• PLANE

CALCULATES connectivity lists (BONDS, HBONDS, PAIRS by using geometric criteria), electrostatic POTENTIAL at selected points, a PLANE passing through an atom selection, converts INTERNAL (relative) into cartesian (absolute) atomic coordinates and vice versa. The first two command words (CALCULATE and for example BOND), must be specified in the correct order, the remaining words can follow in any order.

Syntax

CALCULATE BONDS    INITIALIZE
                   [APPEND]
                   SELECT ... END     [ALL]
                   NEIGHBOR
                   RESIDUE
                   DISULFIDE
                   DISTANCE           [1.71]

         HBONDS  INITIALIZE
                 [APPEND]
                 SELECT ... END  [SELECT ... END]
                 ANGLE real [100.0]
                 DISTANCE real  [3.5]
                 EXCLUDE  inte  [3]
                 HYDROGEN

         PAIRS   (
                 SELECT ... END   SELECT ... END
                 [APPEND] INITIALIZE
                 EXCLUDE  int [3]
                 RANG real  real [0.0  1.5]
                 CLOSEST
                 EACH_CLOSEST
                 MATCH
                      (
                      ATOM
                      RESIDUE
                      SEQUENCE
                      )
                 )

         INTERNAL  SELECT ... END   [SELECT ALL END]

         COORDINATES     SELECT ... END    [SELECT ALL END]
                         [INITIALIZE]
                         APPEND
                         X-AX  [X-AX Y-AX]
                         Y-AX
                         Z-AX

         POTENTIAL    SELECT ... END      SELECT ... END
                     [ SELECT ALL END ]  [ SELECT ALL END ]
                     FROM  SURFACE
                           VOLUME   ATOM
                                    ACCESSIBLE
                           DENSITY
                           POTENTIAL
                           ATOM
                     RANGE real real  [0. 15.]

         PLANE    SELECT ... END

BONDS

• APPEND
• INITIALIZE
• SELECT
• DISULFIDE
• RESIDUE
• NEIGHBOR
• DISTANCE

                   [APPEND]
                   SELECT ... END     [SELE ALL END]
                   NEIGHBOR
                   RESIDUE
                   DISULFIDE
                   DISTANCE           [1.75]

Calculates covalent BONDS from interatomic distances.

APPEND

... APPEND

The CALCULATED bonds will be appended to the list of already existing bonds. Otherwise (INITIALIZE) the bond list (connectivity table) of all atoms will be initialized. APPEND is the default.

INITIALIZE

... INITIALIZE

Before calculating the bond list, the bond list is INITIALIZED.

SELECT

... SELECT ... END

The calculation will be done on the SELECTED atom set. SELECT ALL END is the default.

DISULFIDE

... DISULFIDE

Only sulphur atoms from the selection will be considered by the DISULFIDE bonds calculation.

RESIDUE

... RESIDUE

Only interatomic distances of selected atoms for each separate RESIDUE will be calculated and then checked to form the BONDING list.

NEIGHBOR

... NEIGHBOR

Only interatomic distances for each two consecutive residues will be calculated and then checked to form the bonding list.

DISTANCE

... DISTANCE real

The maximal interatomic DISTANCE for a bond criterion can be changed to any real number. The default value is 1.75AA, exception are the S-S bonds where the default maximal DISTANCE is set to 2.3 A.

HBONDS

• APPEND
• INITIALIZE
• SELECT
• EXCLUDE
• HYDROGEN
• DISTANCE
• ANGLE

                  [APPEND]
                  SELECT ... END  [SELECT ALL END]
                  ANGLE real [90.0]
                  DISTANCE real  [3.5]
                  EXCLUDE inte
                  HYDROGEN

Calculates hydrogen bonds (HBONDS) for the SELECTED atoms. Hydrogen bond donors or acceptors may be only nitrogen and oxygen atoms. Hydrogen bonds with carbon aromatic rings (benzen) as donors or acceptors are not calculated.

APPEND

... APPEND

The calculated hydrogen bonds will be appended to existing ones. APPEND is the default.

INITIALIZE

... INITIALIZE

Before CALCULATING the hydrogen BOND list, the program deletes all present hydrogen bonds.

SELECT

... SELECT ... END

Hydrogens bonds are calculated between two SELECTIONS. When only one is defined then the second one is automatically made equal to the first one.

EXCLUDE

... EXCLUDE inte

The EXCLUDE inte parameter excludes the covalently attached atoms from the hydrogen bonds calculation. The inte is the number of covalent bonds steps from the hydrogen bond donor or acceptor to the compared atom. When inte is -1 then the whole network unit (molecule) is excluded, and only intermolecular hydrogen bonds are calculated. Default EXCLUDE parameter value is 3.

HYDROGEN

... HYDROGEN

Sets the HYDROGEN flag, which means, that the HYDROGEN atoms are present in the atom list and should be used in the calculation.

DISTANCE

... DISTANCE real  (3.5)

Sets the maximum DISTANCE criterion between HYDROGEN bond donor and acceptor atoms to form a hydrogen bond. The default value is 3.5 A. When the HYDROGEN flag is set, then the distance between acceptor and a hydrogen atom is checked. The default distance in this case is 2.5 A.

ANGLE

... ANGLE real

The ANGLE criterion is applied only when the HYDROGEN flag is set, since it calculates the ANGLE between the donor, hydrogen and acceptor atom. Hydrogen bond is created when the calculated ANGLE is larger than the specified value. 100.0 degrees is the default.

PAIRS

• MATCH

                  SELECT ... END
                  SELECT ... END
                  [APPEND] INITIALIZE
                  EXCLUDE  inte [3]
                  RANG real  real [0.0  1.5]
                  CLOSEST
                  EACH_CLOSEST
                  MATCH
                      (
                      ATOM
                      RESIDUE
                      SEQUENCE
                      )
                  )

CALCULATES atom PAIRS between 2 defined SELECTIONS. A PAIR is formed when an interatomic distance is in the specified RANGE ( default values are 0.0 to 1.5A ). EXCLUDES the neighbor atoms ( default value is 3 covalent bonds apart).

INITIALIZES or APPENDS the new pairs to the previous ones.

When CLOSEST is specified, only the PAIR of atoms with the shortest interatomic distance between the two selections will be added to the pair list.

EACH_CLOSEST forms a pair between each atom in the first selection and its closest atom from the second selection.

PAIR list can be inspected with the WRITE command:

> write pair

MATCH

... (
    ATOM
    RESIDUE
    SEQUENCE
    )

Uses additional criteria for pair calculations - ATOM and RESIDUE names and SEQUNCE IDs. It simplifies the calculation when you want to relate atoms or residues with the same name or sequence ID.

> calc pair ( sele resi numb 1 end sele resi numb 2 end range 0. 10 match atom )

INTERNAL

... CALCULATE INTERNAL SELECT ... END

Calculates INTERNAL coordinates from cartesian coordinates and Z-mat-table (ZTABLE) for the selected atoms.

COORDINATES

• for x, y, and z absolute coordinate value) are

... COORDINATES     SELECT ... END    INITIALIZE   X-AX  (X-AX Y-AX)
                        ( SELECT ALL END )  APPEND       Y-AX
                                                         Z-AX

for x, y, and z absolute coordinate value) are

POTENTIAL

• PLANE

                     ( SELECT ALL END )  ( SELECT ALL END )
                     FROM  SURFACE
                           VOLUME   ATOM
                                    ACCESSIBLE
                           DENSITY
                           POTENTIAL
                           ATOM
                     RANGE real real  (0. 15.)

Calculates the electrostatic POTENTIAL at the generated or read points. The first selection defines points belonging to atoms (at least one atom should be confirmed), where the potential will be calculated. The second selection defines atoms to be included in the electrostatic potential calculation. Atom charges are used as the point charges in space. eps = 1.0 The points are selected FROM the specified kind of points. The default RANGE can be changed on order to calculated electrostatic potential only in specified interatomic distance range. Electrostatic potential can be calculated also in the ATOM positions. In this case the points are created at atom positions.

!DIPOLE !DIPOLE moment can be calculated for any desired selection of charged atoms. !The center of positive and negative charge are calculated, so that !"DIPOLE moment" of charged molecules can be calculated too.

!CRYSTAL !Coordinates of atoms can be converted from a crystal space to cartesian !space. First 3 reals are length of unit cell a, b and c, second 3 reals !are angles alpha, beta, gamma and the last is a factor usually 1.

PLANE

Calculates the RMS fit plane of the SELECTED atomic set. Not implemented yet. See SET PLANE instead.

CHARGES

Syntax CHARGE SELECT ... END real

       INITIAL
       EXIT

To a given selection real value CHARGES can be set. See also DEFINE CHARGE.

CLASS

Syntax CLASS SELECT ... END string

       INITIAL
       EXIT

To a given selection class of atom can be set. See also DEFINE CLASS. File: main/doc/color.txt
Last modified: 24-aug-95

COLOR

• RESIDUE
• SEGMENT
• COLOR
• INITIAL
• ANALYSES
• ATOMS
• DEFAULT
• EXIT

> COLOR
        [SELECT ... END]  RESIDUE int1 int2
                          SEGMENT int1 int2
                          COLOR int
                          ANALYSES  AVERAGE
                                    RMS
                                    MINIMUM
                                    MAXIMUM
                                    COLOR  int1 int2 int3
                                    RANGE  AUTOMATIC
                                           CURRENT
                                           DEFINE real real
                          DEFAULT
                          ATOMS int1
                          INITIAL
                          EXIT

The (SET) COLOR commands define color attribute of each individual SELECTED atom. By default all atoms are selected. The colors can be checked at the display by using IMAGE SET commands or with SHOW COLOR SELECT ... END.

RESIDUE

... RESIDUE int1 int2

The RESIDUE specifier colors a selection so that each next RESIDUE has the color value for int2 higher than the previous one. Atoms of the first RESIDUE obtain color int1. Similar rule is applied for the SEGMENT colors.

SEGMENT

... SEGMENT int1 int2

The SEGMENT specifier colors a selection so that each next SEGMENT has the color value for int2 higher than the previous one. Atoms of the first SEGMENT obtain color int1. Similar rule is applied for the RESIDUE colors.

COLOR

... COLOR int1

Sets a single COLOR to the whole atom SELCTION.

INITIAL

Makes atoms invisible (negative color value).

ANALYSES

... AVERAGE  COLOR int1 int2 int3
    RMS
    MINIMUM
    MAXIMUM
    RANGE  AUTOMATIC
           CURRENT
           DEFINE real real

Set colors acording to the analyses aray data. The procedure first finds minimum and maximum value of an ANALYSES array (AVERAGE, RMS, MINIMUM, MAXIMUM) and spans the vaules between the int1 and int2 COLORS. The int3 number is the COLOR step, so that only each int3 color number is taken. The COLOR command has an analogue in FORTRAN "do" loop sentence, which means that you can also inverse the coloring (128 64 -4).

RANGE Interval) of values spanned over the minimal and maximal color can be found by the program (AUTOMATIC), remain from a previous run (CURRENT) or DEFINED explicitly by a user.

ATOMS

... ATOMS int1 int2

Defines a new color for the atom number int1.

DEFAULT

... DEFAULT

Set the DEFAULT set color values to the selected atoms. (See also COLOR ATOMS.)

EXIT

EXIT returns command input back to the MAIN> interpreter. File: main/doc/coord.txt
Last modified: 11-apr-96

COORDINATES

• INITIALIZE
• VALUES
• DEORTHOGONALIZE
• ORTHOGONALIZE
• RESTORE
• KICK
• Example:

> SET COORDINATES  SELECT ... END
                   INITIALIZE
                   VALUES 3*real
                   DEORTHOGONALIZE
                   ORTHOGONALIZE
                   RESTORE
                   KICK  real integer

Sets COORDINATES to the SELECTED atoms. There is no default selection. They can be set explicitly by X, Y and Z VALUES (3*real), INITIALIZED (set to 9999.0), DEORTHOGONALIZED (partial) or its reverse ORTHOGONALIZED.

INITIALIZE

Set COORDINATES of the SELECTED atoms to 9999.0.

VALUES

Set COORDINATES of the SELECTED atoms to the specified x,y and z values.

DEORTHOGONALIZE

Set COORDINATES of the SELECTED atoms to fractional coordinates. The current unit cell data are considered.

ORTHOGONALIZE

Set COORDINATES of the SELECTED atoms from fractional back to orthogonal coordinates. The current unit cell data are considered.

RESTORE

With RESTORE it is possible to restore the atomic coordinate values to their values before the last MINIMIZE, SECONDARY or OBJECT command application. The command should be applied immediately after a catastrophic event, since the saved coordinate data set storage can be modified and therefore disabled with any IMAGE command.

KICK

... KICK real integer

Each atom can be KICKED from its position into a random direction and distance. The real defines the maximum possible shift in x, y or z coordinate. Integer is the seed for applied by the random number generator.

Example:

MAIN> SET COORD SELECT ... END DEORTHOGONALIZE

COPY

• Syntax
• Examples

COPY command sentences copies an property from the first SELECTION to the second one. Two SELECTIONS and a property must always be specified.

Copying is made by pairing atoms (ATOM, CLASS, COORDINATES, CHARGE, COLOR, RADII) or residues (RESIDUE, SEQUENCE) according to their sequential position in the both selections from first to the second. For example atom property of the third atom found in the first selection is copied to the third selected atom found in the second selection. Copying is done from the first selection(A) to the second one(B). Relation is B := A.

Syntax

COPY  RESIDUE         SELECT ... END         SELECT ... END
      SEQUENCE
      COORDINATES
      ATOM_NAMES
      CLASSES
      CHARGES
      COLORS
      RADII
      TEMPERATURE / BVALUES
      WEIGHT
      INTERNAL  DISTANCE
                ANGLES
                DIHEDRALS
                (ALL)
      POINTS    SURFACE
                POTENTIAL

Examples

MAIN> copy coordinate select atom number 1 29 end -
MAIN> select atom number 30 59 end

MAIN> copy sequence select segment number 1 end -
MAIN> select segment number 2 end

File: define.txt
Last modified: 14-mar-95

DEFINE

• SELECT
• BY
  • TOPOLOGY
  • AUTOMATIC
  • ATOMS
• RESIDUE
• NEIGHBOR
• SYMBOL
• INITIALIZE
• PAIRS
• CONSTRAINTS
  • DIHEDRAL
  • INTERACTION
  • MAP
  • NCS
    • FORCE
    • B-FORCE
    • NEXT-GROUP
    • POLAR
• CHECK

Define command sentences are used to define atom CLASS, CHARGE or BOND, ANGLE, DIHEDRAL AND IMPROPER ANGLE parameters from the TOPOLOGY library lists or by an AUTOMATIC procedure and assign them values for energy parameters necessary to carry out energy calculations. Without using the DEFINE command sentence, calculation of most potential ENERGY terms can not be performed.

Additionally distance (PAIRS) and dihedral (CONSTRAINTS) constraints can be defined to enforce desired interatomic distances and dihedral angles during an ENERGY MINIMIZATION procedure.

> DEFINE CLASS
         CHARGES
         BONDS
         ANGLES
         DIHEDRALS
         IMPROPERS CHECK
         CONSTRAINTS DIHEDRAL   4*atom-numb real real   COPY
                     INTERACTION  SELECT ... END  SELECT ... END
                     MAP inte SELECT ... END
                     NCS  SELECT ... END
                          FORCE real
                          B-FORCE real
                          NEXT_GROUP
                          AUTO_GUESS
                          RMS_GUESS
                          SET_GUESS inte 6*real
                          FLAGS 6* inte
                          POLAR
         PAIR         FORCE real
                      DISTANCE real
                      CALCULATE
         INITIALIZE
         BY  TOPOLOGY
             AUTOMATIC  RESIDUES
             ATOMS   x*atom-numb
         SELECT ... END
         NEIGHBOR  string
         SYMBOL  string
         RESIDUE   string

SELECT

... SELECT ... END ...

SELECT ... END and ATOM are the two ways to select the atoms for which force field PARAMETERS are being DEFINED or chosen. With SELECT the whole SELECTION is used while the BY ATOMS option, only the particular energy term for the specified atoms is added to the list.

BY

• TOPOLOGY
• AUTOMATIC
• ATOMS

... BY TOPOLOGY
       AUTOMATIC
       ATOMS

The search for ENERGY terms (BOND, ANGLES, DIHEDRALS and IMPROPERS) is done in the TOPOLOGY library or by an AUTOMATIC procedure or explicitly for each specified ATOM. With SELECT the whole SELECTION is used while with the BY ATOMS option only the particular energy term for the specified atoms is added to the list.

It is recommended to use the AUTOMATIC procedure for generation of BOND and ANGLE lists. The AUTOMATIC procedure should be used with caution for generation of DIHEDRAL and IMPROPER lists. Use it for IMPROPER only when creatiing new TOPOLOGY RESIDUES.

Mostly use the BY TOPLOGY procedure. See file in MAIN_UTILS:def_top_par_19.com.

TOPOLOGY

... BY TOPOLOGY ...

The BY TOPOLOGY procedure can assign atom CLASSES (types) and atomic charges and on their bases generate lists of BONDS, ANGLES, DIHEDRALS and IMPROPERS.

This option covers most of your needs for CLASSES, CHARGES and DIHEDRALS and IMPROPERS assignment.

AUTOMATIC

... BY AUTOMATIC ...

The AUTOMATIC procedure generates an ENERGY term for every possible BOND, ANGLE and DIHEDRAL angle in the specified SELECTION. In order to assign IMPROPERS with the AUTOMATIC procedure, the search for the improper angles should be preceded BY the AUTOMATIC definition for atom CLASSES. The IMPROPERS are assigned only to chiral centers (carbon atom with 3 neighbours or to planar groups).

ATOMS

... ATOMS 2-4*atom-num

ATOMS can be used only with BOND, ANGLE, DIHEDRAL or IMPROPER terms. For BONDS two atoms have to be specified, for ANGLES three and for DIHEDRALS and IMPROPERS four. With the ATOMS the atoms are already specified explicitly. This makes any additional search in TOPOLOGY library as well as explicit RESIDUE reference unneccessary. Used with DELETE ENERGY DIHEDRAL and IMPROPER, combined with the CHECK, it can help to create the desired TOPOLOGY residue. See CLASS and CHARGE as well.

It is assumed, however, that the specified atoms have their ATOM CLASSES already specified, when ATOM CLASSES are not defined no force-constants can be found in the PARAMETER lists of ENERGY terms.

RESIDUE

... RESIDUE string

When RESIDUE is specified then only the TOPOLOGY residue with the name string is used to DEFINE energy terms for the specified SELECTION. NEIGHBOUR and SYMBOL should be combined with the command RESIDUE.

NEIGHBOR

... NEIGHBOR

NEIGHBOR is used for the X-PLOR chain patched residues (PEPT) In those residues atom names are preceded by a one letter code (-, + ) NEIGHBOR is actually a shortened notation of the SYMBOL command which can be applied to a series of neighbouring residues.

MAIN> define residue PEPT neighbour - + select sequence 1H 15 end \
MAIN> dihedral improper

SYMBOL

... SYMBOL string

SYMBOL makes it possible to specify the ENERGY terms for links between two different residues (to use X-PLOR patched residues). The string(s) whow(s) to which SELECTION a certain atom belongs. Up to two different SYMBOLS can be applied. Each SYMBOL definition requires a separate SELECTION.

MAIN> define residue DISU symbol 1 select sequence 1 end symbol 2 \
MAIN> select sequence 122 end  dihedral

INITIALIZE

... INITIALIZE

The command word INITIALIZE initializes the BOND, ANGLE, DIHEDRAL or IMPROPER energy terms lists. With CLASS or CHARGE its use is redundant, since the existing CLASS and CHARGE values of the SELECTED atoms are replaced with the new ones anyway.

PAIRS

... PAIR FORCE       real
         DISTANCE    real
         CALCULATE

The selected PAIRS can be introduced as an additional distance constraint to the energy list. For each selected pair of atoms a FORCE constant can be defined to pull them towards the specified DISTANCE or keep the current one as specified by the CALCULATE command word. The CALCULATE option has to be used for the pair analyses (See ANALYSE PAIR).

CONSTRAINTS

• DIHEDRAL
• INTERACTION
• MAP
• NCS
  • FORCE
  • B-FORCE
  • NEXT-GROUP
  • POLAR

...  CONSTRAINTS DIHEDRAL   4*atom-numb real real   COPY
                 INTERACTION  SELECT ... END  SELECT ... END
                 MAP inte SELECT ... END
                 NCS  SELECT ... END
                      FORCE real
                      B-FORCE real
                      NEXT_GROUP
                      AUTO_GUESS
                      RMS_GUESS
                      SET_GUESS inte 6*real

The MAP, INTERACTION and NCS CONSTRAINTS require one or more selections to be specified. Each selection turns into a KEY so you can check it with a 'SHOW KEY' command. Each KEY includes it string identifier and its group number ('int_ncs__1' is the first NCS interaction key). INITIALIZE preceeding a CONSTRAINT commands sets a group counter to zero and deletes all thereby referred keys.

The DIHEDRAL constraint is the only exeption, it uses the selection that preceeds

DIHEDRAL

... DIHEDRAL   4*atom-numb real real   COPY

Introduces the dihedral CONSTRAINTS for the specified atoms which are included in a SELECTION. The purpose is to maintain or enforce a particular conformation. The four atoms must be specified by their atom names. When the atom is to be searched in next or previous residue then character + or - has to be attached in front of the atom name. The first real number is the target dihedral angle in degrees and the second the force constant.

The command word COPY shows the program to take the target dihedral value from the INTERNAL COORDINATES table. This option makes possible to invert the direction of a peptide chain by keeping the conformation (secondary structure) of a segment as close as possible to the original one.

INTERACTION

... INTERACTION  SELECT ... END  SELECT ... END

You can constraint interactions between atoms to avoid inclusion of undesired overlaps by specifying the first ('active') and the second ('passive') selection. The number of INTERACTION groups is not limited. For example when refining equal molecules in two crystal forms that spatially overlap.

By default no INTERACTION group is defined.

WARNING: After modifying the INTERACTION groups, do not forget to reDEFINE the bonding term lists (BOND, ANGLE, DIHEDRAL, IMPROPER) in order to get the desired effects.

MAP

... MAP inte SELECT ... END

By default atoms interact only with s single map (the last one specified with an ENERGY DENSITY MAP command), the CONSTRAINT MAP command allow you to specify with which MAP a certain atom selection will interact. Each map can have its own selection, and atoms can be in principle included in any number of selections (between none and all). Each MAP has its own force constant (as specified by 'ENERGY DENSITY MAP inte DENSITY SCALE real' command).

NCS

• FORCE
• B-FORCE
• NEXT-GROUP
• POLAR

... NCS  SELECT ... END
         FORCE real
         B-FORCE real
         NEXT_GROUP
         AUTO_GUESS
         RMS_GUESS
         SET_GUESS inte 6*real
         POLAR
         FLAGS 6*inte

NCS energy term is the summ of harmonic FORCES pulling all equivalent atoms within each specified group against their average position. The average atom position is calculated via an RMS fit procedure, which first optimizes the superposition of SELECTIONS within a group to the group first representative and then, after applying the optimized rotation and translation parameters, calculates arithmetic mean of each selected atom coordinates. This averaged model is then transformed by backtransformations to the other NCS GROUP members.

If superposition makes nonsense, try to set and check initial guesses by AUTO_GUESS (performing a RMS fit calculation for the whole group based on the current values, by default all values are zero), RMS_GUESS (result of the RMS COOR ALL calculations) or set your own values (SET_GUESS). The rotations (about X, Y and X axes) are followed by a translation vector.

FORCE

... FORCE real

The FORCE allows you to specify the harmonic FORCE pulling atoms agains their averaged position. Each NCS group can has its own FORCE. When a FORCE constant is a negative number, then the atomic coordinates are simply set to their average value. This is a hard NCS CONSTRAINT, however, it still allows to optimize the NCS rotational and translational parameters during a refinement run.

B-FORCE

... B-FORCE real

The B-FORCE is the harmonic constant pulling B-values of crystallographically differeny but equivalent atoms to their average value.

The default value is 0.004.

NEXT-GROUP

The NEXT_GROUP means that you are starting with a new NCS group. The number of NCS groups is in principle not limited. After finishing an NCS group, you can not edit it any more. If you have made a mistake, start again with 'DEFINE INIT CONSTRAINT NCS'.

POLAR

... POLAR 1 1 1 1 1 1

Rotational parameters for each group can be defined also with POLAR axis description. This makes possible to reatively clearly define an angle of rotation and also fix it (with the third FLAG set to 0). Six flags need to be specified anyway. A zero number means that the parameter is fixed and one that it should be optimized. You can fix also all 6 parameters which essentaily means that the NCS, as defined with a DEFINE NCS SET_GUESS command, is fixed.

CHECK

... IMPROPERS CHECK

CHECK is an option that takes care that each chiral center has always a positive value for an IMPROPER angle. It means, that the current chirallity of a center is accepted and preserved during an energy MINIMIZATION procedure. This option makes possible to deal with L and D amino acids on the basis of the same topological description.

DELETE

• Syntax
• BOND
• ATOM
• PAIR
• HBOND
• ENERGY
• VARIABLE
• MAP

DELETES the SELECTED ATOMS, BONDS, HYDROGEN bonds, PAIRS, ENERGY terms. The SELECTION is required. There is no default selection.

Syntax

DELETE BOND  atom-num1 atom-num2
             SELECT ... END
       HBOND SELECT ... END
       PAIR(S)

       ATOM  SELECT ... END

       ENERGY  BOND        SELECT ... END
               ANGLE
               DIHEDRAL
               IMPROPER

       VARIABLE string
       MAP int

BOND

            SELECT ... END

DELETE BOND atom-num1 atom-num2 DELETES only the BOND between specified atoms when it exists. When an SELECTION is used instead of an atom pair, then only the bonds connecting atoms within the selection are deleted. A covalent bond between a selected atom and one that is not included in the selection is preserved.

ATOM

All the data referring to specified atoms and atoms are deleted. The SELECTION flags for remaining atoms are preserved. The connectivity table (CATBLE) and ZTABLE (connections of internal coordinates) are correspondingly updated as well as the ENERGY term lists.

PAIR

A PAIR of atoms is removed from the PAIR list only when both atoms are SELECTED.

HBOND

A Hydrogen bond is removed from the hydrogen bond list only when both atoms (donor and acceptor) are SELECTED.

ENERGY

              ANGLE
              DIHEDRAL
              IMPROPER
              CONSTRAINT

DELETES from the specified ENERGY term list the contributins of the SELECTED atoms.

VARIABLE

... VARIABLE string

Deletes variables with the given variable name. Wild characters as '*' or '%' can be used as well.

MAP

... MAP inte

Deletes a specified map. When no map is specified (an integer is not given) all maps will be deleted.

DIFFERENCE

Syntax DIFFERENCE RESIDUE SELECT ... END SELECT ... END

            SEQUENCE
            COORDINATES
            ATOM_NAMES
            CLASS
            CHARGE
            COLOR
            RADII
            TEMPERATURE
            WEIGHT
            INTERNAL  DISTANCE
                      ANGLES
                      DIHEDRALS
                      (ALL)
            POINTS    SURFACE
                      POTENTIAL

Syntax is the same as by COPY. Only the relation is different. Relation is here A := A - B. However, the results of a string (RESIDUE, SEQUENCE, ATOM) subtraction is, when the corresponding strings in A and B are the same, blanks and, when they are different, the string in A is not modified. When subtracting RESIDUE names of two SELECTIONS, are the places of mutations easy to see with a

MAIN> write sequence residue

sentence.

EDT

Syntax EDT file_name

Calls the VAX EDIT/EDT editor. When editing is completed, command input is returned to MAIN>. EDT can be called only from the MAIN> (zero level of the command input) and not from command files. File: energy.txt
Last modified: 14-feb-1998

ENERGY

• Syntax
• ALL
• ANGLE
• B-VALUES
  • SCALE
  • BOND
  • ANGLE
  • GROUP
  • MINIMAL
  • MAXIMAL
• BOND
• CON_DIHE
• CUTOFF
• DENSITY
  • ATOMS
  • POLYNOMIAL
  • CONVOLUTION
  • POINTS
  • GRID
• DIELECTRIC
• ELECTROSTA
• EXCLUDE
• HBONDS
• IMPROPER
• LIST
• MATRIX
• NCS
• PAIR
• RANGE
• SELECT
• TRANSLATE
• VDW
• X-TARGET

The ENERGY commands specify parameters for energy calculations and can calculate potential energy (including force gradients) of SELECTED ATOMS (or POINTs). Within ENERGY command the individual ENERGY terms are turned "ON" and "OFF", "CUTOFF" distance for ELECTROSTATIC and van der Waals (VDW) energy terms and "SCALE" is specified. You can inspect these parameters with

> show energy

command. Detailed information about geometry and possible threshold violations of each particular energy term can be inspected using "LIST" and "RANGE" keywords.

"FORCES" can be inspected with

> show forces select ... end
> image sele ... end force real.

DEFINE commands enable ENERGY calculations, so check there first when facing any unexpected behavior.

Related commands are "DEFINE" (define.html, MAIN_UTILS:def_top_par_19.com) "MINIMIZE (minimize.html, MAIN_CMDS:refine.cmds", and"ANALYZE"("anal.txt", MAIN_MENU:analysis.txt")

Syntax

> ENERGY
          ALL        ON / OFF
          ANGLE      ON / OFF
                     SCALE
          B-VALUES   ON / OFF
                     SCALE real
                     BOND real
                     ANGLE real
                     GROUP real
                     MINIMAL real
                     MAXIMAL real
                     OVERALL
                     INDIVIDUAL
          BOND       ON / OFF
                     SCALE
          CON_DIHE   ON / OFF
                     SCALE
          CUTOFF    real
          DENSITY    ON / OFF
                     MAP intg
                     SCALE / RATIO real
                     GRID intg
                     ATOM
                     POINTS
                     POLYNOMI
                     CONVOLUT

          DIELECTRIC   real
          DIHEDRAL   ON / OFF
                     SCALE
          ELECTROS   ON / OFF
          EXCLUDE intg
          HBOND      ON / OFF
                     SCALE
          IMPROPER   ON / OFF
                     SCALE
          LIST
          MATRIX
          NCS        ON / OFF
                     SCALE   real
          PAIR       ON / OFF
                     SCALE   real
          RANGE     real real
          SELECT ... END
          TRANSLATE   VECTOR real real real
                      ATOM   iatom
                      POINT  intg
          VDW        ON / OFF
                     SCALE   real
          X-TARGET   ON / OFF
                     SCALE

ALL

... ALL ON
        OFF

Turns ALL energy terms OFF. The ON command, however, turns on only the default terms (BOND, ANGLE, DIHEDRAL, IMPROPER, ELECTROSTATICS, VDW).

> energy all off

ANGLE

... ANGLE ON
          OFF
          SCALE real

The ANGLE energy controls the ideality of a A-B-C angle, using rotation derivatives for A-B and C-D bonds in the A-B-C plane.

The ON and OFF commands control the status of the ANGLE term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

B-VALUES

• SCALE
• BOND
• ANGLE
• GROUP
• MINIMAL
• MAXIMAL

... B-VALUES   ON / OFF
               SCALE real
               BOND real
               ANGLE real
               GROUP real
               MINIMAL real
               MAXIMAL real
               OVERALL
               INDIVIDUAL

B-VALUE energy is actually a group of energy terms, which all together constitute the B-VALUE energy that can be optimized using

> minimize b-value

commands. The B-VALUE is a term by itself too. It is the pulling force of the atomic B-factors, whereas the BOND, ANGLE, GROUP, MINIMAL and MAXIMAL impose soft or hard con- and re-straints on atomic B-values.

> show temp ...
> anal temp ...

commands give you some insight into the B-values distributions. See also "ANAL_TEM" in MAIN_MENU:analysis.html.

See also related documantation on B-value refinement in MAIN_DOC:refine/refine.html, on menu item "REFINE_B in MAIN_MENU:map_atom.html and the MAIN_CMDS:refine_b.cmds macro.

SCALE

... SCALE real

SCALES the atomic B-factor against the underlaying density map. In the case of X-TARGET optimization, this scale has no effect (to be implemented yet).

> energy b-valu scale = 100.0

BOND

... BOND real

Restraints B-values of two covalently bound groups by a specified harmonic force constant.

ANGLE

... ANGLE real

Restraints B-values of two groups covalently attached to the same atom by a specified harmonic force constant.

GROUP

... GROUP real

Restraints B-values of aall atoms being a member of a DEFINED group (define.html) to the arithmetic middle of the group by a specified harmonic force constant. If the constant is a negative number then the restraint is hard and the shifts in atomic B-values during mininmization are averaged.

Each group can be of any size, the smallest group is individual atom.

MINIMAL

... MINIMAL real

Specifies the lowest B-value limit. MAIN does not except values lower than 2.0. Constraints atomic B-values to the values above the specified MINIMAL border.

MAXIMAL

... MAXIMAL real

Specifies the highest B-value limit. Constraints atomic B-values to the values below the specified MAXIMAL border.

BOND

... BOND ON
          OFF
          SCALE real

The BOND energy controls the ideality of a A-B distance using harmonic constraints.

The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

CON_DIHE

... CON_DIHE   ON / OFF
               SCALE

Controls the dihedral constraints as specified by "DEFINE CONSTRAINTS DIHEDRAL" command (MAIN_COM:define.html).

The ON and OFF commands control the status of the CON_DIHE term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

CUTOFF

... CUTOFF    real

Defines CUTOFF distance for the nonbonding energy terms. Default value is 8 A.

DENSITY

• ATOMS
• POLYNOMIAL
• CONVOLUTION
• POINTS
• GRID

...  DENSITY    ON / OFF
                SCALE real
                MAP intg
                GRID  intg
                ATOMS
                POINTS
                POLYNOMI
                CONVOLUT

DENSITY energy is kind of correlation between placement of a group of ATOMS or POINTS with a density MAP. The term has a SCALE.

ATOMS

... DENSITY ATOMS ...

Calculates energy and derivatives for ATOMS instead of points. Uses POLYNOMIAL or CONVOLUTION terms. POLYNOMIAL is the default.

POLYNOMIAL

... POLYNOMIAL

Each atom density ENERGY contribution is calculated from three second order polynomials approximation. The coeficients for the second order polynomials are calculated by a least square fit procedure from four density points. The points are laying on the line parallel to an crystall cell axis passing through an atomic center position on grid layers (1, 0, +1, +2), whereas the atomic center defines the 0 grid layer. It is positioned between the 0 and +1 grid layer.

The density values of the four density points are obtained by a linear interpolation from their four neighbor grid points which lay in the layer perpendicular to the line direction.

From these polynomials an atomic density energy is calculated as negative of the averaged summ of all three directions contributions scaled by the DENSITY SCALING factor. Derivatives are calculated along each cell axis direction on the basis from each polynomial approximation.

CONVOLUTION

... CONVOLUTION

Calculates energy as the the convolution of underaying electron density map with atomic electron density generated from atomic scattering factors taking into account their B-values. Derivatives are calculated numerically by shifting atom centers in X, Y and Z directions.

Although this seems to be the best possible way top calculate the density correlation, you are advised to use it with caution since it is a computer time consuming method.

POINTS

... DENSITY POINTS

In the case of POINTS DENSITY the energy is a product of the interpolated density at the point positions and the value of each particular point. Combined together with SET CENTER, SET MATRIX and TRANSLATE options, it can be used for optimizing local symmetry, Patterson map superposition by rotational searches, and cross peak correlations of a difference Patterson map. The use of loops is recommended.

> energy all off density on density points density scale 1.0
> set matrix 2 polar 45. 78. 180.
> set center coordinates 40. 41. 67.
> energy matrix 2 translate vector 20. 20. 34. select all end

The DENSITY energy of a POINT selection is the interpolated density from a map to the center position. (The DENSITY energy term is so essentailly a correlation.) The density values are interpolated from the closest GRID intg specified number of grid layers around each selected point position in box (2*2*2=0, 4*4*4=1, 6*6*6=3, 8*8*8=4).

GRID

... GRID inte

Works in combination with the POINTS correlation term.

DIELECTRIC

... DIELECTRIC   real

Defines the dielectric constant for electrostatic calculations. Default value is 1.

ELECTROSTA

... ELECTROSTAT  ON / OFF

Electrostatic calculations are based on interactions of partial atomic charges interacting via Coulombe law.

The command turns ON and OFF the electrostatic term. Its scale is defined vie DIELECTRIC constant.

EXCLUDE

... EXCLUDE intg

The EXCLUDE command defines the level of neighboring atoms to the current atom in nonbonding energy (VdW and ELECTROSTATIC) calculations. The level is defined by integer. For example: CA is bound to N, CB and C. Level 1 means that the nonbonding interactions between atom CA and N, CB or C will be scaled with a scaling factor for electrostatics. No atom will be excluded from nonbonding interactions. The interactions with other atoms are not scaled.

Level 2 means that atoms N, CB and C will be excluded from nonbonding interactions, but that the interactions between their neighbors (HN, -C, CG, O, +N ) and CA will be scaled with the scaling factor. And so on.

The default level for X-PLOR force fields is 3 and scaling constant is 0.4 for the border atoms interaction (electrostatic scale).

However, level -1 means, that atoms comprising a molecule are interacting only with atoms from the other molecules. (A molecule consist of atoms linked into a covalent bonds network.)

HBONDS

... HBONDS ON / OFF
           SCALE

The HBOND energy controls the ideality of hydrogen bond donnor and acceptor distance using week harmonic constraints.

The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

IMPROPER

... IMPROPER ON / OFF
             SCALE

The IMPROPER energy controls the ideality of a A-B-C-D dihedral angle using periodic or harmonic constraints to enforce the planarity or chiralty of the atoms.

The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

LIST

The LIST RANGE real real sets the list flag. The meaning is that all interatomic interactions of all energy terms turned on will be written to the terminal. RANGE sets the threshold values. If no real number is specified, the threshold value is set to 0.0. The first real number relates to geometry violations, and the second one to the energy of interaction. Range command has no effect when the LIST flag is not set.

For bonding terms: BOND, ANGLE, DIHEDRAL, IMPROPER

If range is active then only the terms that have a deviation from the ideal value greater than that specified or an energy term larger than specified, will be printed.

For nonbonding terms: ELECTROSTATIC, VdW

If range is active only the pair of atoms with their absolute energies above the specified threshold will be printed.

Useful for debuging purposes mostly.

MATRIX

... MATRIX inte

Specifies the rotation MATRIX (1-8) which will be applied in point rotations used in calculations of electron density maps correllations.

NCS

...  NCS ON / OFF
         SCALE   real

The NCS (Non-Crystallographic-Symmtry) constraints pull the DEFINED groups against their arithmetic middle position with a group force. Here you can specify also additional overall SCALE value.

PAIR

...  PAIR ON / OFF
          SCALE   real

The PAIR energy controls the distance of a atoms on the PAIR list using harmonic constraints. The target distance value and force are DEFINED for each particular pair on the list.

The PAIR terms enable you to enforce certain interatomic distances (MAK_PAIR).or softly constrain atoms to a certain positions (ANCHORS).

The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

RANGE

... RANGE     real real

Specifies the RANGE (threshold) values above which each interatomic interaction exceeding the threshold will be listed. The first real relates to geometry terms (BOND, ANGLE, DIHEDRAL and IMPROPER), whereas the second relates to to the ENERGY of each particular interactions. The command

> energy all off bond on list sele resi numb 1 end range 0.3

Lists all bonds that deviate for more than 0.3 A from the target value.

SELECT

... SELECT ... END (SELECT ... END)

Two SELECTIONS can be specified. The first selection defines atoms on which forces are calculated, the second selection defines the atoms on which the first atom selection interacts. In order to calculate the potential energy of a molecule, its atoms should be defined in both selections.

When only one SELECTION is defined it is assumed that the second selection is equal to the first one. When no SELECTION is specified no ENERGY calculation is perfomed.

TRANSLATE

... TRANSLATE VECTOR real real real
              ATOM inte
              POINT inte

Specifies the TRANSLATION which will be applied to POINT rotations and translations used in calculations of electron density maps correllations.

The translation vector can be specified explicitely or via an ATOM or POINT position. When ATOMs or POINTs or points are applied and the underlaying map is a Patterson map, then the procedure corresponds to a cross-vector verification.

VDW

...  VDW ON / OFF
         SCALE   real

The VDW energy controls interatomic distances repulsive and attractive Van der Waals distance dependent terms.

The ON and OFF commands control the status of the BOND term, wherase the SCALE allows you to additionally control the strength of the term by scaling it up (real> 1) or down (real< 1). The default scale is 1.0.

X-TARGET

...  X-TARGET ON / OFF
              SCALE   real

Turns ON or OFF the (Fo-Fc)**2 target used in crystallographic refinement. The X-TARGET ON command turns the DENSITY term off.

The X-TARGET uses the currently valied DENSITY MAP for FFT transformation, so be sure that that map is a complete unit cell.

File: main/doc/com/find.txt
Last modified: 24-aug-99

FIND

• Syntax

Use to find in an automate way the best possible position of groups of atoms.

For usages see in MAIN_MENU:auto_stuff.html.

Syntax

FIND





File: fourier.txt

Last modified: 8-feb-98



FOURIER


Syntax
FORWARDS
BACKWARDS
RESOLUTION
FFT
DIRECT
MAP
REFLECTION
ATOMS
B_ADD
EXP_TABL



FOURIER commands perform Fourier Transformations to
calculate structure factors (FORWARD) or maps of electron
density (BACKWARD).  FORWARD is the default.


Releted commands are "REFLECTION" (reflect.html) and "MAKE MAP
(make.html).




Syntax



> FOURIER MAP inte
          ATOMS SELECT ... END
          REFLECTION SELECT ... END
          FFT
          DIRECT
          FORWARDS
          BACKWARDS
          RESOLUTION real real
          B_ADD real
          EXP_TABL    ON
                      OFF





FORWARDS



Structure factors will be calculated.  Either from atoms
directly or by FFT-ing a map.


The forward transform automatically extracts reflections
into the FCALCULATE data array.  Data are not premultiplied
with a resolution dependent temperature factor.  If you want
to scale your data, you need to initiate a reflection
R-VALUE calculation followed by a REFLECTION SET AMPLITUDE
command.



BACKWARDS



An electron density map will be calculated.
A MAP must be specified.


In order to transform a map BACKWARDS (calculate a map from
structure factors), you need to FILL the map first with the
REFLECTIONS FILL command.  Only FWORKSET array fills a map.



RESOLUTION



... RESOLUTION real real




Redefines the resolution range in which an FFT of a map is
performed.



FFT



FFT method will be applied on a map to either transform a
map into structure factors (FORWARDS) or a reciprocal space
map into electron density map (BACKWARDS).



DIRECT



The DIRECT summation method will be applied.
Currently only the FORWARD transformation
(Fcalc from ATOMS or a MAP) can be applied.
You have to specify either "ATOMS" selection or a "MAP".




> fourier refl sele ... end direct forw atom sele ... end
> fourier refl sele ... end direct forw map inte





MAP



... MAP inte




The inte defines the map used in a fourier transformation.



REFLECTION



... REFLECTION SELECT ... END




Selects the reflections to be used in the DIRECT
calculations.




ATOMS



... ATOMS SELECT ... END




Selects the atoms to be used in the DIRECT calculations.



B_ADD



B_ADD is the overall B, which is added to individual atomic
B-factors to reduce the truncation error in FFT based
struture factor calculations.



EXP_TABL



Turn ON and OFF the usage of exponetial tables for generation of
electron density maps (using gaussian form of atomic structure
factors) and in corresponding energy terms.




> make map .. atom dens
> energ dens convolution
> energ x-targ on




Use of tabulated exponetials substantially accelerates electron density
map generation. "ON" is the default.  If your machine is not really fast
don't use the DENSITY CONVOLUTION term.







GRAPH


Syntax
EXIT
OBJECT

space (0.0 0.0 0.0)

SCALE
CHARACTER
Position
COLOR
TEXT
TRANSLATION
RAMACHANDRAN
READ

GRAPH.TEX     19-JUN-1990


GRAPH is a module with prompt: GRAPH>. It is used to displayed
text and two dimensional objects (graphs).  There are 10
possible GRAPH objects that can be manipulated
independently. HIS_RAMA plots the cross of a residue into
Ramachandran plot only into object 1.  To see the results on
the display you must at least once enter the IMAGE DIALOGUE
mode.


WARNING: All GRAPH objects are not stored in the program but
only transferred to the graphic display. The menu option RE_DRAW
will erase them if they are not protected with an IMAGE
FROM command.  If you want to plot the Ramachandran plot or
any other plot, all GRAPH objects must be send to the display
when PLOT mode is already ON. When that is not the case,
first turn the PLOT mode ON and afterwards repeat the GRAPH
commands.



Syntax



EXIT


OBJECT  inte
SCALE   real
CHARACTER    SCALE   real


X-AX    real
Y-AX    real
COLOR  inte
TEXT    string
TRANSLATION     real real real


RAMACHANDRAN


     STEP   real
     ENERGY UNIT  inte
     SELECT ... END
     CROSS
     CELL
     SEQUENCE
     RESIDUE




READ FILE file_name


     UNIT int





EXIT



EXIT returns command input form GRAPH> to MAIN>.



OBJECT


space (0.0 0.0 0.0)

OBJECT inte


OBJECT inte defines the current object and resets the
translation of the current objects to default position in

space (0.0 0.0 0.0)




SCALE

SCALE   real


Defines the SCALING of the current OBJECT.



CHARACTER

CHARACTER   real


Defines the CHARACTER scale of the current OBJECT.



Position

X-AX    real
Y-AX    real
Z-AX    real


Defines the position for the next TEXT command.  It can be
changed interactively by using TEXT_TRN mode.  The default
position is 0.0 0.0 0.0.



COLOR

COLOR  inte


Sets the color that will be used by displaying the following
images.



TEXT

TEXT    string


Sends the TEXT to the current position on the screen.



TRANSLATION

TRANSLATION  3*real


Data used for TRANSLATION of the whole GRAPH OBJECT.



RAMACHANDRAN



... RAMACHANDRAN   STEP real
                   ENERGY UNIT inte
                   SELECT ... END  CROSS
                                   CELL
                                   SEQUENCE
                                   RESIDUE




Displays Ramachandran plot constituents. STEP draws lines in
the frame separated for the real. ENERGY plots the
contouring vectors that are read from the file accessible
under UNIT inte. CROSS, CELL, RESIDUE and SEQUENCE are used
to display a CROSS, squared CELL or RESIDUE name or SEQUENCE
name of SELECTED residues at their position in the
Ramachandran plot.  The SELECT command must precede and not
follow the kind of image.  Otherwise there may be a mass on
the display.


IMPORTANT: dihedral angles PHI and PSI should be present in
INTERNAL coordinates data and PAIR list should be created.
The required condition,however is, that all the selected
atoms are correctly covalently bound.  Apply the following
series of commands




MAIN> make ztable
MAIN> calculate internal
MAIN> make pair ramachandran select ... end




and then enter the GRAPH module and prepare the plot.  The
options ENERGY UNIT and STEP are obsolete now, since any
GRAPH can be displayed with the READ FILE command.  The
RAMACHANDRAN plot background images are made with a READ
FILE command sentence now. See Examples.



READ

READ FILE file.name
READ UNIT int


READS the graphical commands from the specified FILE or from
the FORTRAN logical UNIT number in the the input format for
LWPLOT. This is the way to include any 3-D graphs to the
display list. Graphs may consist of vector lists, dots and
labels. Each GRAPH structure has a name (DISPLY name).


Format


First 6 characters are for the command field (DISPLY, MOVE


...), followed by 24 characters (3 times 8 ) for the X, Y Z


coordinates and 16 for the COLOR (2 times 8) hue and
saturation. The LABEL text continues from the character
number 31 (31 = 6 + 3*8 + 1) to the end of the record.  The
GRAPH FILE should have the following syntax:


Syntax:
DISPLY name
COLOR  hue saturation
MOVE   x y z
DRAW   x y z
LABEL  x y z   THE LABEL TEXT





File: help.txt

Last modified: 23-sept-97



HELP



HTML based documentation is available at //www-bmb.ijs.si/ or
at your local MAIN instalation main/doc/MAIN_index.html.


HELP used as a command word within any valid command sentence
retrieves information from the MAIN Command Reference Manual
documentation files.  You can type it before or after the
command word for which you need some information
However, if you start with HELP you can only retrieve this file.


HELP on Strike window (MENU) items ican be retrieved by
switching to the documentation mode (press 'h' within the MAIN
image window - it is an on/off toggle function) and clicking
on the desired menu items.


IMPORTANT: As MAIN works in two modes (command line and
dialogue) you should bare in mind that IMAGE DIALOGUE enters the
dialogue mode which enables you to use mouse, menu and dials.











IF

IF.TXT     14-OCT-96


The IF statement is useful for MAIN programers, especially
for loop control.


IF ( value operator  value  )   a main command sentence


Comparison operators are:


.LT. less than

.LE. less or equal than

.GT. greater than

.GE. greater or equal than

.EQ. equal

.NE. equal



Values can be integer or real numbers and strings.  You can
only compare values of the same type.


Brackets are obligatory.


When the expression specified ( ... ) is evaluated as true,
then the subsequent command sentence is interpreted,
otherwise the command interpreter skips to the next input line.


To apply loops a loop counter variable should be defined and
the IF statement can serve either to repeat the loop or exit
from the command file:




> set variable iatom = iatom + 1
> if ( iatom .gt. natom ) return
> set center atom iatom
> show image center
> rewind file










File: IMAGE.TXT

Last modified:   18-oct-2007



IMAGE


Syntax
SELECT
PLOTTER

ON
OFF
LWPLOT
RASTER3D
INITIALIZE
UNIT

OVER
MOUSE
HISTORY
Projection parameters

XCENTER
YCENTER
AXCENTER
AYCENTER
VIEW
SCREEN
CENTER

ATOM
SEQUENCE
COORDINATES
CALCULATE

MATRIX
STEREO

SIDE_BY_SIDE
CRYSTAL
ON
OFF
ANGLE
SHIFTS

CLIP
SCALE
CONTRAST

RATIO
ERASE
FROM
INITIALIZE
COLOR
SET
LINE
DELETE
DIALOGUE
FORWARD
Kinds of presentation

Connections
ATOM
FORCE
RESIDUES
SEQUENCE
SEGMENT
MARK
POINTS

SURFACE
VOLUME
NUMBER
POTENTIAL
DENSITY
RIBBON
3ANGLE

MAP

DENSITY
CONTOUR
BOX
GRIDS
ON
OFF
INCLUDE
REMOVE
X-AXIS
Y-AXIS
Z-AXIS
LINES
STICKS
AREA


Examples
Dialog_mode



The IMAGE command sentences INITIALIZE the graphical display
and prepare images of atoms, bond, labels, points and maps.
The DIALOGUE command word transfers the command input to
the interactive devices (DIALS and MOUSE).


Picked atoms are stored in the HISTORY list. Only the atoms
included in the KEY "image" are pickable. The key "image" is
updated each time when an IMAGE of a SELECTION is created,
so that the SELECTION is included into the key "image". The
key image can, however, be modified interactively with a KEY
command.


First an atom must be picked and afterwards a function on
the last picked atom(s) is activated and not reverse.  Atoms
can be sequentially DROPPED from the HISTORY list. The last
picked atom is dropped as the first one.  Each command
picked from the menu is actually translated into one or more
command sentences, that could be in principle also typed in
from the keyboard.



Syntax



SELECT ... END




DIALOG **


GROUP INITIALIZE


      ON / OFF
      NAME string
      INCLUDE int1 int2
      REMOVE  int1 int2
      SHOW
      VISIBLE




ATOM NUMBER


     NAME / SYMBOL
     CROSS
     CLASS
     BALL integer




BOND    [ ]


        DISTANCE
        STICKS  integer




HBOND   [ ]


        DISTANCE
        STICKS  integer




PAIR    [ ]


        DISTANCE
        STICKS  integer




FORCE real


RESIDUE NUMBER


        NAME / SYMBOL




SEQUENCE


POINTS [integer]


       SURFACE  CONTACT
                REENTRANT
                ALL
       3ANGLES
       RIBBONS
       VOLUME
       POTENTIAL STEP real   RANGE real real
                    ( 0.5 )
       DENSITY
       NUMBER   ON / OFF




MARK SELECT .. END


     ON
     OFF




MAP  integer   DENSITY  real  (integer integer integer)


                BOX  integer integer integer
                X-AX
                Y-AX
                Z-AX




STEREO   ON / TRUE


         OFF / FALSE
         CRYSTAL
         SIDE_BY_SIDE
         XCENTER-DIFFERENCE  integer
         ANGLE   real




VIEW   real
SCREEN   real
CENTER   CALCULATE      SELECT .... END


         ATOM      atom-number
         COORDINATES  3*real
                   X-AX real
                   Y-AX real




RATIO   real


SCALE   real


TRANSLATE   real real real


STEP
OVER TRUE


     FALSE




CLIP     TRUE


         FALSE
         Z-AX    real




UNIT integer   SELECT ... END   ...
(UNIT 6 )  (SELECT ALL END)


HISTORY  INITIALIZE


         PICK atom-number
         ATOM    NUMBER           ON  / TRUE
                 NAME / SYMBOL    OFF / FALSE
         RESIDUE NUMBER
                 NAME / SYMBOL
         SEQUENCE
         SEGMENT
         DISTANCE
         ANGLE
         DIHEDRAL
         INTERNAL
         DROP
         CONTINUE  TRUE / or/ FALSE
         NAME    TRUE /or/ FALSE





MENU   OFF /TRUE


       ON  /FALSE
       PAGE int


ERASE
INITIALIZE
DELETE
FROM  (integer)
COLOR integer
SET


PLOTTER (


        )
        ON
        OFF
        UNIT
        LWPLOT
        RASTER3D
        INITIALI





XCENTER   integer
YCENTER   integer
AXCENTER   real
AYCENTER   real


LIGHT  integer    ON


               OFF
               COLOR  3*real
               PHI   real
               PSI   real
               DISTANCE  real
               COORDINATES  3*real
               ANGLE real
               ATTENUATION 2*real
               EXPONENT  real
               AMBIENT
               DIRECTIONAL
               POSITIONAL
               SPOT




SHADOW  integer


REFLEX  BY   integer


        NUMBER integer real





SELECT



... SELECT ... END ...




When a SELECT sentence stands before any other command word
except UNIT it overrides the default main SELECTION which
selects ALL present atoms.  When it stands on some other
positions the SELECTION (second selection) applies only to
the next command word that chooses an atom or point
presentation on image. The two SELECTIONS (main and
secondary) are related by the logical .AND. operator.  The
second image selection is the same as SELECT (main image
selection) .and.  (second image selection) END.



PLOTTER


ON
OFF
LWPLOT
RASTER3D
INITIALIZE
UNIT



... PLOTTER (
     	    )
     	    ON
     	    OFF
     	    UNIT
     	    LWPLOT
     	    RASTER3D
     	    INITIALI





ON



Turns ON plotting.



OFF



Turns OFF plotting.



LWPLOT




RASTER3D




INITIALIZE



It writes the plotter form dependent initialization lines.




UNIT



... UNIT integer




The UNIT command words is used to define the FORTRAN unit to which
the PLOTTER data are sent.  The unit remains the same for all
following image command sentences until a new unit number is
defined via an IMAGE UNIT command sentence.



Turn the PLOT mode ON or OFF.  When the PLOTTER is on,
all the following image
commands will result in image on the screen and its copy on
a file assigned to number under UNIT.  The resulting
file(s), can be converted using LWPLOT to the postscript
language, that can be interpreted by post script laser
printer or by plotters.  The created plot files can be also
read again in GRAPH with the READ FILE command.
By default the PLOTTER mode is turned OFF.



OVER



... OVER TRUE
         FALSE




IMAGE OVER TRUE redwaws the entire molecular image.  The image objects
may get reorganized according to their type, color and their active
mode (ecah active object is drawn separately).



MOUSE



... MOUSE ON
          OFF





Enables or disables the mouse to mimic dials (yo send
motion events).



HISTORY



... HISTORY ...
         INITIALIZE
         PICK atom-number
         DROP






         ATOM    NUMBER           ON  / TRUE
                 NAME / SYMBOL    OFF / FALSE
         RESIDUE NUMBER
                 NAME / SYMBOL
         SEQUENCE
         SEGMENT
         NAME    TRUE
                 FALSE






         DISTANCE
         ANGLE
         DIHEDRAL
         INTERNAL
         CONTINUE  TRUE / or/ FALSE




HISTORY list is a list of PICKED atoms. The HISTORY list
can be INITIALIZED (the count of history atoms is set to 0).
The last PICKED atom can always be DROPPED from the list.
Up to 200 atoms can be PICKED.


When an atom is picked its HISTORY label appears on the
screen. HISTORY label can be composed from ATOM NUMBER and
NAME, RESIDUE NUMBER and NAME, SEGMENT name and SEQUENCE
name. Flag for each component can be set separately.
The visibility of the HISTORY labels can be controlled with
the IMAGE HISTORY NAME TRUE or FALSE command sentence.


! CLASS history label - put it in.



Projection parameters


XCENTER
YCENTER
AXCENTER
AYCENTER
VIEW
SCREEN
CENTER

ATOM
SEQUENCE
COORDINATES
CALCULATE

MATRIX
STEREO

SIDE_BY_SIDE
CRYSTAL
ON
OFF
ANGLE
SHIFTS

CLIP
SCALE
CONTRAST




XCENTER



... XCENTER   integer




Sets the xcenter of the screen relative to the absolute
xcenter(axcenter). The default value is 0.0.



YCENTER



... YCENTER   integer




Sets the ycenter of the screen relative to the absolute
ycenter(aycenter). The default value is 0.0.


!4 WIND   integer integer
!     Defines the upper right corner of the screen in screen coordinates.
!     The lower left corner has 0, 0  x and y values respectively



AXCENTER



... AXCENTER   integer




Sets the absolute xcenter value.



AYCENTER



... AYCENTER   integer




Sets the absolute ycenter value.



VIEW



... VIEW   real




Sets the distance from the viewer to the image center along
the Z axes. The default value is 500.0. Check with SHOW VIEW.



SCREEN



... SCREEN   real




Sets the distance from the viewer to the screen plane
along the Z axes or field of view falue. The default
value is system dependent.  Check with SHOW SCREEN.




CENTER


ATOM
SEQUENCE
COORDINATES
CALCULATE



... CENTER




Sets the image center to



ATOM



... ATOM      atom-number




Sets the CENTER to the specified ATOM position.



SEQUENCE



... SEQUENCE    string




Sets the CENTER to the CA atom of the residue with the
first found SEQUENCE string.  When the residue has no CA
atom then the center is set to the position of the first
atom in the residue.


If there are several residues with the same SEQUENCE id
then the first found is taken.  If you want to center on
some other residue with the chosen SEQUENCE id then apply




> IMAGE CENTER CALCULATE SELECT ... END




command.




COORDINATES



... COORDINATES  3*real




Sets the CENTER to specified COORDINATES.




CALCULATE



... CALCULATE SELECT ... END




Sets the IMAGE CENTER to the CALCULATED average of the
coordinates of the given SELECTION. The default SELECTION
are ALL atoms.



MATRIX



... MATRIX   integer  Z-AX real X-AX real Y-AX real ...




Sets the specified rotation matrix for orientation of the
image around specified axes by angle in degrees. Matrix 1
is the default matrix and is used in image processing.  See
also SET MATRIX.



STEREO


SIDE_BY_SIDE
CRYSTAL
ON
OFF
ANGLE
SHIFTS



... STEREO  ON  / TRUE
            OFF / FALSE
            CRYSTAL
            SIDE_BY_SIDE
            ANGLE real
            SHIFTS int int   int int   int int




Stereo commands manipulate stereo projection parameters,
the current mode and switch between stereo and mono
modes.  Default values are installation dependent.


STEREO item on several pages and keyword touch 's' toggle
between stereo ON and OFF.



SIDE_BY_SIDE



When stereo is ON the SIDE_BY_SIDE stereo mode splits
the screen into left and right viewports.  Default
stereo angle is adjusted for the relaxed eye (positive
angle).  For crosseyed stereo set a negative angle
value.



CRYSTAL



Defines the crystal eyes stereo mode.



ON



Turns the stereo projections ON.



OFF



Turns the stereo projections OFF.  Images will apppear
in a single viewport.



ANGLE



ANGLE sets the difference in view angle (image is
rotated along y) between the left and right image.  For
the CRYSTAL eyes stereo the ANGLE difference is actually
doubled, since left and right image are rotated into
opposite directions.  The default value is 3.0 degrees.


The value can be set interactively using
the DIAL_VIEW item (page 2) dial set.



SHIFTS



... shifts 3 * 2 int




If stereo windows don't overlap well adjust the shifts for
each window.  Each pair of numbers shifts a window for a
certain number of pixels in X and Y.  The first pair is for
the 3-D IMAGE window, the second for the menus on the side
and the third for the dials window.  the shifts must be
specified before you turn the stereo on.  Set the stereo
angle to 0.0 and start typing shifts.  (Don't use glasses
when doing it.)  When the two images almost ideally overlap
you have done it.


It is a bit anoying, but once you have the parameters
insert the command into the .main file (after an image init command).




> image stereo shifts 0 0  0 0  0 0




is the default.



CLIP



... CLIP TRUE / ON
         FALSE / OFF
         Z-AXIS  real




When the automatic clipping is ON (set TRUE) then the
clipping planes are defined automatically so that the
complete IMAGE appears on the screen.  The option shouldn't
be applied for larger molecules since it slows down the DIAL
respond, However, the IMAGE is displayed with optimal depth
contrast.  The default flag is set to OFF and the default
Z-AXIS value is set to 20.0.



SCALE



... SCALE real




SCALE defines a scaling factor for the image objects.
The image scaling factor should be positive.



CONTRAST



... CONTRAST real




Specifies the contrast between front and back of an image.  Interval
is between 0 and 1.0.  1.0 means no contrast depth (depth cueing off).
The default number is hardware and system version dependent.



RATIO



... RATIO real




Sets the scaling factor for ATOM CROSSES.



ERASE



... ERASE  string




ERASES the screen and clears the programs memory from saved
images.  The default argument is *, which means that all
displayed objects will be ERASED. When image object is
explicitly defined only the image labeled with the string is
deleted.  See also IMAGE FROM.



FROM



... FROM  integer




Protects displayed IMAGES from erasure. The images bellow
the integer number can not be deleted with command IMAGE
ERASE. When no image object number is specified, as the
default value the last image object is taken.



INITIALIZE



... INITIALIZE




INITIALIZES the graphic device and established connections.


!WINDOW
!Draws the window borders in specified COLOR.



COLOR



... COLOR integer




Sets the current COLOR for drawing objects on the screen.
See IMAGE SET.



SET



... SET




Disables the current COLOR set by the last COLOR command.
The program takes the atomic SET colors as specified in
module SET_COLOR.



LINE



... LINE integer




Defines the line type to be used when drawing vectors.
Default is continues line. It doesn't work on PS330.



DELETE



... DELETE ...




When the DELETE flag is set, the following IMAGE commands do
exactly opposite from the usual IMAGE command sentence.  The
images of selected atoms are deleted from the program's
memory and cannot be redrawn any more.



DIALOGUE



... DIALOGUE (real)




Transfers the control from terminals keyboard to the DIALS
and mouse.  A specified real number changes the current DIAL
scaling factor by multipling it.



FORWARD



... FORWARD




Transfers the control from command line mode (keyboard) to
DIALS and a mouse.  The difference between this and the
DIALOGUE command is that this one changes the mode also when
issued in a command file, whereas the DIALOGUE command has
no effect.



Kinds of presentation


Connections
ATOM
FORCE
RESIDUES
SEQUENCE
SEGMENT
MARK
POINTS

SURFACE
VOLUME
NUMBER
POTENTIAL
DENSITY
RIBBON
3ANGLE

MAP

DENSITY
CONTOUR
BOX
GRIDS
ON
OFF
INCLUDE
REMOVE
X-AXIS
Y-AXIS
Z-AXIS
LINES
STICKS
AREA





Connections



... BONDS   [LINES]
    HBONDS  DISTANCES
    PAIRS   STICKS integer




When in COLOR mode is on, all connections between atoms
appear in one color, while when the SET mode is on, each
connection is divided in 2 parts of equal length, colored
according to part's atom color.  DISTANCE displays
distances of the selected connections.  Connections can be
displayed also as STICKS (cylinders) with the specified
RADIUS and DENSITY of polygons.  See SET STICKS ...  An
integer that can be specified after command word STICKS is
a flag that tells whether the polygons are shaded smoothly
(more than 0 ) or not ( less or equal 0).



ATOM



... ATOM NUMBER
         NAME / SYMBOL
         CROSS
         CLASS
         BALL integer




ATOM NUMBERS and NAMES / SYMBOLS can be drawn near the
selected atom center.  CROSS is drawn through the atomic
center. The length of cross lines is specified by the RATIO.
CLASS displays atom classes or atom types as specified by an
SET CLASS or DEFINE command sentence.  It is useful for
identifying atom types when building a new residue into
topology libraries.  ATOM BALLS (spheres) are drawn with the
currently valid REFLECTION properties and chosen BALL
definition (see SET BALL).



FORCE



... FORCE real




Draws FORCES acting on atoms as calculated by the last
ENERGY or MINIMIZE command sentence. The FORCE IMAGE is a
vector with origin at the atom center and is pointing
(pushing) the atoms in the direction of the gradient.
(Pushing with the positive scaling value and pulling with a
negative one.)  The FORCE unit is kcal/A. When FORCE
scaling factor is 1.0 then is the length of the 1 kcal/Amol
force 1A.



RESIDUES



... RESIDUE NUMBER
        NAME / SYMBOL




RESIDUE NUMBER and NAMES or SYMBOLS of selected atoms are
displayed.



SEQUENCE



... SEQUENCE




SEQUENCE symbols can be drawn on the place of residue
numbers.



SEGMENT

SEGMENT NUMBER


        NAME / SYMBOL




SEGMENT NUMBER and NAMES or SYMBOLS of selected atoms are
displayed.



MARK



... MARK SELECT ... END
         ON
         OFF




MARKS selected atoms with a star.  It is usually activated
automatically when KEYS active, passive, image and anchor
are being modified from the SELECTIONS menus.  The MARKS can
be turned ON or OFF.



POINTS


SURFACE
VOLUME
NUMBER
POTENTIAL
DENSITY
RIBBON
3ANGLE



... POINTS [integer] ...




Since each POINT is related to an atom, they can be also
SELECTED with a SELECT ... END sentence.  The integer
following POINTS is optional.  Since on Silicon Graphics
machines size of points is not directly adjustable, increasing
level from 0 to 1 creates larger spots on screen and slows
down dial respond substantially.  1 is recommended to be
used for preparing slides.



SURFACE



... SURFACE REENTRANT
            CONTACT
            ACCESSIBLE
            ALL




Points of REENTRANT, CONTACT or both SURFACES (ALL) are
drawn.  Colors are taken from the atom_color array
(the SET mode) or are defined by the color command.



VOLUME



... VOLUME  ATOM
            ACCESSIBLE




The use of volume points is now obsolete, because their
function is more than replaced with operations on the MAP(s).



NUMBER



... NUMBER   ON    / TRUE
             OFF   / FALSE




The NUMBER flag can be set ON or OFF. When it is on, the
value at a point will be displayed as well. The point values
can be either SURFACE, DENSITY, POTENTIAL or VOLUME.



POTENTIAL



... POTENTIAL STEP real
              RANGE real real




When a POTENTIAL or DENSITY points are selected, then the
colors of points will be chosen + and - from the defined
color for STEP value. Each STEP the color is increased or
decreased by 1. When RANGE is specified then only the points
in the range will be colored in specified color and drawn.
SET flag for atom coloring is meaningless when STEP or RANGE
are activated.



DENSITY



... DENSITY STEP real
            RANGE real real




When a POTENTIAL or DENSITY points are selected, then the
colors of points will be chosen + and - from the defined
color for STEP value. Each STEP the color is increased or
decreased by 1.  When RANGE is specified then only the points
in the range will be colored in specified color and drawn.
SET flag for atom coloring is meaningless when STEP or RANGE
are activated.



RIBBON



... RIBBON LINES
           STICKS
           RGB
           COLOR




Displays ribbons as LINES or STICKS of corresponding color or atom
color definition.


See also "SET RIBBON" comamnd in (MAIN_COM:set.html)



3ANGLE



... 3ANGLE LINES
           AREA
           RGB
           NORMAL
           INVERT





Displays surfaces with filled surfaces eitheras in a single color or
corresponding atom color definition.


When RGB each triangle may get variable color, which is interpolated
between the colors of each triangle point according to the distance.


NORMAL may be also INCERTED - which enables to look at the surface
from its inside.



MAP


DENSITY
CONTOUR
BOX
GRIDS
ON
OFF
INCLUDE
REMOVE
X-AXIS
Y-AXIS
Z-AXIS
LINES
STICKS
AREA



... MAP  intg   DENSITY /CONTOUR real  (integer_x integer_y integer_z)
                BOX / GRIDS integer_x integer_y integer_z
                ON
                OFF
                INCLUDE (int)
                REMOVE
                X-AXIS
                Y-AXIS
                Z-AXIS
                AREA ON
                     OFF
                LINES
                STICKS ON
                       OFF
                       DENSITY int
                       RADIUS  real




MAP IMAGE command control displaying of maps.
SHOW MAP reveals some map details.



DENSITY



... DENSITY real




Displays the specified MAP at a certain density level.


CONTOUR is a synonym.



CONTOUR



... CONTOUR real




Displays the specified MAP at a certain density level.



BOX



... BOX integer_x integer_y integer_z





GRIDS



... GRIDS integer_x integer_y integer_z





ON



Turns map redrawal (recontouring) on, so that a RE_MAP will
recontour the map at the current center of the screen.  This
is the default, but you can turn a map recontouring also
OFF.



OFF



Turns map redrawal (recontouring) OFF, so that a RE_MAP command
will not recontour the map at the current center of the screen.



INCLUDE



... (int)




You can INCLUDE or REMOVE a map from the display list of
image of objects and teher by from the screen.  By default a
map image is part of the background image (number 0).
You can insert it into some other image object and so move
the map on the screen as a part of movement attached to atoms
(rotations, translations etc...).



REMOVE



Maps whicch are parts of the image displayed on a screen can
be REMOVED from the displayed list and later on INCLUDED as
well.  A shortcut is to press keys from '1' to '0' and maps
will be included and removed from the display.



X-AXIS



Maps can be contoured as lines along a certain axis (X-AXIS,
Y-AXIS, Z-AXIS) or with all three projections simultaneously
(LINES) with STICKS ON or OFF.



Y-AXIS



Maps can be contoured as lines along a certain axis (X-AXIS,
Y-AXIS, Z-AXIS) or with all three projections simultaneously
(LINES) with STICKS ON or OFF.



Z-AXIS



Maps can be contoured as lines along a certain axis (X-AXIS,
Y-AXIS, Z-AXIS) or with all three projections simultaneously
(LINES) with STICKS ON or OFF.



LINES



Turns STICKS and AREAS presentation of maps off and turns
the default LINES (wire) presentations.



STICKS



...  STICKS ON
            OFF
            DENSITY int
            RADIUS  real




Maps contours can be displayed as STICKS (when turned ON) of
various precesion (DENSITY) and RADIUS (thickness).



AREA



... AREA ON
         OFF




Displays MAP as a solid polygonal surface when turned ON.



Examples





MAIN> image select pep end bond select atom name CA end  -
MAIN> residue name




Displays bonds of the key "pep" and at positions of each CA
included in the key "pep" also its residue name




MAIN> image color 60 map 3 dens 0.9 5 5 5




Displays in color 60 map number 3 at density level 0.9 in a
box 5 grids in all directions from the center.



Dialog_mode



The DIALOG mode can be entered only from MAIN> directly and
not from a command file. The IMAGE and ATOMIC
transformations can be driven by dials and commands picked
from menus combined with picked atoms in the HISTORY list.


Menu commands are actually shortened notations for command
sentences.  Some of resulting command sentences appearing in
manual within square brackets [] are written by the program
and later on executed.  Command interpreter does not
distinguish between the sentences typed in from the
keyboard and the ones written by the program.  The command
sentences written by the program itself are also stored
into the file INPUT.COP before they are executed. So even
if no update of coordinates in a file has been done between
the run, all the changes off structural data could be
retrieved afterwards.  In the case of computer or program
crash or a mistake the user's effort is not lost as long
data from the file are accessible.







INTERNAL


SYNTAX
EXIT
SELECT
SET

INTERNAL
VARIABLE
ZTABLE

SHOW
SYMBOL
NUMBER
VARIABLE
CONSTANT
EXAMPLES

INTCOOR.TXT        23-FEB-1993


In INTERNAL module internal coordinates (DISTANCES, ANGLES and
DIHEDRAL ANGLES) and internal coordinates connectivity table
(ZTABLE) can be edited.  Directly by defining values explicitly
or indirectly by defining variables and their values.  Each
internal coordinate may have its own variable name as well as a
single variable name  may be shared by a group of internal
coordinates.  ZTABLE, however, consist only of atomic number
references.



SYNTAX

SET   INTERNAL   VARIABLE  DISTANCE


                 CONSTANT  ANGLE
                           DIHEDRAL
                           (ALL)
                 DISTANCE   real
                 ANGLE      real
                 DIHEDRAL   real
                 (ALL)      3*real






      VARIABLE  STRING real
                       AUTO      DISTANCE
                                 ANGLE
                                 DIHEDRAL
                                 (ALL)






      ZTABLE  ATOM-NUM DISTANCE   atom-num
                       ANGLE      atom-num
                       DIHEDRAL   atom-num  [(0), 1 or -1]
                       (ALL)      3 x atom-num [(0), 1 or -1]




SHOW  INTERNAL   VARIABLE  DISTANCE


                 CONSTANT  ANGLE
                           DIHEDRAL
                           (ALL)
                 DISTANCE
                 ANGLE
                 DIHEDRAL
                 (ALL)






      VARIABLE  string  LIST






      ZTABLE  atom-num DISTANCE
                       ANGLE
                       DIHEDRAL
                       (ALL)




SYMBOL
(NUMBER)


VARIABLE
(CONSTANT)


IDENTIFY  atom-num


          atom-symbol





EXIT

EXIT


EXIT   exits the INT_COOR modul and returns to MAIN.



SELECT

SELECT ... END


A command will allways act on the last defined SELECTION.  By
default all atoms are SELECTED.



SET


INTERNAL
VARIABLE
ZTABLE

SET



INTERNAL

INTERNAL


Sets the distance, angle, dihedral or all internal coordinates
a real value.
Using VARIABLE command word the variable flag for the selected
internal coordinates of atoms is set.
The CONSTANT unsets the variable flags.
The CONSTANCE or VARIABLE ought to be used first otherwise a real
value for specified internal coordinate specification is required.



VARIABLE

VARIABLE


Connects the selected internal coordinates with a variable name.
If a variable name exists (differs from 4 blanks('    ')),
a real value can be seted to all
the internal coordinates connected with that variable name.
If AUTO is specified then the string is a root for automatic
assigning of varible name. Each time a variable name is assigned to
specified internal coordinate, a number is increased for 1 and added.



ZTABLE

ZTABLE


The connections in the table can be overriden by typing in
the new connections. When changing the second angle specification
into the dihedral angle specification two numbers are required.



SHOW

SHOW


Shows the data fields than can be set.
VARIABLE shows only the first value of chosen variable.
When the user wants to see the list of all the values, that
can be different than the command word LIST should be used.
While showing the ztable the output can be changed from numbers
to atom symbol and vice versa by using the SYMBOL or NUMBER command
word.



SYMBOL




NUMBER



SYMBOL and NUMBER commands are used to set the symbol flag (fsymb)
that changes from atom-number to atom symbol and vice versa
in input and output. By default the numbers are required to
identify the atoms.
When symbol flag is set then the user shoul type in the atom
symbol. The atom with this symbol will be found in the selected range
if it is uniquely defined.
When '-' stnands before the atom symbol
then the first atom with that identifier, counting from the
first atom in the selection down, will be found.
When '+' stnands before the atom symbol
then the first atom with that identifier, counting from the
last atom in the selection up, will be found.



VARIABLE




CONSTANT



VARIABLE and CONSTANT commands are used to set the variable_display
flag (fvari).
When fvari flag is set then variable names are displayed
if they exist on the place of internal coordinate value, if
SHOW INTERNAL command sentence is used.



EXAMPLES





      set var a auto angle
      generates variables for angles a1, a2, ... a56, untill the end
      of selection.







Io_control


Syntax
CLOSE
OPEN
INQUIRE
REWIND
RETURN
STREAM
@
SUBROUTINE
Examples

io_control.txt           17-Oct-1996


Input/output group of command sentences are used to access
data files on disk in order to read or write data or
redirect command input.  READ and WRITE command sentences
are described separately.



Syntax







CLOSE UNIT int


INQUIRE variable "PROMPT"


OPEN UNIT int FILE file_name READONLY


                             WRITE_ENABLE


REWIND UNIT int


       FILE




RETURN


STREAM UNIT int


@ file_name
< file_name



CLOSE

CLOSE UNIT int


CLOSES the currently OPENED file on FORTRAN UNIT int.



OPEN

OPEN  UNIT int


      FILE file_name
      READONLY
      WRITE_ENABLE
      OVER_WRITE
      APPEND
      FORMATTED
      UNFORMATTED
      RECORD_LENGTH int




OPENS access to the FILE name file_name on FORTRAN UNIT int.
Default options are FORMATTED, READONLY files with variable
record length (0).  To create a new FILE and write into it,
the FILE must be OPENED using the WRITE_ENABLE command word.
OVER_WRITE means that a file will be overwritten if it
exist.  Otehrwise a new file will be opened.
RECORD_LENGTH int defines fixed records (when greater than 0).
FORMATTED and UNFORMATTED file attributes need no explanation.


You can use your own environments under UNIX to shorten file
names or to make your command files the same throughout
various computers, even UNIX and VMS environments.  An
environment string must end with a colon as 'MAIN:' and
should be defined as '/metka/dus/main/'.  There is no
translation of environment strings under VMS, whre you
should use the assign or define VMS commands.



INQUIRE

INQUIRE VARIABLE string


        REAL
        INTEGER
        CHARACTER
TEXT "SOME PROMPT WITH AN EXPLANATION"
        GLOBAL
        LOCAL




INQUIRES a value for a variable directly form the terminal,
regardless from where the current command input comes from.
VARIABLE string gives the variable name.  INTEGER, REAL or
CHARACTER variables can be inquired.  There is no default
type recognition, so you have to specify the variable type
you want.  The specified variables can be LOCAL or GLOBAL.
The TEXT inside "" appears at the beginning of a line as a
prompt.


An INQUIRE sentence is used for example when PLOT has been
activated from the IMAGE menu asking for the name of the
output file.  The command is also quite often used to obtain
some input from the menu macros.



REWIND

REWIND UNIT int


       FILE




REWINDS file OPENED under FORTRAN UNIT int or REWINDS the
current command input file. The later is utilized in loops.



RETURN

RETURN


RETURNS the command input to the calling input level.  It can
be used in the command files entered with the '@' or STREAM
command sentence. RETURN from the default command input level
has no effect.


It deletes all local variables.



STREAM

STREAM UNIT int


Transfers the command input to the file accessed under
FORTRAN UNIT int. 10 levels of command STREAMING are allowed.
After RETURN command the input file is not closed as by the
@ or<.



@

@ file_name     integer
< file_name     real


                strings




Transfers the command input to the file file_name. 10
levels of @ command are allowed (the stack for input files
has 10 places).  When command interpreter reaches RETURN or
end of file the file is closed.  The default file_name
extension is '.com', so that it doesn't have to be
specified.


Arguments of integer, real or character type can be passed to a
command file macro via the 'by value' mechanism.  On the lower level
they are interpreted with the SUBROUTINE command, which assignes
variable types to each particular arguments.  This way created
variables exist only locally within the current command macro
procedure. They are deleted when the RETURN command is invoked.



SUBROUTINE

SUBROUTINE INTEGER int


           REAL    real
           CHARACTER string




Creates local variables transferred through the macro
calling command @ and assigns them local names.  ANy
combination and number of variable names and types can be
applied.  Naturally, the transffered variables must match by
their type and number.




> subroutine real r1 integer GG ...





Examples





MAIN> open unit 1 file gly.dat write






MAIN> close unit 2






> return






MAIN> stream unit 99






MAIN> @>utils/protein.bond






> @some_macro int II real r1 real r2 ...












JOIN

JOIN.TEX   19-OCT-91


syntax:
JOIN   atom-number  atom-number


       RESIDUE   SELECT ... END   SELECT ... END




JOINS atoms by forming covalent bonds or 2 SELECTED
RESIDUES into 1. The RESIDUES should follow each other.
Joining  of two SEGMENTS can be achieved by the RENAME
command sentence.







KEY

KEY.TEX    19-OCT-91


Syntax
KEY   string    SELECT ... END


                DROP
                INITIALIZE




User can define his own KEY(s) that can be later used in
SELECT statements.  The KEY name can be up to 10 characters
long string.  When a key and a MAIN tag have the same name,
then the KEY value will prevail. In a SELECT sentence the
signs like % and * can be used in order to access more than
one KEY at a time.


Keys can be DROPPED of INITIALIZED. By DROPPING only the
particular KEY is deleted, while by INITIALIZE all defined
KEYS are gone. Also by INITIALIZING a string, as a dummy
key, must be typed in.


Use SHOW KEY or SHOW SELECTIONS to see the list of defined
KEY(s) and number of SELECTED atoms in each one.


When no atom is SELECTED in the specified KEY, a warning
message appears.







MAKE


BOND
CTABLE
ZTABLE
PAIR

Syntax
INITIALIZE
APPEND
INVERT
SELECT ... END
SEQUENCE
ATOM
RAMACHANDRAN

POINTS

Syntax
INITIALIZE
APPEND
FROM

ATOMS
BONDS
MAP

PICK
WEIGHT
RANGE
CUT
CENTER
RADII
BOX
AROUND
LOCAL



ATOMS

POINTS
COORDINATES
MERGE

DISTANCE
RESIDUES


MAP

Syntax
CHARACTER
NUMBER
REAL
COMPLEX
INTEGER
INTG*2
GRID
AUTO_GRID
CELL
FROM
INITIALIZE
SET
ZERO
SELECT
BOX
AROUND
FILL
REMOVE
EXPAND
SHRINK
COPY
SCALE
RESCALE
SHIFT
RESHIFT
INVERT
ROTATE
TRANSLATE
ADD
MULTIPLY
MERGE
CUT
RADIUS
WEIGHT
RMS
ANALYZE
ATOM

RADII
MASK
CLEAR
DENSITY
SYMMETRY
DISTANCE
FUNCTION
HIGHER

OVER
NEW

SEGMENT

MAKE.TEX     29-MAR-94


The command word order is important only for the first 2
command words (MAKE BOND ...).  The remaining command words
can follow in any order.  Something is MADE from something
else. For example a covalent BOND list is made from the
TOPOLOGY library.



BOND

MAKE BOND  FROM RESIDUES


                ZTABLE
                TOPOLOGY
                ATOM  atom-num1 iatom-num2  DROP
                                            APPEND
           APPEND
           INITIALIZE
           SELECT ... END




BONDS and CTABLE are only two different ways of the
connection table presentation. By make BONDS covalent BONDS
are created or their multiplicity (bond order) is modified.
MAKE BOND makes or modifies the covalent BONDS of the
SELECTED atoms


from RESIDUES (by connecting CA atoms), or

from the distance connections in the ZTABLE or

from the TOPOLOGY library or

from a pair of ATOMS (atom-num1/2) specified by their
atom numbers.



When after an ATOM definition DROP or APPEND is applied, the
BOND order of that particular bond can be increased or
decreased.  The bond list can be INITIALIZED. By default the
newly created BONDS are APPENDED to already existing ones.



CTABLE



BONDS and CTABLE are only two different ways of presentation
of the connection table. So see MAKE BOND.



ZTABLE

MAKE   ZTABLE  FROM   CTABLE / BONDS


                      TOPOLOGY
               (APPEND)
               INITIALIZE
               SELECT ... END (ALL)




ZTABLE records are parts of INTERNAL coordinates records. In
the ZTABLE the reference atoms for the distance, angle and
dihedral angle are stored.


The ZTABLE can be created from the CTABLE by a search
through the neighbouring atoms. However, since the reference
atoms, should have lower number than the atom they define,
the order of the atoms influences the ZTABLE and can result
in the ``holes'' in it. A hole in ZTABLE is, when an atom
has less than 3 reference atoms.  The holes can be corrected
in the INTERNAL_COORDINATE module.  The ZTABLE can be
INITIALIZED or the new references can be APPENDED to already
existing ones. The default SELECTION is the ALL.



PAIR


Syntax
INITIALIZE
APPEND
INVERT
SELECT ... END
SEQUENCE
ATOM
RAMACHANDRAN



MAKES a PAIR list by adding a single pair (atom-num1/2) or
the whole set of pairs.



Syntax



MAKE   PAIR   atom-num1 atom-num2
              INITIALIZE
              APPEND






              SELECT ... END    SELECT ... END
              SEQUENCE
              ATOM
              INVERT






              RAMACHANDRAN





INITIALIZE



... INITIALIZE




INITIALIZE the PAIR list (Sets the pair counter to zero).



APPEND



... APPEND ...




APPEND is the opposite from INITIALIZE. This is the default.



INVERT



... ... INVERT




INVERTS the second column of the PAIR list, so that the last
in the column becomes the first one and so on.



SELECT ... END



... SELECT ... END




Usually 2 SELECTIONS have to be defined, since the PAIR
generation pairs the first atom from the first SELECTION
with the first from the second SELECTION, the second from
the first selection with the second from the second
selection and so on. The pair generation stops when no more
atoms are found in the first or in the second selection.



SEQUENCE



... SEQUENCE




PAIRS only atoms that belong to the residues with the same
SEQUENCE name.



ATOM



... ATOM




PAIRS ATOMS of a residue from the first SELECTION with a
residue in the second SELECTION by matching the atoms
according to their ATOM NAMES.



RAMACHANDRAN



... RAMACHANDRAN




Generates PAIRS of atoms so that their INTERNAL dihedral
coordinates represent PHI and PSI dihedral angels of the
peptide chain.  Only one SELECTION is required. So generated
pair list is necessary for displaying the RAMACHANDRAN plot
with the GRAPH routines.



POINTS


Syntax
INITIALIZE
APPEND
FROM

ATOMS
BONDS
MAP

PICK
WEIGHT
RANGE
CUT
CENTER
RADII
BOX
AROUND
LOCAL





Major purpose of the following conversions is to extract
information from electron density MAPs, that can be used
either for density maxima analyzes (in a map skeletonization
cross vector verification or in identification for solvent
sites) for correlation of atomic model with electron density
(FROM ATOMS and BONDS).


The MAKE POINTS can serve also as intermediate storage of
positions and density in conversions between ATOMS and MAP(S).



Syntax



MAKE POINT INITIALIZE
           APPEND
           FROM ATOMS MAP inte
                      SELECT ... END
                BONDS MAP inte
                      SELECT ... END
                      DIVISIONS   inte
                MAP inte LOCAL  inte
                         PICK   real2 real2  real3
                         WEIGHT real1 real2
                         RANGE  real1 real2
                         CUT
                         CENTER  (see SET CENTER)
                         RADII  real1 [real2]
                         BOX  6*inte





INITIALIZE



... INITIALIZE




INITIALIZES the POINT list. (Sets the POINT counter to zero.)



APPEND



... APPEND




APPENDS newly created points to the present ones.  This is the
default.



FROM


ATOMS
BONDS
MAP

PICK
WEIGHT
RANGE
CUT
CENTER
RADII
BOX
AROUND
LOCAL




... FROM ...




POINTS will be created either from ATOMS, along covalent BONDS
or at grid positions of a MAP.  The word FROM is here to
increase readability of the syntax.



ATOMS



... ATOMS SELECT ... END
         MAP inte




When ATOM is specified POINTS are created from the SELECTED
atom positions and the density is calculated from the 8
closest MAP grid points by a linear interpolation algorithm.
There is no default SELECTION or MAP.



BONDS



... BONDS SELECT ... END
         MAP inte
         DIVISON  inte




POINTS are calculated along the covalent BONDS between the
SELECTED atoms.  The 'inte' specifies the number of
DIVISIONS (points) generated along each BOND.  The density
at each point is calculated from the chosen MAP by a linear
interpolation algorithm from the 8 closest map grid points.
There is no default SELECTION or MAP.



MAP


PICK
WEIGHT
RANGE
CUT
CENTER
RADII
BOX
AROUND
LOCAL



... MAP inte LOCAL  inte
             PICK   real2 real2  real3
             WEIGHT real1 real2
             RANGE  real1 real2
             CUT
             CENTER  (see SET CENTER)
             RADII  real1 [real2]
             BOX  6*inte
             AROUND 3*inte




POINTS are extracted from a MAP with a search algorithm.
For description see below.



PICK



... PICK   real1 real2  real3 MAP ...




PICKS POINTS in a chosen MAP with a second order Polinomyal
search around each grid point that has higher density than
real1. Polinomyal coefficients are defined by a least square
fit procedure from the 125 surrounding MAP grid points.
POINTS that have lower calculated value than real2 and that
are more than real3 of GRID in any direction away from the
origin grid point are rejected. (This is a computationally
slow procedure. Its use has been replaced by the WEIGHT
option.)



WEIGHT



... WEIGHT (real1 real2)




Applies the WEIGHTING algorithm for the point search. Map
grid points, which density values are in the specified range
real1 real2 (RANGE can be specified with the RANGE or with
the WEIGHT command), are transformed to POINTS so, that
first the intervals of grid points laying along the X
direction with the density values inside the range are found
and then their WEIGHTING CENTER is calculated. Weights are
the density values, and the generated point obtains the
weighting center coordinates.



RANGE



... RANGE  real1 real2




From each MAP grid point with the density value in the
specified density range, a density POINT is generated.



CUT



...




By default the points are generated anywhere in the space
from the current (IMAGE) CENTER for the specified BOX sizes.
With the CUT the points can be generated only within the MAP
boundaries. The generation of points outside MAP boundaries
is not performed.



CENTER



... CENTER ...




See SET CENTER for the CENTER definitions.



RADII



... RADII real1 [real2]




Defines the RADIUS of the sphere around the CENTER, inside
which points are to be generated.  When both RADII are
specified then only the grid points at the distances between
the specified RADII from the CENTER are chosen.



BOX



... BOX 6*int




The area for the point generation can be defined also
exactly in the grid coordinates by the BOX command. The BOX
is defined from the point (int1, int2, int3) to the point
(int4, int5, int6). (CUT can modify the boundaries.)
The default BOX is the whole map.



AROUND



... AROUND 3*int




The AROUND redefines the BOX by setting new limits.  New BOX
expands for specified number of grid points away from the
CENTER position in all directions.



LOCAL



... LOCAL inte




POINTS are created at positions of the LOCAL maxima as found
by a MAKE MAP LOCAL sentense, their density value is however
taken from the MAP.



ATOMS


POINTS
COORDINATES
MERGE

DISTANCE
RESIDUES


MAKE  ATOMS SELECT ... END


            MERGE   DISTANCE  real
                    RESIDUE


!                   RING  inte


            FROM  ATOMS
                  BONDS
                  COORDINATES  3*real
                  POINTS  REINDEX




MAKES ATOM(S) from POINTS, position (COORDINATES) or modifys
the atoms by the ATOM MERGE procedures that on the base of
connectivities rearranges the atom arrays.  By default all
atoms are selected.



POINTS



... POINTS   REINDEX




Makes ATOMS (as dummies with the ATOM NAME 'X ') in positions
of all SELECTED POINTS. All newly created atom are joined
within a single residue and segment. WEIGHT of the atom is
filled with the point value.  REINDEX is an option that, after
an atom has been created at the current point position,
modifies the point atom index to the newly created atom.



COORDINATES



... COORDINATE 3*real




Only one atom at position 3*real (x,y,z) is created.



MERGE


DISTANCE
RESIDUES



... MERGE    SELECT ... END
             DISTANCE real
             RESIDUE




Reduces the number of atoms by MERGING the SELECTED atoms
into each other.



DISTANCE



... DISTANCE real




When DISTANCE is specified, the atoms forming covalent BOND
pairs that are closer than the specified DISTANCE, are MERGED
together.  The MERGED atom has coordinates of the arithmetic
middle of the pair and keeps all covalent BOND connections to
the rest of the atoms.  Atoms are MERGED in many cycles so
that finally there is not a single pair that could be MERGED
accoridng to the specified DISTANCE criterion.  However, a
pair of atoms connected only to each other can not be MERGED.



RESIDUES



... RESIDUES




All atoms inside a covalent BONDING network are MERGED into
a single ATOM placed at their arithmetic middle. No covalent
bonds are kept.



MAP


Syntax
CHARACTER
NUMBER
REAL
COMPLEX
INTEGER
INTG*2
GRID
AUTO_GRID
CELL
FROM
INITIALIZE
SET
ZERO
SELECT
BOX
AROUND
FILL
REMOVE
EXPAND
SHRINK
COPY
SCALE
RESCALE
SHIFT
RESHIFT
INVERT
ROTATE
TRANSLATE
ADD
MULTIPLY
MERGE
CUT
RADIUS
WEIGHT
RMS
ANALYZE
ATOM

RADII
MASK
CLEAR
DENSITY
SYMMETRY
DISTANCE
FUNCTION
HIGHER

OVER
NEW



The MAKE MAP inte command acts on the referenced MAP usually
exploiting data present in the FROM map.


Each MAP has a header including cell constants, GRIDS and a
BOX (or a layout) and array of density data (grid points).
Data are stored in arrays of character*1 (CHARACTER),
integer*2 (INTG*2), integer*4 (INTEGER), real*4 (REAL or
NUMBER) and complex (COMPLEX) values.  Full functionality
can be exploited only with REAL*4 maps.  The code does not
fully support maps in integer*2, integer*4 or complex form
so please stick to the examples.


A grid point is masked when its value is 255 (character*1
MAP) or greater than 9999.0 (of the real*4 MAP). A grid
point is assumed to be empty when its value is 0 (character
map) or smaller than -9999.0 (real*4) map.  All values in
between the masked and empty region are considered as
electron density region.



Syntax



MAKE MAP  inte   FROM inte
                 INITIALIZE  inte
                 BOX   6 * inte
                 GRID inte inte inte
                 CHARACTER
                 NUMBER






                 LOCAL
                 AROUND inte
                 SET    inte  inte real
                 ZERO
                 COPY
                 ATOM  RADII
                       MASK real
                       CLEAR real
                       DENSITY
                       DISTANCE real
                       HIGHER
                       SYMMETRY  [inte]
                 SELECT ... END
                 FILL  inte
                 REMOVE  inte
                 EXPAND
                 SHRINK
                 ROTATE   MATRIX inte
                          RMS
                          CENTER  3*real
                 TRANSLATE    VECTOR   3* real   DISTANCE real
                              RMS
                 CENTER
                 ADD
                 OVER
                 MULTIPLY
                 SCALE   real
                 RESCALE
                 INVERT
                 MERGE  WEIGHTED real1 real2
                        HIGHER
                 CELL
                 CUT / DENSITY   real
                 RADII     real
                 WEIGHT   LINEAR
                          GAUSSIAN
                 ANALYZE  STEP  inte
                          RANGE real





CHARACTER

MAKE MAP 1 FROM 0 CHARACTER ...


A new CHARACTER*1 MAP is to be created.



NUMBER

MAKE MAP 1 FROM 0 NUMBER ...


A new real*4 MAP is to be created. NUMBER is synonym of REAL.



REAL

MAKE MAP 1 FROM 0 REAL ...


A new real*4 MAP is to be created. REAL is synonym of NUMBER.



COMPLEX

MAKE MAP 1 FROM 0 COMPLEX ...


A new COMPLEX map is to be created.



INTEGER

MAKE MAP 1 FROM 0 INTEGER ...


A new integer*4 map is to be created.



INTG*2

MAKE MAP 1 FROM 0 INTG2 ...


A new integer*2 map is to be created.



GRID



... GRID 3*inte




In the case when a new map is created FROM 0 MAP (no map), the
number of grid points per unit cell length must be defined to
build it. BOX has to be defined explicitly as well. The map
cell constants are taken from the current MAIN cell
constants. By default the cell constants are set to 1.0 A for
the lengths and 90.0 degrees for the angles.


See also AUTO_GRID.



AUTO_GRID



... AUTO_GRID real




When AUTO_GRID is used, the number of grdi points along each
unit cell axes are calculated from the used unit cell and
resolution limits of the diffraction data used:




 ngrid = ucell / resol_max * auto_grid




The default AUTO_GRID multiplier is 3.05 but you can provide
your own value.



CELL



... CELL




Fills the map by the values of grid points of the reference
(FROM) map applying all crystal symmetry operations. The CELL
MAP should at the beginning be INITIALIZED to an empty map,
since only the points different from 0(character map) and
smaller than -9999 in the real map are overwritten by the
program.


When CELL is used within the same command as INITIALIZE
then, it only defines a unit cell BOX.



FROM



... FROM inte




Assigns the FROM inte MAP as the reference MAP.  When the
reference map does not exist (the FROM inte is 0), then a new
map can be created only if the GRIDS, BOX or AROUND and
INITIALIZE options of the MAKE MAP are specified. It is
recommended to have read the CELL constants, since their
default values are 1.0 1.0 1.0 and 90.0, 90.0, 90.0.



INITIALIZE



... INITIALIZE inte




Creates and INITIALIZES a map. The reference (FROM) MAP is
required. By default the new map is filled with zeros [0].
If some other value is desired it should be specified by the
inte.



SET



... SET inte inte real




SETs all grid points stored inside the specified integer
interval to the real value.


When combined with the BOX command it is possible to limit
the SET command to a ceratin map region (BOX).


By character maps the integer numbers [0-255] refer to the
internal program presentation of density values and not to the
real density values themselves.



ZERO



Sets the whole map to ZERO regardles of a map grid point
value.  This command was added because sometimes intervals
specified through a SET command were not enough.



SELECT



... SELECT ... END




A SELECTION is applied by ATOM mask or density generation,
or when the boundaries (BOX) of the INITIALIZED map are
defined indirectly AROUND an atom SELECTION.  For the syntax
see SELECT.



BOX



... BOX 6* inte




BOX defines the positioning of the new map in grdi oordinates. By
default (when no BOX or AROUND SELECTION are specified) the map size
is copied from the reference (FROM) map. The first 3 inte define the
origin point of the new map (the lowest grid point
coordinates), whereas the last 3 inte define the highest grid point
coordinates.


BOX can be used also in combination with the SET command.
CELL command word with INITIALIZE generates a unit cell BOX.



AROUND



... AROUND inte




Sets the new MAP boundaries AROUND the SELECTED atoms
with a boundary of inte grid points.  The inte can be also a
negative number. It works only when a map is INITIALIZED.



FILL

MAKE MAP int1 FROM int2 FILL int3


FILLS the holes in the MAKE MAP mask, when the number of
grid points from an empty grid point to the masked region
along the X, Y or Z axes on both sides is smaller than the
specified int3.  The MAP int1 and the referenced FROM map
are assumed to be equal by size and content at the
beginning of the procedure.


It is an opposite of MAKE MAPE REMOVE.



REMOVE

MAKE MAP int1 FROM int2 REMOVE int3


REMOVES grid points from the MAKE MAP mask, when along the
X, Y or Z axes an all sides in the range of int3 grid
points an empty grid point in the masked region is found.
The MAP int1 and the referenced FROM map are assumed to be
equal by size and content at the beginning of the
procedure.


It is a kind of contrary of MAKE MAPE FILL.



EXPAND



... EXPAND




EXPANDS a masked region for one grid point.  Any grid point
whose neighbor is at least one masked point is turned to a
mask.



SHRINK



SHRINK a masked region for one grid point.  Any MASKED point
that has at least one neighbor point not masked becomes
empty.




COPY



... COPY




Copies the density values from the reference (FROM inte) map
to the masked map (MAKE MAP inte) grid points.  See also
MAKE MAP INVERT.



SCALE



... SCALE real




SCALES all density points of a MAKE MAP by a real number.



RESCALE



... RESCALE




RESCALE modifies a MAKE MAP first by subtracting its average
value from each density grid point and then dividing by its
sigma value.  A new average value of the grid points that are
either not masked or empty becomes zero, and their standard
deviation 1.



SHIFT



... SHIFT real




Shifts a map grid point values for the specified real.



RESHIFT



... RESHIFT




Shifts a map so that its average density region value is
RESHIFTED to zero.



INVERT



... INVERT




INVERT is similar to the COPY command, it however allows to
combine the COPY with SHIFT, RESHIFT, SCALE and RESCALE of
the map.  To be used for solvent regions flipping (Abrahams,
Act. Crys. D52, 30-42) with SCALE -1.0 and RESHIFT.



ROTATE



... ROTATE   MATRIX inte
         RMS
         CENTER  3*real






... TRANSLATE    VECTOR   3* real   [real]
                 RMS




Each masked point is translated and rotated by the specified
TRANSLATION and ROTATION parameters as defined below into
the FROM map electron density. Density at a masked point is
then defined by interpolation from the corresponding 8
surrounding points of the reference map.  WAKE UP, this
place is a very common source of error, since it appears
somehow 'self-evident', that density is rotated into the
mask, and not vice versa (as the program actually operates).


The order in which TRANSLATION and ROTATION operators are
specified is also important.  When TRANSLATION is defined
before ROTATION then it is also applied before and vice versa.
Points are translated for the specified vector. The fourth
real is optional, when it is specified then the vector gives
only the direction, the length of translation is specified by
the fourth number. RMS takes the translation vector obtained
from the RMS fit routine.  ROTATION parameter MATRIX inte
defines the rotation matrix (1 to 8 ).  RMS takes rotational
parameters from the last RMS fit calculation. The CENTER
redefines the center of rotation. By default it is set to
the origin (0.0, 0.0, 0.0).  When there is NO TRANSLATION, the
translation vector should be specified anyway by the VECTOR
0.0 0.0 0.0 syntax.



TRANSLATE



... TRANSLATE    VECTOR   3* real   [real]
                 RMS




See MAKE MAP ROTATE.



ADD



... ADD




Two maps can be ADDED within MAIN. When a larger set of
character*1 maps have to be averaged, the maps should be
written as files to a disk and averaged by the program
AVEMAP. For real*4 maps there are no limitations. You have to
remember that only the density points are ADDED together and
that empty and masked points remain unchanged.  ADDING of a
density point with an empty or masked point results in an
empty point, thus removing the inconsistant points from
different molecular envelopes.



MULTIPLY



... MULTIPLY




Two real*4 maps can be MULTIPLIED within MAIN. It should be
remembered that only the density points are MULTIPLIED
together and that empty and masked points remain unchanged.
MULTIPLYING of a density point with an empty or masked grid
point results in an empty point.



MERGE



... MERGE WEIGHT real1 real2
          HIGHER




MERGES density values at the same grid points of a unit cell
FROM the specified MAP and the MAKE MAP together and writes
the result into the MAKE MAP.  When a grid points in a FROM
map is empty or masked, the MAKE MAP is not influenced.  When
a grid point in a MAKE MAP is empty or masked, the value from
a FROM map is copied into the corresponding MAKE MAP grid
point.  In the case when the MAKE MAP is a CHARACTER*1 map,
value of a grid point is simply copied from the FROM map.


The WEIGHTED alternative premultiplies values of each merging
points from the FROM (real1) and MAKE MAP (real2) map and then
add them together, while by HIGHER option the FROM map
replaces the point values of the MAKE MAP only when they both
have the same sign and the FROM map has more extreme values.
(Used is a density combination application.)



CUT

MAKE MAP 2 FROM 1 CUT real


CUT and DENSITY are synonyms that define the density threshold
below which no grid points from the FROM map will contribute
to the total density sum in a sphere defined with RADIUS real.
The sum of electron density will be WEIGHTED by the distance
if required and written to the specified MAP.  The WEIGHTED
sum corresponds to the standard solvent flattening procedure
described by Wang (Wang et. al., 1985).  After this the summed
map is to be ANALYZED, and afterwards a proper envelope with a
specified portions of the density can be chosen.



RADIUS

MAKE MAP 2 FROM 1 RADIUS real


See MAKE MAP ... CUT.



WEIGHT



... WEIGHT  LINEAR
            GAUSSIAN real




Uses the distance WEIGHTING when summing density points
within a sphere.  Either LINEAR or GAUSSIAN weights within
the specified RADIUS are used.  MAKE MAP FROM WEIGHT
LINEAR RADIUS real CUT 0.0 is the standard real space
solvent flattening (Wang 1985, Meth. Enzym.  115).
Resulting map is then used for envelope calculation based on
map histogram (MAKE MAP ANALYZE).


GAUSSIAN gives better results.



RMS



... RMS LINEAR
        GAUSSIAN real




Is essentially the same as the WEIGHTed procedure.  The
difference is that here the weighted RMS deviations of the
local density is summed instead of the density by itself.
(the idea originates from Abrahams and Leslie, 1996, Acta
Cryst. D52)



ANALYZE

MAKE MAP 2 ANALYZE  STEP  inte


                    RANGE real




After a map has been ANALYZED with an ANALYZE MAP command
sentence, its grid points have been counted for each density
interval.  This list can be accessed either by the STEP
command, where the density values below the STEP are set to
a CLEAR area, and values above the STEP are set to a MASKED
area.  RANGE values can be defined between 0.0 and 1.0,
where a STEP closest to the specified RANGE of the map
interval histogram is chosen.  0.0 means no points are cut
away into the CLEAR area and 1.0 means that all points are
CLEARED.  See also MAKE MAP CUT.



ATOM


RADII
MASK
CLEAR
DENSITY
SYMMETRY
DISTANCE
FUNCTION
HIGHER



... ATOM RADII
         MASK    real
         CLEAR   real
         DENSITY
         HIGHER
         SYMMETRY inte
         FUNCTION   GAUSSIAN
                    LINEAR




Uses atoms to create MASK, CLEAR density or generate
electron density in a map also by applying symmetry
operations.



RADII



Instead of a fix number, the current atomic RADII settings
(SET RADII command) are used.  Use this option when trying
to avoid overlap between local and crystal symmetry related
molecules.  (See: SET RADII OVERLAP real real SELECT ... END
SELECT ... END)



MASK



... MASK real   SELECT ... END




Defines a MASK: sets values of grid points that are closer
than the specified real radius (in Angstroems) to any
SELECTED atom.  If RADII has been specified, then atomic
radia are taken from the atomic radii settings.  The
character MAP grid points are set to 255 and the real MAP
grid points to 9999.



CLEAR



... CLEAR real   SELECT ... END




CLEARS a map region: sets values of grid points that are
closer than the specified real (in Angstroems) to any
SELECTED atom.  If RADII has been specified, then atomic
radia are taken from the atomic radii settings. The
character MAP grid points are set to 0 and the real MAP grid
points to -9999.



DENSITY



... DENSITY  SELECT ... END




Adds a gaussian approximation of electron density of an atom
to the grid points of a map region.  Works only for real*4
maps.  Use it in combination with ATOM SYMMETRY [int1 int2].
Consequent usage of MAKE MAP RESCALE is recommended.



SYMMETRY



... SYMMETRY [int1 int2]




Acts only in combination with ATOM DENSITY commands.
Spacegroup symmetry operations can be applied to generate
electron density throughout the whole unit cell.  By default
all crystal symmetry operations are applied, however you may
select only a particular one or a range of symmetry oparations
by specifying only one or a two numbers.  Numbers are the
consecutive symmetry operations.



DISTANCE



... DISTANCE real




See FUNCTION.



FUNCTION



... FUNCTION real LINEAR
                  GAUSSIAN real




Instead of the 5 GAUSSIAN approximations (from
crystallographic TABLES), LINEAR or a single GAUSSIAN
density function is used.  With LINEAR the grid points
within the specified RADIUS (the first real) around the atom
obtain the values according to their distance from the atom
(1.0 - DIST/ RAD ).  With GAUSSIAN density is distribution
is calculated with a (exp(-dist**2/ sigma) so that the
second real tells how many sigmas fall into the specified
radius.



HIGHER



... HIGHER




By default density of an atom is added to the value at the
grid point.  THE HIGHER option replaces the old value with
the new one when the new one is HIGHER than the old one.  To
be used with iterative map skeletonisation procedures as
part of density manipulation procedures, where atoms are not
regularly distributed along a skeleton.



OVER



The OVER flag is effective only in combination with a map
INITIALIZation (generation) when no MAP number was
explicitly specified. The created map will replace the last
map.  It is an opposite to NEW which places the newly
created map after the last currently present.



NEW



The NEW flag is effective only in combination with a map
INITIALIZation (generation) when no MAP number was
explicitly specified. The newly created map will be appended
to the current number of maps.  It is an opposite to OVER
which places the newly created map on the place of the last
map.



SEGMENT

MAKE SEGMENT SELECT ... END


             FROM    ATOM
                     RESIDUES




Reorganizes the SEGMENT structure.


Using the FROM ATOM option (it is the default), each network
of covalently bound atoms is reorganized so that they form a
new SEGMENT. Each created SEGMENT consist of only one RESIDUE.
The residue structure of SELECTIONs is destroyed.


With the FROM RESIDUE option, all residues, connected with the
next residue in the row via a covalent BOND are joined within
a single SEGMENT name.





File: menu.txt

Last modified: 29-sept-94



MENU


PAGE

INITIALIZE
ADD
REMOVE
LIST
COPY

BLOCK

ADD
CREATE
DELETE
DOCUMENT
REMOVE
COLOR
INITIALIZE
ITEM
RENAME
SHOW
LIST

DEFAULT
DOCUMENT
LIST
Examples



> MENU BLOCK  string  ADD / CREATE
                      DELETE / REMOVE
                      DOCUMENT file_name
                      COLOR int
                      INITIALIZE
                      ITEM  string  ADD
                                    MODIFY
                                    REMOVE
                                    RENAME string
                                    SHOW
TEXT "string ..."
                      RENAME string
                      SHOW / LIST
     DEFAULT
     DOCUMENT ON
              OFF
     LIST
     PAGE int  INITIALIZE
               ADD  string
               REMOVE  string
               COPY  int
               LIST




MAIN DIALOG mode MENU appears in the window named
STRIKES.  MENU is organized in PAGES.  Only a single MENU
PAGE is displayed at a time.  EACH MENU PAGE can be
composed of MENU BLOCKS.  Some BLOCKS are defined inside
the program, some can be loaded and organized while the
program is running.  A MENU BLOCK is a group of ITEMS,
where each ITEM is designed to perform a specific task
related to the other ones within a single BLOCK.


With MENU command sentences it is possible to
(interactively) edit MAIN menu structures (PAGES, BLOCKS
and ITEMS).



PAGE


INITIALIZE
ADD
REMOVE
LIST
COPY



...  PAGE int ...




Any PAGE menu command, except LIST, sets the current MENU
page ass well.



INITIALIZE



... INITIALIZE




INITIALIZES a menu page (removes all BLOCKS entries).



ADD



... ADD string




ADDs the specified menu BLOCK to the current menu page.



REMOVE



... REMOVE string




REMOVES the specified menu BLOCK from the current page.



LIST



... LIST




LISTS all the BLOCKS within the current page.



COPY



... COPY int




Copies the BLOCK composition from the COPY page to the
current page.



BLOCK


ADD
CREATE
DELETE
DOCUMENT
REMOVE
COLOR
INITIALIZE
ITEM
RENAME
SHOW
LIST



...  BLOCK   string  ADD / CREATE
                     DELETE / REMOVE
                     DOCUMENT file_name
                     COLOR
                     INITIALIZE
                     ITEM  string   ...
                     RENAME string
                     SHOW / LIST




Each MENU BLOCK has its own COLOR, name, documentation file
and can be composed of a reasonable number of ITEMS.  Each
ITEM has a name which is connected with a single command
sentence.



ADD



ADDs another menu BLOCK to already existing ones. BLOCK
contains no ITEMS, is not exposed on any PAGE and has
COLOR 1 (white). ADD is a synonym for CREATE.



CREATE



CREATES another menu BLOCK. Synonym for ADD.



DELETE



DELETES a menu BLOCK.  (Only user created blocks can be
deleted.)



DOCUMENT



... DOCUMENT file_name




The string 'file_name' is the file from which DOCUMENTation of
the BLOCK will be retrieved when MENU DOCUMENT mode is ON.



REMOVE



See DELETE.



COLOR



... COLOR inte




Specifies or changes COLOR of a MENU BLOCK.



INITIALIZE



INITIALIZES the specified BLOCK. (Sets its item count to
zero and color to 1 (white).)



ITEM



...  ITEM  string   ADD    TEXT ...
                    MODIFY TEXT ...
                    REMOVE
                    RENAME string
                    SHOW
...    TEXT "string(s)"




Each ITEM has its own identifier and corresponding
command string (TEXT).  ITEMs can be ADDed, REMOVED,
RENAMED, MODIFIED and viewed (SHOW).  The TEXT command
must follow an ADD or MODIFY proposal.  An ITEM can be
viewed (SHOW) as soon as it exist.




MAIN> menu block YYY item STR_ON rename STR_OFF
MAIN> menu block YYY item STR_OFF text "<str_off.cmds"





RENAME



RENAMES the current BLOCK identifier to something else.



SHOW



SHOWS BLOCKs ITEM composition.  It is a synonym for LIST.



LIST



LIST is a synonym for SHOW.



DEFAULT



... DEFAULT




Restores original composition of MENU PAGES by keeping
contents of each USER editable menu BLOCK unchanged.



DOCUMENT



... DOCUMENT ON
             OFF




Turns the MENU DOCUMENT mode ON or OFF. When the document mode
is ON description of each hited menu ITEM and its BLOCK is
written to the standard output.  No MENU commands are accepted
except the page changes.  If you want to apply the menu
commands you have to turn the document mode OFF again. OFF is
the default.





LIST



... LIST




Displays LIST of available MENU BLOCKs.



Examples





MAIN> menu block USER_1 init
MAIN> menu block USER_1 item AROUND add text "<around.inp"
MAIN> menu block USER_1 item DUMMIES add -
text "image col 1 select aro .and. weight 0.9 1.1 end atom cros"
MAIN> menu block USER_1 item DELE_RES add text "user_3.inp"
MAIN> menu block USER_1 item SYMMETRY add text "<user_4.inp"
MAIN> menu page 2 add USER_1




Initializes the menu BLOCK USER_1 and ADDs four ITEMS
(AROUND, DUMMIES, DELE_RES and SYMMETRY) and connects
each item with a command file "<user_1.inp" or a single
command sentence and includes the menu menu BLOCK USER_1
to the second menu page.







File: minimize.txt

Last modified: 14-feb-98



MINIMIZE


Syntax
SELECT
KEY
BY
STEP
IMAGE_STEP
WRITE
LIST-GENERATION
PHASE

STEPS
SELECT
MACRO
KICK
FREE

POSITION
B-VALUES
BASE
RESCALE



MINIMIZES a potential ENERGY function of the SELECTED ATOMS for a
specified number of steps and writes the results.  All ENERGY terms
turned on are applied in the procedure.  POSITIONS, B-VALUES and
TRANSLATIONAL and ROTATIONAL parameters of a single rigid body can be
optimized.


Before a POSITIONAL or B-VALUE minimization starts, the current data
are saved internaly.  See also MAIN_COM:energy.html and "UN_DO menu
item MAIN_MENU:xray_build.html.


Related commands:




> show energy
> energy
> save coor restore





Syntax



  MINIMIZE  STEP  inte[50]
            WRITE_STEP inte
            IMAGE_STEP inte
            BY CONJUGATED
               BODY
            SELECT ... END (SELECT ... END)
            KEY [select active end select passive end]
            LIST_GENERATION  ON
                             OFF
            TRANSLATE 3*(real inte)
            POLAR 3*(real inte)
            XYX-AXES 3*(real inte)
            GAIN_R-VALUE real
            POSITION
            B-VALUES  OVERALL
                      INDIVIDUAL
            PHASE  (
                    STEPS inte
                    MACRO file_name
                    SELECT ... END
                    FREE SELECT ... END
                    KICK ( = real
                           SEED inte
                           LINEAR
                           SQUARE
                           EXPONENTIAL
                         )
                    )
            BASE =    real
                 KICK real  (not working yet)
            RESCALE ON
                    OFF





SELECT



... SELECT ... END




Usually two SELECTIONS are defined. The first one is
allowed to move and the second one serves at the interaction
background to the first one. When only one selection is defined
program assumes that the second one is equal to the first
one.



KEY



... KEY




Assumes that the SELECTIONS are already defined as KEYs.  The
first one as the KEY named ``active'' and the second as the
KEY named ``passive''.  These selection are usually defined
through the interactive MENU items.  See also MINIMIZE SELECT.



BY



... BY CONJUGATED
       BODY




With CONJUGATED gradient MINIMIZATION (this is the default)
the position of each atom from the first SELECTION is
optimized separately, whereas using rigid BODY minimization
the placement of the whole SELECTION as a single entity
(GROUP) (rigid BODY) is optimized. The placement of POINTS in
a map can be optimized only with the BODY method.



STEP



... STEP inte




The starting number of MINIMIZATION STEPS is 80.



IMAGE_STEP



... IMAGE_STEP inte




The IMAGE defines the number of MINIMIZATION STEPS after the
molecular model IMAGE is redrawn (replaced with the new
coordiates).  The default value is 0, which means that the
IMAGE is not updated during the MINIMIZATION.  IMAGE is
updated after the minimization is done.  (This option is
currently disabeled.)



WRITE



... WRITE inte




With WRITE inte (5 is the default), the number of MINIMIZATION
STEPS is defined after which the ENERGY summary is written to
the terminal.



LIST-GENERATION



... LIST-GENERATION ON
                    OFF




Turns ON/OFF the generation of lists for calculation of
nonbonded energy terms (VDW and ELECTROSTATIC), ON is the
default.  The nonbonded interaction list generation
considerably speedes up energy calculation, when the nonbonded
energy terms are requested.



PHASE


STEPS
SELECT
MACRO
KICK
FREE



...  PHASE (
             STEPS inte
             MACRO file_name
             SELECT ... END
             FREE SELECT ... END
             KICK ( = real
                    SEED inte
                    LINEAR
                    SQUARE
                    EXPONENTIAL
                   )
           )




PHASE commands deal with structure factor and maps used in refinement.


Bra-kets can enclose a set of PHASE keywords.  If you not use them you
have to start from the command PHASE again to reach each additional
PHASE keyword.



STEPS



... STEPS inte




Zero is the default number, meaning rephasing is of, It is the number
of MINIMIZATION steps after which a new structure factor set is
calculated.  The PHASE step number is meaningless unless the DENSITY
ENERGY term is turned ON.



SELECT



... SELECT ... END




Only the first selection (active) contributes to new map generation,
the following structure factor calculation and difference map
generation.  (DENSITY MAP should be properly defined. See ENERGY
DENSITY.)  The second is used for "R-FREE" assesment.



MACRO



... MACRO file_name




When PHASE MACRO is defined, then the new structure factors are to be
calculated within that macro and not as by the default procedure.
This is the way how to incorporate density modification procedures as
well as various crystal form into a refinement procedure and thereby
not break continuity of the gradient search by restarting it after
each structure factor calculation.  WARNING: You should, however, take
care that the phasing and the difference map calculation make sense.



KICK



... KICK ( = real
           SEED inte
           LINEAR
           SQUARE
           EXPONENTIAL
          )




KICKING of structure factors during a refinement procedure
results in convrgence problems of the refinement.



FREE



... SELECT ... END




Defines a selection of reflections that will be applied in R-FREE
factor calculation.  You must, however, take care that the reflections
from this selection are not included in the selection used in
refinement.  See also MAIN_CMDS:refine.cmds,
MAIN_DOC:refine/refine.html.



POSITION



... POSITION




POSITION is the switch in a MINIMIZE command that turns the B-VALUE
optimization off and turns the POSITIONAL optimization on.



This is the default.



B-VALUES



... B-VALUES  OVERALL
              INDIVIDUAL




B-VALUES turns the POSITIONAL optimization off and turns the B-VALUES
optimization ON.  POSITION optimization is the default.  The B-VALUES
flag has no effect when rigid BODY optimization is requested.


INDIVIDUAL B-VALUES are optimized for each defined GROUP.  The
smallest group can consist of one atom. See "DEFINE GROUP" and ENERGY
B-VALUE commands.


OVERALL B-VALUE is optimized (actually calculated) on the basis of
Wilson plot statistics.




> mininimize b-values overall sele ... end step 3




See also MAIN_DOC:refine/refine.html, define.html, energy.html.



BASE



... BASE = real




Sets the empty region of the unit cell to a specified value.




RESCALE



... RESCALE ON
            OFF




RESCALES the generated map before its Fourier transformation
in order to introduce a real-space solvent correction.  The
default is OFF.


See also MAKE MAP RESCALE.










OBJECT


Syntax
inte
SELECT
BOND
DISTANCE
ANGLE
DIHEDRAL
TRANSLATE
ROTATE
SYMMETRY
FROM
SET

OBJECT.TEX          23-nov-91


Activated OBJECT are defined in order to interactively (by
dials) manipulate conformations of models without actually
changing the coordinates data. The OBJECTS are supposed to
be defined via MENU commands, though they can be changed and
also manipulated manually via command sentences. Each OBJECT
obtains a KEYED SELECTION. The SELECTIONS can be changed also
after the OBJECTS have been already defined. Up to 30
activated OBJECTS are allowed to be set simultaneously.  The
SYMMETRY OBJECTS have to be defined manually.



Syntax







OBJECT inte   SELECT ... END


              BOND     atom-num atom-num (atom-num)
              DISTANCE  atom-num1 atom-num
              ANGLE    atom-num atom-num atom-num
              DIHEDRAL atom-num atom-num atom-num atom-num
              TRANSLATE
              ROTATE atom-num
              SYMMETRY     MATRIX  inte
                           TRANSLATION   inte inte inte
              SET    TRUE
                     FALSE
                     INITIAL
                     BOND  real
                     ANGLE  real
                     DISTANCE real
                     DIHEDRAL real
                     TRANSLATION  3*real
                     ROTATION    9*real






              FROM   int2
                     AUTO





inte

OBJECT inte ...


Defines the identity number of the OBJECT on which to following
function is activated.



SELECT



... SELECT ... END




Defines the SELECTION on which the specified function acts.
The name of the OBJECT'S KEY is a 4 character string
``ob__''.  The ``__'' are replaced with the OBJECT identity
number.



BOND



... BOND atom-num1 atom-num2 [atom-num3]




Activates rotation around the BOND atom-num1 atom-num2. The
atom-num3 is optional. Usually it is chosen from the
neighbours of atom-num2 by the program itself.



DISTANCE



...  DISTANCE  atom-num1 atom-num2




Activates translation of the SELECTION along the vector
atom-num1 atom-num2.



ANGLE



... ANGLE  atom-num1 atom-num2 atom-num3




Activates rotation of the SELECTION around axes that goes
through atom atom-num2 and is perpendicular to the plane
defined by the 3 atoms.



DIHEDRAL



... DIHEDRAL atom-num1 atom-num2 atom-num3 atom-num4




Activates rotation of the SELECTION around bond atom-num2
atom-num3.



TRANSLATE



... TRANSLATE




Activates TRANSLATION of the SELECTION in X Y and Z
components.



ROTATE



... ROTATE atom-num




Activates ROTATION of the SELECTION around X Y and Z axes.
The CENTER of ROTATION is at the position of atom atom-num.



SYMMETRY



... SYMMETRY     MATRIX  inte
                 TRANSLATION   inte inte inte




Activates crystallographic SYMMETRY operations on the given
object.  It acts only with a link to an activated parent
OBJECT. When the parent is moved (ROT_TRAN) also the
children are following its rotations and translations with
the chosen SYMMETRY operations plus the additional
TRANSLATIONS in whole number fractional coordinates. The
SYMMETRY operation MATRIX inte is the sequential number
taken from the list of SYMMETRY MATRICES that should be
already read before.



FROM

OBJECT inte FROM   int0


                   AUTO




The changes of the activated OBJECTS can be dependent from
each other.  The OBJECT int0 is the parent of the OBJECT
inte. That means, that whatever happen to the parent
OBJECTS, happen to the children as well.  The command word
AUTO tells the program to find the parents, if they exist,
from the SELECTIONS of the activated OBJECTS. An OBJECT is a
child, when a parent OBJECT can be found. A parent OBJECT
includes the complete SELECTION of its' child.



SET



... SET    TRUE
           FALSE
           INITIAL
           BOND  real
           ANGLE  real
           DISTANCE real
           DIHEDRAL real
           TRANSLATION  3*real
           ROTATION    9*real




The values of activated OBJECTS' functions are normally
defined interactively with DIALS. They can be checked with a
SHOW OBJECT command.  In the case of restarts or since the
user would like to do it manually, The values can be set
directly. For BOND, ANGLE, DISTANCE and DIHEDRAL it is
enough to specify 1 value, while for the TRANSLATION the
whole vector is is required and for ROTATION the whole 3x3
matrix.  The values can be any moment INITIALIZED - set to
starting point, the current OBJECT definition can be
accepted (SET TRUE) (the coordinates are accordingly
changed) or rejected (SET FALSE). Either rejection or
confirmation of the current OBJECT'S status, eliminates the
OBJECT'S definition and the KEY connected to it.







POINT


Syntax:
SELECT
SURFACE
RADIUS
DENSITY
RATIO
RANGE
STEP
PLANE
VOLUME
Examples

POINT.TXT          20-nov-91


Points can be generated on one or more surface levels or in
a rectangular box defined by maximum and minimum x, y, and z
values.



Syntax:



POINTS  INITIALIZE
        APPEND
        SURFACE    REENTRANT
                   CONTACT
                   ( ALL = CONTACT + REENTRANT )
                   ACCESSIBLE
        VOLUME
        PLANE   3*realx/y/z, 3*real (sx/sy/sz), 3*inte (x/y/z)
        SELECT ... END
        RADIUS real (1.4)
        DENSITY real  (4.0)
        RANGE real real
        STEP real





SELECT



... SELECT ... END




Two SELECTIONS are required for generation of a Connolly
SURFACE.  The first one is the one on which atoms points are
generated and the second one serves to cut away the inner
points, that wouldn't be generated if the whole molecule
would have been chosen.  For syntax see SELECT.



SURFACE



... SURFACE    REENTRANT
               CONTACT
               ALL (= CONTACT + REENTRANT )
               ACCESSIBLE




Calculates the Connoly surface ( by the Connoly algorithm ).
The atomic radii should be specified by the SET RADII.  Three
kinds of SURFACES can be calculated: CONTACT, REENTRANT
and ACCESSIBLE. Points of CONTACT and REENTRANT surfaces lie
for the atomic RADII far away from atoms, while points of
the solvent ACCESSIBLE surface represent the boundary to
which the centers of solvent atoms can still approach.  The
ACCESSIBLE surface is mathematically the same as the CONTACT
surface, only the atomic radii are enlarged for the solvent
radius.



RADIUS



... RADIUS real




Defines the RADIUS of the solvent molecules.



DENSITY



... DENSITY




Defines the DENSITY of points. Default value is 4.0 point
per square A.  Higher number means more points. 4.0 is well
enough when the protein as whole is suppose to be inspected.
For smaller parts it is reasonable to increase it.



RATIO



... RATIO real




RATIO is the real number with which atomic radii are
multiplied.



RANGE



... RANGE real1 real2




RANGE is the distance from VdW radii of atoms out in space
in which the surface points are generated.



STEP



... STEP real




When surfaces are generated in a RANGE then STEP is the
distance between the 2 consecutive layers of SURFACE.



PLANE



... PLANE   3*real x/y/z, 3*real sx/sy/sz, 3*inte x/y/z




The PLANE command words offers a possibility to generate
points in a 3-D lattice. From the origin (3*real x/y,z),
step size in each direction (3*real sx/sy/sz) and number of
steps (3*inte x/y/z) the 3-D lattice is generated.



VOLUME



The VOLUME points options are more than replaced with the
MAP operations.



Examples



MAIN> point surface all ratio 1.2 select all end select all end






MAIN> point surface all select activ_site end -
MAIN> select protein end dens 7.0 initialize






MAIN> point plane -2. -2. -2. 1. 1. 1. 5 5 5





Last modified: 17-JUL-96



RADII


Syntax
CONSTANT
OVERLAP

Fle: radii.txt


The atomic radii are applicable for molecular images
and molecular envelope generations.



Syntax



SET RADII   SELECT ... END * real
                             INITIAL (0.0)
                             VdW
                             CHARGE
                             CONSTANT real
                             OVERLAP real real
            EXIT




To a given selection VdW, CHARGE or nonnegative real value
RADII can be set. EXIT should be used to return back to


MAIN>.





CONSTANT



... CONSTANT real




Sets a CONSTANT radius value to all selected atoms.



OVERLAP



... OVERALP real real




Using the OVERLAP option it is possible to avoid overlap of
molecular envelopes between two specified SELECTIONS.  The original
molecule and its crystal or local SYMMETRY mates.  The first
real specifies the minimal radius and the second real the
maximal atomic radius.  Each atom from the first selection
that is further than double maximal radius away from any atom
from the second selection obtains the maximal radius.  The
atoms that are closer than that obtain half of the closest
interatomic distance.  When the distance is shorter than
minimal radius, atomic radii are set to 0.0.





File: read.txt

Last modified: 10-FEB-95



READ


Syntax
COORDINATES
ATOMS
SCATTERI
ELEMENTS
BONDS
CTABLE
ZTABLE
INTERNAL
POINTS
TOPOLOGY
CELL
SYMMETRY
MAPS
FIRST
REFLECTIONS

CSN




When no UNIT number or file is specified, the READ UNIT is
the current input, either the terminal or a command file.
The number of atoms is changed only when cartesian or
internal coordinates are read.  The FILES are opened with
the READONLY option.



Syntax



READ UNIT int
     FILE string
       ATOMS   DEFAULT           ATOM_UNI      INITIALIZE
               CARD         [ANGSTROEM]   APPEND
               PDB          NANOMETER     OVER   SELECT ... END
               XPLOR
               DISCOVER
               AMPAC
               GROMOS
               DIAMOND
        SCATTERI
        ELEMENTS






        BONDS ()       |  INITIALIZE
                    NUMBERS  |   APPEND
        CTABLE         |   FIRST   atom-num
        HBONDS         |           SELECT ... END
        ZTABLE         |






        INTERNAL  (GAUSS)   ATOM           INITIALIZE
                   AMPAC     (ANGSTROEM)    (APPEND)
                                            OVERWRITE   FIRST *
        POINTS  ()
                SURFACE           CONNOLLY      INITIALIZE
                VOLUME            GAUSSIAN86    (APPEND)
                POTENTIAL         G80           FIRST *
                DENSITY
        TOPOLOGY   CARD          (APPEND)
                   XPLOR          INITIALIZE
                   DISCOVER
                   GROMOS
                   (MAIN)
        PARAMETERS XPLOR
         SEQUENCE
         CELL
         SYMMETRY
         MAP  (CHARACTER)     OVERWRITE int
              NUMBER
              ALPHA
              PROTEIN
              XPLOR
              CCP4





COORDINATES



See READ ATOMS.



ATOMS



... ATOMS                        ATOM          INITIALIZE
                    CARD                       APPEND
                    PDB          NANOMETER     OVER      SELECT ... END
                    XPLOR
                    DISCOVER
                    AMPAC
                    GROMOS
                    DIAMOND




ATOMIC coordinates can be read in different formats.  The
program uses angstroems units.  INITIALIZE starts reading
from zero number of atoms.  APPEND adds the atoms to the
previously known ones in the program.  OVERWRITE finds the
FIRST atom number in the SELECTION and replaces the atomic
coordinates after the first found atom and leaves the atom
and residue structures untouched.


Formats:
DEFAULT, CARD, PDB, XPLOR, DISCOVER, AMPAC, GROMOS, DIAMOND


The format without a name is the DEFAULT format. It tries to
find an atomic name or atomic element number and 3 coordinates
for X, Y, and Z. The format is free and the order of data is
not important. When a real number is not found, the program
assumes that the coordinate is zero.


CARD is the CHARMM format.


DIAMOND is the format used by FRODO and EREF.


PDB or XPLOR reads Brookhaven Data Bank and XPLOR PDB.


DISCOVER is the format from BIOSYM Inc. (DISCOVER, INSIGHT).


GROMOS is the Groningen package format.


AMPAC and GAUSSIANnn are program packages for quantum
mechanical calculations.


Units:


ANGSTROEM units are the default.


NANOMETER accepts that the coordinates in NANOMETERS and
multiplies them by 10. In GROMOS format the NANOMETER units
are set automatically.


ATOM means that coordinates have to be converted from atomic
units to Angstroems. Atom units are quite often used in
quantum mechanical calculations.



SCATTERI



SCATTERING factors for each ELEMENT can be read in form of
an ELEMENT id (and also as atomic number) followed by 10 or
less real numbers (the 5 gaussian presentation as appearing
in the International tables.)



ELEMENTS



Each atom has its ATOMIC NUMBER and ELEMENT id.  When read
each atom gets its ATOMIC NUMBER based on comparison with
the ELEMENT id-s table.  Each ELEMENT id, which is a string,
can be replaced by reading a line consisting of an ATOMIC
NUMBER and the new ELEMENT id string.  Replacing C with E
for example:




>read element
> 6 E
>




If a new name is not unique, then it can not replace the old
one.  All characters are converted to capital letters.
See also WRITE ELEMENTS.



BONDS



... BONDS  NUMBER




A file containing only the atom numbers is read when there is
the NUMBER command word.



CTABLE



... CTABLE




A connection table can be read. This make sense only when
atoms are in the same order as they were when the CTABLE was
written.



ZTABLE



... ZTABLE




A Z-mat-connection table is used for conversions between the
INTERNAL (relative) and cartesian COORDINATES (absolute).
Each atom can have a ZTABLE record.



INTERNAL



... INTERNAL GAUSSIAN
             AMPAC




Reads INTERNAL coordinates and ZTABLE with the INITIALIZE or APPEND
options. GAUSSIAN or AMPAC formats can be read.



POINTS



... POINTS  ()
    SURFACE           CONNOLLY       INITIALIZE
    VOLUME            GAUSSIAN86    (APPEND)
    POTENTIAL         G80           FIRST *
    DENSITY




SURFACE, VOLUME, electrostatic POTENTIAL or DENSITY POINTS can
be READ. The default is SURFACE points.  When the read points
are to be transformed into some other kind (VOLUME,
electrostatic POTENTIAL or DENSITY) then the kind should be
explicitly specified.


There are three formats of point records available (CONNOLLY,
GAUSSIAN86 and G80).  Only the CONNOLLY format includes the
complete information for each point. The GAUSSIAN86 and G80
formats are only used to READ electrostatic potentials.


The POINT counter can be set to 0 (INITIALIZE) or left
unchanged (APPEND). Each point has one or more atomic
indices that tell the program to which atom a point belongs.
By default they are not changed when using the CONNOLLY
format.  With  GAUSSIAN and G80 all the points in the file
are by default assigned to the last atom. The default can be
changed by the FIRST option, so that the number of the first
atom found in the SELECTION is supposed to be the atomic
index 1 from the points.  This is achieved simply by adding
the difference to each atomic index.



TOPOLOGY



... TOPOLOGY  MAIN
              CARD          (APPEND)
              XPLOR          INITIALIZE
              DISCOVER
              GROMOS




MAIN format is the default. MAIN topology libaries are the
only ones that can be used for model building and energy
calculations.


The X-PLOR (XPLOR) TOPOLOGY files can used for energy
minimization procedure, however, new residues can not be built
from scratch from X-PLOR topology files.  The conversion to
MAIN topology files is rather simple, so that you should in
general try to convert your XPLOR topology files in MAIN
format.


The DISCOVER topology file of MOLEDT - DISCOVER format can be
used can be used for model building (CLASSES, CHARGES, BONDS
and INTERNALS are read).


The GROMOS and CARD (CHARMM) topology files can be used for
atom name corrections and partial atomic charges assigneent
(only CLASSES and CHARGES are read).



CELL



... CELL




Cell constants (a, b, c, alpha, beta, gamma) are read in
free format. Title line(s) beginning with a '*' is required,
when you try to read the cell constants from your terminal.



SYMMETRY



... SYMMETRY




SYMMETRY operations are read in the form used by the
international tables for crystallography. Only a single group
of crystallographic symmetry operations can be handeled at
once in the program. When MAP files in PROTEIN or MAIN formats
are read the symmetry operations are included automatically.



MAPS



... MAPS  CHARACTER     OVERWRITE int
          REAL (NUMBER)
          ALPHA
          CCP4
          PROTEIN
          XPLOR




Maps can be read by MAIN as character*1 or real*4 maps.  The
default map format is the CHARACTER. The real*4 maps require
the NUMBER format qualifier. PROTEIN, XPLOR and ASCII CCP4
maps are transformed into the real*4 maps.  ALPHA maps are a
character*1 presentation written hexadecimally.  ALPHA, XPLOR
and ASCII CCP4 maps are all text files that can be transferred
between any hardware.


ASCII CCP4 maps are output from a CCP4 program called
mapexchange.


PROTEIN maps are automatically scaled to 1 sigma.


The OVERWRITE qualifier means, that the map stored under the
specified map number will be overwritten and that all maps
with higher consecutive numbers are lost.



FIRST



... FIRST  atom-num
           SELECT ... END




The FIRST atom can be specified directly as an atom number
or found as the first atom in the SELECTION.



REFLECTIONS


CSN



... REFLECTIONS INITIALIZE
                RESOLUTION  real real
                LIMITS int int int
                FRIEDEL
                RE_READ
                MAIN
                XPLOR
                CSN




When INITIALIZING the data arrays RESOLUTION limits have to
be specified and cell constants known to the program.


Reads a reflections file (with INDEX, FOBS, PHASE, SIGMA,
FCALC, COMPLEX, POLAR, WEIGHT, TEST).  FOBS can have PHASE
too.  FCALCs can be presented as COMPLEX numbers or as POLAR
(amplitude and phase).  Format is free.


The lower HKL limits are desired, in order to reduce data
storage. If you don't know what to do set the LIMITS to
zeros and use keyword RE_READ to get the exact values.
RE_READ will read the reflection file twice in the case of a
limits problem. It however makes sense that for future
readings the limits are correctly set in order to avoid the
unneccessary, time consuming second pass through a reflecion
file.


TEST keyword flags are stored in the reflection KEY 'TEST'
which can be used later on for R-FREE calculations.


Program interprets an XPLOR reflection file as well.



CSN



Specifies the CSN format.  The follwoing keywords are processed
INDEX, FOBS, SIGMA, IOBS, ISIGMA, FOM, PA, PB, PC, PD,
however, only INDEX, FOBS, SIGMA and FOM are understood.








File: reflect.txt

Last modified: 17-jul-96



REFLECTIONS


Syntax
EXPAND
FILL-MAP
KEY
KICK
MOVEFCFO
PHASES
R-VALUES
RESOLUTION
SELECT

ALL
CENTRIC
DEFINED
FCALCULA
FOBSERVE
FWORK
H-INDEX
K-INDEX
L-INDEX
MODUL
MULTIPLI
NONCENTR
R-VALUES
RANDOM
RESOLUTI
SHELL
SIGMA
UNDEFINE

SET
SHELLS
SYMMETRY
SOLV_FLA
WEIGHTS
SHOW
TWINS



REFLECTION commands manipulate reflection data and structure
factors.  They are used for proper scaling and structure
factor manipulation including an R-VALUE calculation that
finally leads to FILL-MAP and its FOURIER BACK TRANSFORM.


There are three data structures FOBSERVED, FCALCULATED and
FWORKSET that can be manipulated with REFLECTION commands.
FOBSERVED are usually amplitudes of a measured data set
(read from a file), FCALCULATED array is automatically
filled with a MAP FOURIER transformation, FWORKSET is used
to prepare a map (wirh FILL-MAP command) for FOURIER map
BACK transformation.



Syntax



> REFLECTION
              EXIT
              EXPAND
              FILL-MAP  inte
              KEY string SELECT ... END
              MOVEFCFO
              KICK   (
                     = real
                     SEED
                     LINEAR
                     SQUARE
                     EXPONENT
                     )
              PHASES     STATISTICS
                         FROM      FOBS
                         TO        FCALC
                                   FWORK
                         SAYRE-EQ
              R-VALUES     TEMPERAT real
                           B-WILSON
              RESOLUTION real real
              SELECT ... END
              SET    AMPLITUDE
                     PHASE
                     SCALE FOBSERVE  expresion + - * / expresion
                           FCALCULA
                           FWORKSET
                        expresion as FOBSERVE * ^ / real
                                     FCALCULA
                                     FWORKSET
              SHELLS   inte
              SHOW    KEYS
                      TWINS
                      REFELCTIONS
              SOLV_FLAT real
              SYMMETRY inte inte
              WEIGHTS    CONSTANT
                         SIGMA
                         A_SIGMA real
                         R-VALUES





EXPAND



... EXPAND FCALCULATE
           FOBSERVED
           FWORKSET




EXPANDS specified structure factors applying SYMMETRY
operators in specified RESOLUTION range to the HKL limits as
generated by the last READ REFLECT INIT command.



FILL-MAP



... FILL-MAP inte




Specifies a complex map that will be filled with structure
factors form the WORKSET as a preparation step for a
following FOURIER (FFT) map BACK TRANSFROM.



KEY



... KEY string SELECT ... END
               INITIALIZE
               DROP




A selected set of structure factors can be addressed using
a KEY name in consequent REFLECTION commands.  It is
an analogue of atom selections KEY.



KICK



... KICK   (
           = real
           SEED inte
           LINEAR
           SQUARE
           EXPONENT
           )




FCALC are kicked inside the given kick value (maximum
distance) which has a LINAR (resol * kick), SQUARE (resol**2


* kick) or EXPONETIAL ( k * exp(-resol**2 * B) * kick)


dependance from resolution.


Centric reflections are kicked only along real or imaginary
componet, whereas the noncentric reflactions are kicked
randomly.



MOVEFCFO



Moves the curent values of FCALC into FOBS (real and
imaginary part).



PHASES



... PHASES (
           STATISTICS   FROM     FOBS
                        TO       FCALC
                                 FWORK
           SHIFT
           SAYRE-EQUAT
           )




STATISTICS is used for comparison of phases between two
structure factor sets




> refl phase ( stati from fobs to fcalc )




The rest is not working yet.



R-VALUES



... R-VALUES TEMPERAT real
             B_REFINE
             RESCALE
             FIXED





Linear R-VALUE matches are calculated between FOBSERVED and
FCALCULATED for the number of specified reflection shells.


Each resolution obtains independent scaling factor (K).
Once they are calculated you can turn the default RESCALE of
with the FIX keyword and calculate an R-FREE value:




> refle select .not TEST end r-val rescale
> refle select      TEST end r-val fix




A resolution dependent TEMPERATURE factor can be set or
refined (B_REFINE is the default).  Use at least 3
shells to get a reasonable B-value.



RESOLUTION



... RESOLUTION real real




RESOLUTION can limit any of the REFELCTION operations to a
limited resolution range, however, the resolution range of
reflections can not be expanded beyond the resolution limits
set at the beginning (within a READ REFLECTION) sentence.


A yet more flexible way is to use SELECT commands.



SELECT


ALL
CENTRIC
DEFINED
FCALCULA
FOBSERVE
FWORK
H-INDEX
K-INDEX
L-INDEX
MODUL
MULTIPLI
NONCENTR
R-VALUES
RANDOM
RESOLUTI
SHELL
SIGMA
UNDEFINE



... SELECT ... END




Use of () and logical operators (.AND., .NOT., .OR.) between
tags is allowed.


Tags define whether a particular reflection should be chosen
or not.



ALL



Select all reflections.



CENTRIC



Select only centric reflections.



DEFINED



Select only defined reflections (FOBS are not zero).



FCALCULA



... FCALC real real




Select reflections with their FCALC in a range of their
amplitudes.



FOBSERVE



... FOBS real real




Select reflections with their FOBS in a range of their
amplitudes.



FWORK



... FWORK real real




Select reflections with their FWORK in a range of their
amplitudes.



H-INDEX



... H_INDEX inte inte




Select reflections with their H-INDEX within
the given interval.  When only one integer is given,
the second is equal to the first one.  The command




> refl select h-index 4 .and. k-index 3 .and. l-index 2 end




will select the reflection with HKL values 4,3,2.



K-INDEX



... K-INDEX inte inte




Select reflections with their K-INDEX within
the given interval.  When only one integer is given,
the second is equal to the first one.



L-INDEX



... L-INDEX inte inte




Select reflections with their H-INDEX within the given
interval.  When only one integer is given, the second is
equal to the first one.



MODUL



... MODUL inte inte




Selects among defined reflections by modul and remainder.
For example




> refl select modul 12 3 end




selects the 3rd 15th and so forth refelctions.



MULTIPLI



... MULTIPLI inte inte




Selects reflections within a given mulitplicity range.  When
only one integer is specified, the second one becomes equal
to the firts one.



NONCENTR



Selects noncentric refelctions.



R-VALUES



... R-VALUES real real




Select reflections in a given R-VALUE range.



RANDOM



... RANDOM int1 int2




Select randomly among defined reflections a partition (int1)
with a given seed (int2).  Default int1 value is 12 and
default int2 (seed) is variable RAN_SEED.




> key TEST select random 12 end





RESOLUTI



... RESOLUTION real real




Select reflections in a given RESOLUTION range.



SHELL



... SHELL inte inte




Select reflections within given SHELLS.  When only one
integer is given, the second becomes equal to the first one.



SIGMA



... SIGMA real real




Select reflections with the given AMPLITUDE/SIGMA values
ratio range.



UNDEFINE



Selectc UNDEFINED reflections (not read FOBS).



SET



 ... AMPLITUDE
     PHASE
     SCALE FOBSERVE  expresion + - * / expresion
           FCALCULA
           FWORKSET
        expresion as FOBSERVE * ^ / real
                     FCALCULA
                     FWORKSET




SET commands enables you to perform various structure factor
calculations that are a basis for density map calculations:
Either as difference maps (Fwork = Fobs*2. - Fcalc*1,
Fobs*1. - Fcalc*1.), Patterson maps (Fwork = Fobs^2.),
correlations maps (for the fast solvent flattening procedure
(Fwork = Fcal * 1.0 * Fwork * 1.), fast translational search
etc...)


You can set AMPLITUDE, PHASE or AMPLITUDE and PHASE.


Any of reflection arrays (FOBSERVED, FCALCULATED or FWORK)
can be SCALED in accordance with the constants obtained by
the last R-VALUES calculation.  FOBSERVED array is divided
with the constants while the FCALCLATED and FWORKSET arrays
are multiplied with them.


The current WEIGHTS for FOBS and FCALC are applied.  Default
values are one, but you can also read WEIGHTS of FOBS with
PHASES to calculated a figure of merit map.



SHELLS



... SHELLS inte




Specifies number of SHELLS that are used in a R-VALUE
calculation and in a REFLECTION SET calculation (when
SCALING an data array).



SYMMETRY



... SYMMTERY inte (inte)




Can limit a FILL-MAP command to apply only the specified
symmetry operations.  By default all symmetry operations are
used.



SOLV_FLA



... SOLV_FLAT real




Sets Fcalc to the values for Fast solvent flattening based on
Leslie, Acta Cryst. (1987) A43, 134-136.



WEIGHTS



...  WEIGHTS    CONSTANT
                SIGMA
                A_SIGMA real
                R-VALUES




Not perfect yet.  So use CONSTANT to switch from a Figure of
Merit (FOM) weights obtained by reading a reflection file to
constant weights.  Sigma A values are only estimated and not
refined.



SHOW



... KEYS
    TWINS
    REFELCTION





TWINS



... ON
    OFF
    MATRIX 9 * real
    INITIALIZE









File: rename.tex

Last modified:     19-OCT-91



RENAME


Syntax
SELECT
ATOM
RESIDUE
SEGMENT
CHAIN
SEQUENCE
APPEND
REMOVE
INSERT
DELETE
AUTOMATI
BACKWARD
EXAMPLES




Syntax



 RENAME  SELECT ... END
         ATOM  string
         RESIDUE  string
         SEGMENT  string
         CHAIN    char
         SEQUENCE string
           INSERT
           DELETE
           APPEND
           REMOVE
         AUTOMATI  [inte]
         BACKWARD  [inte]




The atomic character data (ATOM, RESIDUE,
SEGMENT names and SEQUENCE IDs) of the SELECTED atoms can
be modified using the RENAME command sentence.  This can
save a lot of effort required to transfer the atomic
coordinate files between different programs. The time
consuming editor use can be avoided.


The INSERT/DELETE and APPEND/REMOVE are operating only on
SEQUENCE names.   APPEND appends a character
after the current sequence names,



SELECT



... SELECT ... END




The standard selection subcommand.



ATOM



... ATOM string




RENAMES the selected atoms to something. (CD1 to CD).




> rena sele atom  name CD1 .a resi name ILE  end atom CD





RESIDUE



... RESIDUE string




RENAMES the selected RESIDUE names tosomething. (SOL to H20).




> rena sele resi name SOL  end resi H2O





SEGMENT



... SEGMENT string




RENAMES the selected SEGMENTs to something. (SOL to WAT).




> rena sele segm name SOL  end segm WAT





CHAIN



... CHAIN




RENAMES chain identifiers of the given selection.  In a combination
with AUTO flag only the first found chain gets the given character,
each following chain gets also the following characters from the ASCII
table.




> rename chain A sele segm name MOL1 end






> show chain




See also "MAKE CHAIN" commad in make.html.



SEQUENCE



... SEQUENCE string




If no additional command wrod follows then the whole selection
obtains the new sequence ID, otherwise the string following
the SEQUENCE keyword is used as a root (APPEND, INSERT,
AUTOMATI, BACKWARD) or not considered at all (DELETE, REMOVE).




> rename sele resi numb 4 end seq A4
> rename sele active end seq A auto
> rename sele active end seq A append





APPEND



APPENDs the specified SEQUENCE character after the current
sequence IDs.



REMOVE



REMOVES the last character from the sequence names.



INSERT



Inserts the specified SEQUENCE character before the current
SEQUENCE id string.



DELETE



Deletes the first character of the sequence names.



AUTOMATI



... AUTOMATI [int]




Each additional residue will obtain the sequence ID root plus
the current counter.  The default start is 1.



BACKWARD





EXAMPLES





> rename select atom name CD1 .and. residue name ILE end atom CD






> rename select residue number 1 end sequence -2






> rename sequence 33A select residue number 33 end






> rename select segment numb 1 end sequence A insert
> rename select segment numb 2 end sequence B insert






> rename select inhibitor end sequence I append






> rename sequence 33A select residue number 33 end




This rename will change the sequence IDs of a selection so that each
seq ID starts with B and a consecutive number from 1 to nn is
appended to it. (AUTOGENERATE)





> rename select active end seq B auto





Give new segment name to the specified selecttion of atoms.  Be aware
that the selection should contain complete residues, otherwise the
command will not behave as you expect.




> rename sele active end segm MOLA





File: temp.txt

Last modified: 2-feb-1999



RIBBON


Syntax
DENSITY  real
INITIALI
N_LINES
RADIUS
REFINE
SELECT
SEPARATION
STEPS   int



Defines parameters used in ribbon presentation of a protein fold.
RIBBON parameters are initialized from "SET".



Syntax



SET  RIBBON AUTOMATI
            COIL
            DENSITY  real
            EXIT
            HELIX
            INITIALI
            N_LINES int
            RADIUS  real
            REFINE  int
            SELECT ... END
            SEPARATION
            STEPS   int
            STRAND





DENSITY  real



Specifies DENSITY (number of points) defining the curvature of each
stick.  Default is 6.



INITIALI




N_LINES



... N_LINES int




Number of lines for the line presentation. Default is 3.



RADIUS



... RADIUS  real




Specifies RADIUS for of the ribbon stick. Default is 0.3.



REFINE



... REFINE  int




Specifies the number of REFINEMENT steps used during ribbon generation.



SELECT



... SELECT ... END




The usual select command - used in connectiosn with HELIX and STRAND.



SEPARATION

.. SEPARATION real


SEPARATION between two LINES.  Default is 0.2.



STEPS   int



Specifies the number of interpolation STEPS between two CA atoms.





File: main/doc/com/rms.txt

Last modified: 10-jan-96



RMS


Syntax
SELECT
PAIRS
COORDINATES

ALL
BOTH
ROTATION
TRANSLATION
POLAR
GUESS
INITIAL_GUESS
FLAGS
EIGEN

CHARGES
TEMPERATURE
B-VALUES
RADII
INTERNAL
POINTS
MAPS




With the RMS (Root Mean Square) command sentence it is
possible to compare (calculate a RMS deviation) between two
different data sets (atomic COORDINATES, CHARGES, RADII,
INTERNAL COORDINATES or POINTS) and also optimize the
rotational matrix and translational vector for superposition
atomic COORDINATES of two given SELECTIONS or a PAIR list,
so that the RMS of compared coordinates gives a minimum.



Syntax



RMS   SELECT ... END         SELECT ... END
      PAIR
      COORDINATES    ()
                     ALL / BOTH
                     TRANSLATE
                     ROTATE
                     POLAR
                     FLAGS 6 or 3 inte
                     INIT / GUESS 6 * real
                     EIGEN






      CHARGE
      RADII
      INTERNAL  DISTANCE
                ANGLES
                DIHEDRALS
                (ALL)
      POINTS    SURFACE
                POTENTIAL






      MAPS 2*inte





SELECT



... SELECT ... END





PAIRS



... PAIRS ...




Two SELECTIONS define an implicit pair list, while the PAIR
keyword accesses PAIRS as they appear in the PAIR list.


Points can not be PAIRED by the
PAIR command word - 2 SELECTIONS should be specified.



COORDINATES


ALL
BOTH
ROTATION
TRANSLATION
POLAR
GUESS
INITIAL_GUESS
FLAGS
EIGEN



...  COORDINATES
                 ALL / BOTH
                 TRANSLATE
                 ROTATE
                 POLAR
                 FLAGS 6 or 3 inte
                 INIT / GUESS 6 * real
                 EIGEN




Coordinates of atoms can be also matched by a fitting
procedure, when one of the command words (ALL, BOTH, ROTATE
or TRANSLATE) follows the COORDINATE command. The
coordinates of atoms are not actually moved.  Only the
parameters for rotation and translation are found and saved
in programs memory.  The parameters can be shown with a SHOW
RMS or SAVE RMS. The rotational matrix used for the fitting
procedure is the matrix number 8.


Remember: ROTATION is performed before TRANSLATION.


The two RMS choices (SELECT and PAIR) are equivalent.




> rms coordinates all select MOL_A end select MOL_B end






> make pair  select MOL_A end select MOL_B end
> rms coordinates all pair




Related coomands:




> save rms




The coordinates of the atoms and points can be ROTATED and
TRANSLATED into the position found by the RMS fit routine,
by first using ROTATION and later TRANSLATION and not vice
versa.  Center of rotation is implicit (coordinate system
origin).




> rotate atom sele MOL_A end rms
> translate atom sele MOL_A end rms





ALL



ROTATIONAL and TRASLATIONAL fit is performed.  BOTH is a synonym
of ALL.



BOTH



ROTATIONAL and TRASLATIONAL fit is performed.  BOTH is a synonym
of ALL. See "RMS COORDINATES ALL".



ROTATION



Only ROTATIONAL atrix is optimized.



TRANSLATION



Only TRANSLATIONAL vector is optimized.



POLAR



ROTATION angles are by default rotations about X, Y and X.
POLAR keyword switches to POLAR rotational axis description
(phi, psi, kappa) instead of the default choice.



GUESS



... GUESS 6*real


Sometimes the procedure does not converge.  In such cases it makes
sense to start with some other INITIAL GUESS values.
A common problem are 2-fold axis.



INITIAL_GUESS



Is a synonym of GUESS.  See "RMS COORDINATES GUESS".



FLAGS



... FLAGS 6*inte




With flags you can fix some fitting parameters.  For example
you know that your rotational axis is a perfect 2-fold and
you want to enforce it.  ZERO means that a variable is kept
fixed and 1 that it is optimized during the RMS optimisation
procedure.




> rms coor all polar pairs guess 0. 0. 180. 0. 0. 0. \
> flags 1  1    0  1  1  1





EIGEN



... EIGEN




When EIGEN values based rotation matrix construction is
performed then always all 6 parameters are fitted.
Currently this option is not capable to extract rotation angles.
The resulting rotation matrix is the number 8.



CHARGES



... CHARGES ...




Calculates RMS deviation of atomic CHARGES between the two
atomic SELECTIONS.



TEMPERATURE



... TEMPERATURE ...




Calculates RMS deviation of atomic TEMPERATURE factors
(B-VALUES) between the two atomic SELECTIONS.



B-VALUES



... B-VALUES ...




Calculates RMS deviation of atomic TEMPERATURE factors
(B-VALUES) between the two atomic SELECTIONS.



RADII



... RADII ...




Calculates RMS deviation of atomic RADII between the two SELECTED
coordinate lists.



INTERNAL



... INTERNAL  DISTANCE
              ANGLES
              DIHEDRALS




Calculates RMS deviation between the two specified INTERNAL
coordinate lists.



POINTS



... POINTS    SURFACE
              POTENTIAL




Compares pairs of points (SURFACE or POTENTIAL) according to
their values.



MAPS



... 2*inte




RMS deviation of density values between two specified maps
can be calculated.  It is required that the maps are
identical in grids and box.







ROTATE


Syntax
BOND
ATOM
POINTS
Examples

ROTATE.TEX     6-dec-91


A SELECTION of ATOMS or POINTS is ROTATED around a point in
space (CENTER).  The ROTATION is specified via an MATRIX (in
case of ATOM or POINT rotations) or as ROTATION around a BOND.



Syntax



ROTATE BOND atom-num1 atom-num2 (atom-num3) -
              (SELECT CUT atom-num1 atom-num2 END )
               SELECT ... END
               ANGLE real






        ATOM  SELECT ... END
              MATRIX inte
              CENTER ATOM atom-num
                     COORDINATE  3*real
                     CALCULATED







        POINTS   SURFACE    SELECT ... END
                 VOLUME     MATRIX inte
                 DENSITY    CENTER ...
                 POTENTIAL





BOND



...  BOND atom-num1 atom-num2 (atom-num3) -
          SELECT ... END
          ANGLE real




The SELECTED atom coordinates are ROTATED around the
specified BOND for the specified ANGLE.  It is not necessary
that atom-num1 and atom-num2 are connected by a covalent
bond. When a third atom (atom-num3) is specified it doesn't
have to be connected to atom-num2. When the third atom is
omitted then the program looks for it in the connection
table for a neighbour of atom-num2.  The default atom
SELECTION is the group of atoms that are on the side of the
atom-num2 of the covalent bond atom-num1 atom-num2 (SELECT
CUT atom-num1 atom-num2 END ).



ATOM



... ATOM  SELECT ... END
          MATRIX inte
          RMS
          CENTER ATOM atom-num
                 COORDINATE  3*real
                 CALCULATED




ROTATES the SELECTED atoms around the specified CENTER by
multiplying atomic coordinates with the specified rotational
MATRIX. The ROTATIONAL
MATRICES can be specified by the SET MATRIX int ... command
sentence. There are 8 matrices available. Using RMS the last
RMS fit parameters are used to create the ROTATIONAL MATRIX.
The default CENTER for the transformation is the coordinate
system origin. Other CENTER positions can be chosen (the
current image center - CALCULATED, an ATOM position or
some other point in space - COORDINATES ).



POINTS



... POINTS   SURFACE    SELECT ... END
             VOLUME     MATRIX inte
             DENSITY    RMS
             POTENTIAL  CENTER ...




Work on the same way as the ROTATE ATOM command with the
only difference, that the points can be selected also
by  their kind (SURFACE, VOLUME, POTENTIAL, DENSITY).



Examples





MAIN> rotate bond 3 4 angle 30.






MAIN> rotate atom select segment number 3 end -
MAIN> matrix 3 center atom 4






MAIN> rotate points potential select number segment 4 end -
MAIN> rms center calculated





File: save.txt

Last modified: 3-apr-95



REFLECTIONS





> SAVE      (OVER)  FILE string (APPEND)   \
        VIEW
        VARIABLE




SAVE commands are extracting data from the program in a form
of MAIN commands.  So it is possible to restart an
interactive image session exactly with the same VIEW
parameters as you have finished.  This option is useful for
PLOT file generation as well.







SECONDARY

SECONDARY.TEX   21-nov-91


Syntax
SECONDARY


       EXIT
       SELECT ... END  ALPHA
                       BETA
                       PARALLEL
                       PHI  real
                       PSI  real




The module SECONDARY sets some basic secondary structure
elements like ALPHA helix, antiparallel BETA strand and
PARALLEL beta strand. Besides PHI and PSI angles can be
defined explicitly.





File: select.txt

Last modified: 5-apr-2004



SELECT


Operators
Tags

Syntax
BY
ALL
ANALYSIS
AROUND
BETWEEN
CHARGE
CLASS
COLOR
CTABLE
CUT
ELEMENTS
HISTORY
IMAGE
INTERNAL
MAIN
ATOM
RESIDUE
SEGMENT
CHAIN
MAP
NEIGHBOUR
PATH
PLANE
RINGS
SEQUENCE
TEMPERATURE
WEIGHT

Examples:



The SELECT subsentence can be included in almost any MAIN
command sentence. It allows you to perform the desired
operations on a limited ATOM or POINT SELECTION.  In most
cases ALL atoms are selected by default, sometimes (as in a
DELETE command) such default is not acceptable, and a
selection must be specified.


The SELECT ... END subsentence assigns each atom
a flag value 1 for (true) or 0 for (false).


In general a SELECT sentence looks like this:




MAIN> ... SELECT  tag1 .OR. tag2 .AND. ( .NOT. tag3 ...) .XOR. tag4 END




The user can combine the tag(s) with logical operators
.AND., .OR., .NOT.  and brackets (). Up to 10 levels of
brackets are allowed. Logical operators .AND. and .OR. act
between 2 tags, while .NOT. acts on one only.


Recursive use of the SELECT sentence is possible only
indirectly with the help of KEY(s). The SELECT sentence uses
the result of a previous one as a tag.



Operators



Operators allow you to combine tags with logical relations:


".NOT." works on a single following tag by inverting each
atomic flag (on to off and off to on),

".OR." combines the preceeding and the following tags so
that result is on when any of the two atomic flags is on and
the result remains off when both of the two flags are off,

".AND." combines the preceeding and the following tags so
that result is on when both of the two atomic flags are on and
the result is off when any of the two atomic flags is off.

".XOR." combines the preceeding and the following tags so
that result is on when both of the two atomic flags differ and
the result is off when any of the two atomic flags are equal.




Tags


Syntax
BY
ALL
ANALYSIS
AROUND
BETWEEN
CHARGE
CLASS
COLOR
CTABLE
CUT
ELEMENTS
HISTORY
IMAGE
INTERNAL
MAIN
ATOM
RESIDUE
SEGMENT
CHAIN
MAP
NEIGHBOUR
PATH
PLANE
RINGS
SEQUENCE
TEMPERATURE
WEIGHT



Tag is a synonym for an atom property or its description.
Through tags you can reach particular group of atoms and
combine them by applying brackets and logical operations.
Tags refer to ATOM NAMES, atomic TEMPERATURE factors, atomic
positions regarding to a PLANE or a CENTER, ...


MAIN differentiates between small and capital letters.  The
star sign '*' and the percent sign '%' have special meaning
when atoms are selected according to their NAMES or KEY(s).
The star allows any further character, and the percent sign
allows any character on that particular place.


See also section "Operators".



Syntax





BY    BOND


      PAIR
      RESIDUE
      SEGMENT
      SEQUENCE




string (KEY(s))


ALL


ANALYSIS AVERAGE   real   real


         RMS       real   real
         MINIMAL   real   real
         MAXIMAL   real   real




AROUND   KEY      string                        DISTANCE real


         CENTER   ATOM      atom-num
                  CALCULATED
                  COORDINATES real real real




ATOM MODULUS inte  inte [inte]  (*)


     NUMBER  inte [: inte inte ]
     NAME    string [strings ...]
     CLASS   string




BETWEEN   inte inte


BOND    PAIR     inte


        NUMBER   inte
        RANGE real1 real2




CHAIN  MODULUS inte  inte [inte]   (*)


       NUMBER  inte [inte]
       NAME    string [strings ...]
       SIZE    inte inte





CHARGE  real real


CLASS   string


COLOR   inte inte


CTABLE   inte inte


CUT      atom-num   atom-num


ELEMENTS int1 int2


HISTORY


IMAGE


INTERNAL   DISTANCE   real real


           ANGLE      real real
           DIHEDRAL   real real




MAP   inte [1] real real


MAIN


NEIGHBOUR atom-num inte


PAIR   inte


PATH inte inte


PLANE  inte real real


RESIDUE MODULUS inte  inte [inte]   (*)


        NUMBER  inte [: inte]
        NAME    string




RINGS


SEQUENCE string [: string] [string ...]


SEGMENT MODULUS inte  inte [inte]   (*)


        NUMBER  inte [: inte]
        NAME    string [strings ...]
        SIZE    inte inte




TEMPERATURE  real real


WEIGHT   real real


(*) ATOM NAME is equivalent to NAME ATOM.  Word order is also
not important for combinations of words as RESIDUE and SEGMENT
with words NAME, NUMBER and MODULUS.



BY



... BY   BOND       ...
         PAIR
         RESIDUE
         SEGMENT
         SEQUENCE




BY is a special tag operator that can precede any other tag
including a KEYED SELECTION. It means that atoms that are
covalently bound (BOND), form a PAIR, are in the same
RESIDUE or SEGMENT or have the same SEQUENCE name as any of
the tagged atoms, will be SELECTED. Operators BY RESIDUE,
SEGMENT or SEQUENCE operators SELECT also the tagged atoms,
while the BY BOND and PAIR don't.



ALL



... ALL ...




Selects ALL atoms. In some command sentences (DEFINE, IMAGE,
WRITE) it is the default SELECTION so that it doesn't always
have to be explicitly specified. In general, ALL atoms are
SELECTED, unless a selection is required.



ANALYSIS



... AVERAGE   real   real
    RMS       real   real
    MINIMAL   real   real
    MAXIMAL   real   real




Select analysis data (AVERAGE, RMS, MINIMAL or MAXIMAL) within the
given range for ATOM or RESIDUE selection.



AROUND



... AROUND KEY string
           CENTER   ATOM atom-num
                    CALCULATED
                    COORDINATES real real real
           FROM string
           DISTANCE real




The AROUND tag selects atoms that are AROUND any atom from the
KEY or AROUND a specified point in space (CENTER) for the
specified DISTANCE.  The CENTER can be defined either by an
ATOM position, by the current IMAGE center (CALCULATED) or
specified directly with COORDINATES. In order to speed up the
calculation, it is reasonable to limit the search only to the
atoms FROM the specified key.



BETWEEN



... BETWEEN int1 int2




Selects all atoms included in the covalent bond network between the
two specified atoms.  (Used for selection of all atoms between two CA
atoms to specify rotation of the whole peptide bond subunit.)



CHARGE



... CHARGE real real




SELECTS atoms with their partial atomic CHARGES in a specified
range.



CLASS



... CLASS string




SELECTS atoms with specified atom CLASSES.



COLOR



... COLOR inte




SELECT atoms with the specified COLOR.



CTABLE



... CTABLE inte inte




Selects atoms with the number of covalently attached neighbors between
"int1" and "int2".



CUT



... CUT  atom-num1   atom-num2




SELECTS the atoms, that are included in the network of
covalent bonds, starting at the atom-num2 away from the
atom-num1.  This is a shortcut to the procedure, where you
should first cut the bond (atom-num1 - atom-num2), then
select all atoms included in the covalent bond network on the
side of atom-num2 and at the end join the atoms again.



ELEMENTS



... ELEMENTS int1 [int2 ...]




SELECTS atoms with the given element number (atomic number).
More than one number can be specified at a time.



HISTORY



... HISTORY




SELECTS atoms from the HISTORY list.



IMAGE



... IMAGE




Selects displayed atoms.



INTERNAL

INTERNAL   DISTANCE   real real


           ANGLE
           DIHEDRAL




SELECTS the atoms whose INTERNAL coordinate (DISTANCE, ANGLE
or DIHEDRAL angle) is in the specified range. Internal
coordinates and Z_TABLE are required.



MAIN

MAIN


Selects the MAIN chain amino acid residue atoms (C,O,CA,H,N).
Its equivalent is ATOM NAME C O CA H N.



ATOM



... ATOM MODULUS  inte  inte [inte]
         NUMBER  inte [inte]
         NAME    string [strings...]
         CLASS   string




Selects ATOMS according to their NAME(S), CLASS, consecutive
NUMBER in a range or MODULUS operator.



RESIDUE



... RESIDUE MODULUS inte  inte [inte]
            NUMBER  inte [inte]
            NAME    string [strings...]




Selects RESIDUES according to their NAME(S), consecutive
NUMBER in a range or MODULUS operator.  See ATOMS for
a further description of NAME.



SEGMENT



... SEGMENT MODULUS inte  inte [inte]
            NUMBER  inte [inte]
            NAME    string [strings...]
            SIZE    inte inte




Selects SEGMENTS according to their NAME(S), consecutive
NUMBER in a range or MODULUS operator.  SEGMENT SIZE
selects segments that include number of atoms within
the specified limits.




CHAIN



... CHAIN MODULUS inte  inte [inte]
          NUMBER  inte [inte]
          NAME    string [strings...]
          SIZE    inte inte




Selects CHAINS according to their NAME(S), consecutive
NUMBER in a range or MODULUS operator.  CHAIN SIZE
chains of atoms that include number of atoms within
the specified limits.




MAP



... MAP  inte real real




Select atoms within the specified (electron) density range.
The density at an atom center is calculated from the MAP
inte by linear interpolation.



NEIGHBOUR



... NEIGHBOUR atom-num inte




SELECTS all the atoms that are within the range of the inte
steps form the central atom-num. 1 step is one covalent
bond.  With 0 only the atom atom-num is selected, with 1 its
NEIGHBOURS, with 2 NEIGHBOURS of the NEIGHBOURS and so on.
With inte -1 the whole molecule (network of covalent bonds
starting at the atom-num) is SELECTED.



PATH



... PATH inte1 inte2




SELECTS atoms on the covalent bond network on the direct path betwen
the two specified atoms.



PLANE



... PLANE inte real1 real2 ...




SELECTS atoms that are located in the specified distance range (real1
and real2) distances from the PLANE inte.  Distances are calculated
from the scalar product between the atomic position and the plane
equation and can be negative.  Planes are defined with a SET PLANE or
CALCULATE PLANE command sentence.



RINGS



SELECTS atoms involved in RINGS of covalent networks.



SEQUENCE



... SEQUENCE string (string) ...




SELECTS the residues between the residues with the specified
sequence names. When only residues with a single SEQUENCE
name are to be found, then the second string is redundant.




TEMPERATURE



... TEMPERATURE  real real ...




SELECT atoms with TEMPERATURE factors in the specified
range.



WEIGHT



... WEIGHT real real ...




SELECT atoms with crystallographic WEIGHTING factors in
the specified range.



Examples:





MAIN> write select all end coordinates




Selects all atoms and writes their coordinates to the
terminal.





MAIN> key a select atom name C* N* O* .and. .not.
MAIN> ( main .or. residue -
MAIN> name A* ) .and. segment number 2 10 end




Assigns to key 'a' all atoms, which ATOM NAME starts with C,
N or O and are not ( the MAIN chain atoms or their RESIDUE
NAME doesn't start with an A ) and are included in segments
with their consecutive numbers from 2 to 10.




MAIN> key inhibitor select segment number 1 : 3 5 end




Assigns the atoms included in the segment
number 1 to 3 and 5 to the KEY inhibitor.





MAIN> key water select residue name HOH end




Assigns to key water all residues with names HOH





MAIN> ... select around key inhib distance 4.5 from water end




SELECTS atoms that are closer than 4.5A to key inhib and
belong to key water. (Two solvation shells).





MAIN> key bond_to_C  select by bond atom name C* end




SELECTS all atoms that are covalently bound to atoms with name
starting with the letter C (carbons). When two C* atoms are connected
to each other, then they are both SELECTED.







File: set.txt

Last modified: 18-oct-2007



SET


Syntax
LEVEL
DIALS

READ
WRITE
DROP
FROM
TRANSLATION
CENTER
SCALE
CLIPPING
ROTATION
VIEW
SCREEN
STEREO
COLOR
INITIALIZE
CHARACTER
OBJECT
IMAGE_parameters
ANGLE, 4-STEREO XCENTER, 8-CHARACTER scale)
GRAPH

TEXT
OBJECT

TRANSLATE
SCALE
CHARACTER
ROTATE



DISPLAY
VARIABLE
STICK
BOND
MATRIX
INITIAL
PLANES
INVERT
GEOMETRY

AUTO
VALEUS
SELECT
DISTANCE
ANGLE
DIHEDRAL
INTERNAL_COOR
ALIGN

RMS
CENTER
B-VALUES
TEMPERATURE
COORDINATES
RADII
RIBBON
WEIGHTS
SECONDARY



The SET command sentences are used to SET some values or
parameters relevant for atomic records (B_VALUES, WEIGHTS,
COLORS, RADII, COORDINATES, SECONDARY - these modules can be
entered also from MAIN directly), GEOMETRY relations, they
control DIALS assignment and parameters relevant for general
MAIN control (VARIABLES, LEVEL, MATRIX, CENTER)...



Syntax



SET
    B-VALUES
    BOND   ATOMS       FORWARD 3*atom-num  BACKWARD
            POINTS
    CHRAGES
    LEVEL       inte
    DIALS .....
    DISPLAY     int1 int2 int3 int4






    VARIABLE    string   real/inte/string






    MATRIX   int0    INITIALIZE
                     X-AX   real  (in degrees)
                     Y-AX   real
                     Z-AX   real
                     NUMBERED     9 * real
                     * inte
                     \ inte
                     DEORTHOGONAL
                     ORTHOGONAL
                     SYMMETRY inte
                     TRANSPOSE
                     INVERSE
                     COPY
                     RMS
                     POLAR_ANGLES 3*real (psi, phi, kappa) or (phi, psi, kappa)
                     ATOM atom-num atom-num atom-num


!    AUTODIALS   inte  INITIALIZE
!                      STEP real
!                      TIME_STEP real




     PLANE     ATOM  atom-num1 atom-num2 atom-num3
               NUMBERS 4*real
               SELECT ... END
               INITIALIZE
               DROP  [inte]






     INITIALIZE






     RMS   3*real 3*real






     RIBBON AUTOMATI
            COIL
            DENSITY  real
            EXIT
            HELIX
            INITIALI
            N_LINES int
            RADIUS  real
            REFINE  int
            SELECT ... END
            SEPARATI
            STEPS   int
            STRAND






     STICK DENSITY int
           RADIUS real







     CENTER    ATOM          atom-num
               CALCULATE     [SELECT ... END]
               COORDINATES   3*real
               SEQUENCE      string
               POINT         inte






     INVERSE/CHANGE   atom-num1 atom-num2






     GEOMETRY   DISTANCE       2*atom-num
                ANGLE          3*atom-num
                DIHEDRAL       4*atom-num
                INTERNAL_COOR  4*atom-num
                ALIGN          2*atom-num
                VALUES      real [real real]
                AUTO
                SELECT ... END





LEVEL



... LEVEL inte




Sets the message level (errors, warnings, debugging data). A
lower value results in fewer messages and a higher in
more. The starting LEVEL value is 0.  You can set any
number, also only values between -5 and 5 differ in effect.



DIALS


READ
WRITE
DROP
FROM
TRANSLATION
CENTER
SCALE
CLIPPING
ROTATION
VIEW
SCREEN
STEREO
COLOR
INITIALIZE
CHARACTER
OBJECT
IMAGE_parameters
ANGLE, 4-STEREO XCENTER, 8-CHARACTER scale)
GRAPH

TEXT
OBJECT

TRANSLATE
SCALE
CHARACTER
ROTATE





... DIALS   inte  TRANSLATION     []
                                  X-AX
                                  Y-AX
                                  Z-AX
                  CENTER          ()
                                  X-AX
                                  Y-AX
                                  Z-AX
                  SCALE
                  CLIPPING
                  ROTATION        []
                  VIEW
                  SCREEN
                  STEREO          ANGLE
                                  XCENTER
                  COLOR  inte  string
                  INITIALIZE
                  CHARACTER
                  OBJECT  inte    BOND
                                  ANGLE
                                  DIHEDRAL
                                  DISTANCE
                                  ROTATION
                                             X-AX
                                             Y-AX
                                             Z-AX
                                  TRANSLATION
                                             X-AX
                                             Y-AX
                                             Z-AX
                  READ
                  WRITE
                  IMAGE_PARAMETERS
                  DROP
                  GRAPH     TEXT   string
                            OBJECT inte   TRANSLATE   ALL
                                                      X-AX
                                                      Y-AX
                                                      Z-AX
                                          SCALE       ALL
                                                      X-AX
                                                      Y-AX
                                                      Z-AX
                                          CHARACTER
                                          ROTATE      ALL
                                                      X-AX
                                                      Y-AX
                                                      Z-AX
                  FROM inte





SETs the DIAL definitions. The DIALS are not set through an
IMAGE command sentence to allow the use of a single command
word (DIAL) to enter the DIAL-OG mode and to assign
functions to DIAL-S.  Most dial definitions are governed by
the program itself or can be picked from menus when MAIN is
in the DIALOG mode.  Each DIAL has a label, that tells what
is the function of the dial and to which object it is
attached (in the case of OBJECT and GRAPH DIALS).  Sometimes
it is necessary to do DIAL_SAV from menu so as not to lose
some dial definitions. Up to 10 different dial sets can be
stored and restored.  A dial set is a combination of 8 dial
functions.



READ



... READ




It is called using DIAL_RST menu item (dial restore) in
DIALOG mode.  It READS (restores), the next dial set from
the list.  So one after another all the saved dial sets can
be restored.



WRITE



... WRITE




It is called using DIAL_SAV menu item (dial save) in DIALOG
mode.  It WRITES (saves), the current dial set to the list.
The dial set is stored as last and the pointer is moved to
it. The rule is written last, read first.



DROP



... DROP




DROPS (forgets) all dial definitions to the consecutive
number inte2, that is set by the SET DIAL inte FROM inte2
command.  (It sets the list count to inte2. By default this
number is equal to 0.)  It is called automatically when the
current geometry of the active OBJECTS is accepted
(OBJ_ACCEP) or rejected (OBJ_REJEC) in DIALOG mode.



FROM



... FROM inte2




Protects the dial set definitions as saved on the list from
deletion, by SETing the lowest value to which the dial set
count can be DROPPED.  By default it is set to 0, which
means none of the dial sets is protected.  This command is
used for example to protect the Ramachandran plot GRAPH
manipulation during a model building session.




TRANSLATION



... TRANSLATION     []
                    X-AX
                    Y-AX
                    Z-AX




Sets 3 [] or a single DIAL to transfer the translations of
the image in X, Y or Z direction. The rotation center of the
image remains unchanged and may even move out of the screen.



CENTER



... CENTER          []
                    X-AX
                    Y-AX
                    Z-AX




Sets 3 [] or a single DIAL to control the translation of the
rotation center of the image in X, Y or Z direction. The
rotation center remains all the time in the middle of the
screen, so the image is shifted. (This is the default.)



SCALE



... SCALE




Controls SCALING of the IMAGE. The value should be negative
for the PSnnn devices, since their coordinate system is
left-handed.



CLIPPING



... CLIPPING




Controls the distance between the two CLIPPING
planes. CLIPPING of the image occurs in the Z direction.



ROTATION



... ROTATION        []
                    X-AX
                    Y-AX
                    Z-AX




Sets 3 [] or a single DIAL to control the rotation of the
image around the rotation center in X, Y or Z direction.



VIEW



... VIEW




Controls distance from the VIEWER eye position to the center
of the image. MAIN uses perspective view.



SCREEN



... SCREEN




Controls the distance between the VIEWER to the imaginary
SCREEN on which the image objects are projected.  In GL or
OpenGL environment this parameter is related to the field of
view.



STEREO



... STEREO ANGLE
           XCENTER




Controls the STEREO ANGLE and separation (XCENTER) of the
image rotation centers along the X axes for side by side
stereo.



COLOR



... COLOR inte  string




A dial controls color of an image object.  A dial is defined
in DIALOG mode by first activating the color mode and then
clicking an image object.



INITIALIZE



... INITIALIZE




Restores the INITIAL definition of the DIALS (X,Y and Z
center translations, scaling, X, Y and Z axes rotations and
clipping).



CHARACTER



... CHARACTER




Controls the character size.



OBJECT



... OBJECT inte ...




The active OBJECTS of MAIN are the SELECTIONS of atoms on
which particular functions are activated in order to control
the spatial changes of molecules interactively. When an
OBJECT is activated from the DIALOG mode the DIALS are
assigned to it automatically.





... BOND
... ANGLE
... DIHEDRAL
... DISTANCE
... ROTATION []
             X-AX
             Y-AX
             Z-AX
... TRANSLATION []
                X-AX
                Y-AX
                Z-AX




The assigned DIAL rotates a BOND, changes an ANGLE, a
DIHEDRAL angle, moves along the vector connecting the last
twoclicked atoms (DISTANCE). Three DIALS are assigned to
ROTATE around all 3 axes or only one DIAL to ROTATE around
one (X-AX or Y-AX or Z-AX).  Definitions for the TRANSLATION
of the OBJECT follow the same rules as the ones for
ROTATION.



IMAGE_parameters



... IMAGE_parameters




SETs the view parameters DIAL set.  (1-SCREEN, 2-VIEW,

ANGLE, 4-STEREO XCENTER, 8-CHARACTER scale)




GRAPH


TEXT
OBJECT

TRANSLATE
SCALE
CHARACTER
ROTATE




... GRAPH ...




Controls the GRAPH objects (TEXT - translations inside a
GRAPH OBJECT) and a GRAPH OBJECT as a whole. (Its
orientation, translation and scaling.)



TEXT



... TEXT   string




String is a name of an IMAGE object.



OBJECT


TRANSLATE
SCALE
CHARACTER
ROTATE



... OBJECT inte





TRANSLATE



... TRANSLATE   ALL
                X-AX
                Y-AX
                Z-AX




TRANSLATION of a GRAPH OBJECT assigned with ALL, defines 3
DIALS, one for each direction, while the X-AX, Y-AX or Z-AX
define 1 DIAL for each separate direction.



SCALE



... SCALE       []
                X-AX
                Y-AX
                Z-AX
                ALL




SCALING of a GRAPH OBJECT can be coupled (ALL), which means
that SCALING in ALL three directions is the same, and is
governed with a single DIAL. Each axis can also be scaled
independently (X-AX, Y-AX, Z-AX) using one DIAL per axis.
With no ([]) explicit specification four DIALS are assigned,
one for each of the possible SCALING controls.



CHARACTER



... CHARACTER




Controls the CHARACTER size of the GRAPH OBJECT.  Only works
under PHIGS graphics interface (on HP and ESV systems).



ROTATE



... ROTATE      ALL
                X-AX
                Y-AX
                Z-AX




The ROTATION of a GRAPH OBJECT is controled along each axes
(X-AX, Y-AX, Z-AX).  If you want to adress rotation about
ALL three of them similtaneously use command ALL intstead of
three separate dial definition commands.



DISPLAY

,,, int1 int2 int3 int4


The four integer values may override deafult size and origin position
of the windows during the image initialization.  The first pair
defines the uper left corner of the image window, whereas the second
pair defines the maximal size of dislpay available for the
application.  When X-server sizes are smaller than the user defined
ones, the X-server default values prevail.



VARIABLE



... VARIABLE string0 REAL
                     INTEGER
                     CHARACTER
                     LOCAL
                     GLOBAL
                     = inte/real/string1
                     SEGMENT  SELECT ... END
                     RESIDUE
                     SEQUENCE
                     ATOM




SETs the VARIABLE adressed with the string0 to a value that
can be either an INTEGER, a REAL number or a CHARACTER
string. The program normally recognizes the kind of VARIABLE
from the argument.  You are however advised to explicitly
specified the type.  Variables can be assigned as GLOBAL or
LOCAL ones.  The GLOBAL are seen throughout of the program
run, while the LOCAL ones exist only on the particular macro
level.  A RETURN deletes them.


Values of character variables can be extracted from a
selection of SEGMENT, RESIDUE or ATOM NAMES and SEQUENCE
IDs.


Integer number can be extracted from the first selected
ATOM, RESIDUE or SEGMENT.


The variables can be further applied in any command sentence
at the place of required input data (integer or real numbers
and strings).  The only exception is this command sentence,
where the string0 is assumed to be the variable name
explicitly and not its value.  The VARIABLE name string0 can
be any string up to 10 characters long.  Character variable
values can be up to 80 characters long.


See sections "INQUIRE" and section "DELETE VARIABLE".





> inquire real global variable XX text "GIVE ME A REAL NUMBER:"





STICK



... DENSITY int
    RADIUS real




SETS the stick RADIUS and DENSITY (number of circle divisions).



BOND



... BOND ATOM      FORE atom-num atom-num  atom-num
         POINT     BACK




BOND FORE atom-num atom-num transforms the atom coordinates
so that the specified BOND is in direction of the X axes and
with the origin at the first specified atom.  BACK does the
opposite transformation. It returns only one level back.


Using two consecutive BOND FORE commands without the BOND
BACK command in between, the user can not return to the
original coordinate system any more.



MATRIX



... MATRIX int0 INITIAL
                X-AX   real  / in degrees
                Y-AX   real
                Z-AX   real
                NUMBERED     9 * real
                * inte
                \ inte
                INVERT
                TRANSPOSE
                DEORTHOGONAL
                ORTHOGONAL
                POLAR_ANGLES phi psi kappa  (or phi psi kappa)
                SYMMETRY inte
                COPY inte
                RMS
                ATOM atom-num atom-num atom-num




MATRICES int0 (1 to 8) can be set.  MATRIX 1 and 8 are used
for the image processing (8 is the stereo pair).  MATRIX 6
is the matrix that is used to define a rotation around a
single axis (X-AX, Y-AX, Z-AX).


The command




MAIN> set mat 3 init x-ax 3. y- 45. z- 90. y- -34. z- 3.45 y- 1890.




will result in matrix 3 that is composed of the 6 specified
rotations.  Matrices can be defined explicitly by NUMBERED
input of the 9 consecutive real numbers.  MATRICES can be
COPIED, INVERTED, TRANSPOSED, multiplied (*), divided (/),
INITIALIZED (set to a unit matrix), specified by the POLAR
angles or by symmetry operations, or as DE/ORTHOGONALIZATION
matrices or calculated from the last RMS fit rotational
parameters.


WARNING: Whenever you transfer or interchange matrices between
various programs you do always have to check the consistency
of matrix definitions.  They should be all the same but they
are not!!!



INITIAL



Sets all program variables and data to the initial state
(ONLY ATOMS AND COVALENT BONDS ARE LEFT).  Don't use it unless
you are really in trouble because of a bug.


!2 POINTS
!POINTS   inte   PASCAL
!                TRIANGLE
!                SURFACE
!
!     Sets the level in pascal triangle rule generation
!     for points on the atom surface.



PLANES



... PLANES   ATOM  iatom iatom iatom
             NUMBERED  4*real
             SELECT ... END
             INITIALIZE
             DROP  (inte)




ATOM creates a plane through the first three SELECTED atoms.
NUMBERED requires the normal to the plane (a, b,c) and the
d. [ a*X + b*Y + c*Z + d = 0 ]


SELECT ... END creates a plane that goes through 3 first
atoms in selection.  (will be used to calculate the RMS
plane)


INITIALIZE the number of planes to 0. 10 is maximum.


DROP  (inte) one or more plane from the stack.


inte .le. 0 : DROPS the last inte planes

inte .gt. 0 : DROPS the specified plane and fills


  its place with the last one on the list



inte not specified : DROPS the last plane from the list





INVERT



... INVERT atom-num1 atom-num2




Interchanges positions of the two atom chains at a chiral
center.  (INVERTS the chirality). The chiral center atom is
the atom to which both specified atoms (atom-num1 and
atom-num2 ) are attached by a covalent bond. Each atom chain
includes all atoms connected via covalent bonds to atoms
atom-num1 or atom-num2 apart from the chiral center.



GEOMETRY


AUTO
VALEUS
SELECT
DISTANCE
ANGLE
DIHEDRAL
INTERNAL_COOR
ALIGN



...  GEOMETRY   DISTANCE     2*atom-num
                ANGLE          3*atom-num
                DIHEDRAL       4*atom-num
                INTERNAL_COOR  4*atom-num
                ALIGN          2*atom-num
                VALUES      real [real real]
                AUTO
                SELECT ... END





AUTO



... AUTO




It is the default option.  The desired parameter (DISTANCE or
ANGLE) is searched in the forcefield parameter library.



VALEUS



... VALUES real [real real]




The neccessary number of target values is hereby explicitly
defined.  One VALUE for BOND, ANGLE, DIHEDRAL and three
values for INTERNAL coordinates need to be
specified. DISTANCES are in AA and angles in degrees.



SELECT



... SELECT ... END




By default only the first specified atom is moved, the
others are used as reference points only.  If you want to
move SELECTIONS you have to specify them explicitly.



DISTANCE



... DISTANCE     2*atom-num




Moves the SELECTION in the direction of the vector going
from atom-num1 to atom-num2, for the DISTANCE that is the
difference between the specified real and the distance
between the atom-num1 and atom-num2.  The specified real can
also be a negative value. When atom-num1 is a part of the
SELECTION the resulting distance between the atoms atom-num1
and atom-num2 is the specified real. When AUTO is chosen
instead of an explicitly defined VALUE then the required
distance is searched in the list of BOND ENERGY parameters
(according to the atom CLASSES).



ANGLE



... ANGLE  atom-num1   atom-num2   atom-num3




Rotates the SELECTION around the normal to the plane defined
by the atoms atom-num1/2/3 and going through atom-num2.  The
ANGLE of rotation is calculated so that when the atom-num1
is included in the SELECTION, the resulting angle between
atoms atom-num1/2/3 is the specified real.  When AUTO is
chosen instead of an explicitly defined VALUE,  the
required angle is searched in the list of ANGLE ENERGY
parameters (according to the atom CLASSES).




DIHEDRAL



... DIHEDRAL atom-num1 atom-num2 atom-num3 atom-num4




Rotates the SELECTION around the bond atom-num2 atom-num3.
The angle of rotation is calculated so that when the
atom-num1 is included in the SELECTION, the resulting
DIHEDRAL angle between the atoms atom-num1/2/3/4 becomes
equal to the specified real.  When AUTO is chosen instead of
an explicitly defined VALUE, the required dihedral
angle is set to 180o.




INTERNAL_COOR



... INTERNAL  atom-num1 atom-num2 atom-num3 atom-num4




It combines the translation and rotations of the SET
DISTANCE, ANGLE and DIHEDRAL angle into one entity. For
description see SET DISTANCE, SET ANGLE and SET DIHEDRAL.
Its VALUES parameter however consist of 3 real numbers
meaning a distance andgle and dihedral angle.



ALIGN



...  ALIGN 2*atom-num




ALIGNS two atoms or a SELECTION so that the two appear to
each other at the specified (or bond) distance with their
attached neighbors at a reasonable geometrical criteria.  It
as a construction that may not always work.



RMS



... RMS 6*real




SETs the rotational and translational parameters that are
usually obtained via the RMS COORDINATES ALL ... procedure.
The first 3 parameters are the rotational angles around the
X-axes, Y'-axes and X"-axes and the second 3 parameters are
the translational vector"the translational vector.



CENTER



...  CENTER    ATOM          atom-num
               CALCULATE     [SELECT ... END]
               COORDINATES   3*real
               SEQUENCE      string
               POINT         inte




SETs the CENTER (also IMAGE center) coordinates:


to the position of an ATOM, specified by its atom-num,

to the arithmetic mean of the SELECTION,

to the specified COORDINATES X, Y and Z (3*real),

to the residue with the SEQUENCE name "string",


  (the coordinates of the CA atom are chosen. When
  the residue has no CA atom, then the first atom
  appearing in the chosen residue),



to the POINT with the sequential number inte.
CENTER coordinates can be SHOWN.




B-VALUES



See under the same keyword directly from MAIN (MAIN_COM:temp.html).



TEMPERATURE



See under the same keyword directly from MAIN (MAIN_COM:temp.html).



COORDINATES



See under the same keyword directly from MAIN (MAIN_COM:coord.html).



RADII



See under the same keyword directly from MAIN (MAIN_COM:radii.html).



RIBBON



See under the same keyword directly from MAIN (MAIN_COM:ribbon.html).



WEIGHTS



See under the same keyword directly from MAIN (MAIN_COM:weight.html).



SECONDARY



See under the same keyword directly from MAIN (MAIN_COM:secondary.html).









SHOW


Syntax
UNIT
FILE
IMAGE

AUTO_DIA
BALL
CENTER
CLIPPING
COLOR
CONTRAST
DIALS
FONT
HISTORY
LIGHTS
LIST
MATRIX
RATIO
REFLECTI
SCALE
SCREEN
STEREO
STICK
TRANSLAT
VIEW_CEN
WINDOW

ATOM
BOX
RESIDUE
SEGMENT
SIZES
PLANES
POINTS
MATRIX
KEY
SELECTION
CHAIN
VARIABLES
TOPOLOGY
PARAMETERS
ENERGY
FORCES
DENSITY
OBJECTS
COLOR
CHARGE
CLASS
RADII
WEIGHT
TEMPERATURE
DISTANCE
ANGLE
DIHEDRAL
INTERNAL
Examples

SHOW.TEX       14-nov-91


The SHOW command sentence is to be used for interactive
control of data (ATOM, BOND, RESIDUE, SEGMENT, SELECTION
number, IMAGE parameters ...)  and for some data analyses
and statistics.  Each of the SHOW command group can be
continued within the same command sentence by starting a new
command group at the end of the previous.  Most of the
parameters that can be SET can be also SHOWN.



Syntax



UNIT int


FILE string


      IMAGE
               ALL
               AUTO_DIA
               BALL
               CENTER
               CLIPPING
               COLOR
               CONTRAST
               DIALS
               FONT
               HISTORY
               LIGHTS
               LIST
               MATRIX
               RATIO
               REFLECTI
               SCALE
               SCREEN
               STEREO
               STICK
               TRANSLAT
               VIEW_CEN
               WINDOW






      BOX    SELECT ... END
      BOND
      ATOM
      RESIDUE
      SEGMENT
      SIZES






      PLANE  LIST
             ANGLE int int
             DISTANCE atom-num int







      POINTS   SURFACE ALL                 RESIDUE
                       CONTACT            RANGE  real real
                       REENTRANT           STEP   real
                       ACCESSIBLE






               VOLUME  ALL
                       ATOM
                       ACCESSIBLE






               DENSITY






               POTENTIAL







      TEXT






      MATRIX






      KEY / SELECTION






      VARIABLES






      TOPOLOGY LIST
               RESIDUE string
                           ATOM string CHARGE CLASS / ALL
                           INTERNAL_COORDINATES
                           ZTABLE_CONNECTIONS
                           VARIABLE_NAMES
                           GROUP_NUMBER
                           BOND
                           DIHEDRAL
                           IMPROPER






      PARAMETERS    BOND  string
                    ANGLE string
                    DIHEDRAL string
                    IMPROPER string
                    VdW    string






      ENERGY






      FORCES        SELECT ... END






      DENSITY       SELECT ... END
                    RESIDUE






      OBJECTS






      COLOR SELECT ... END
      RADII  SELECT ... END
      CHARGE SELECT ... END
      CLASS  SELECT ... END
      WEIGHT SELECT ... END
      TEMPERATURE   SELECT ... END
                    RESIDUE
                    LIST
                    STEP
                    RANGE






      DISTANCE   atom-num  atom-num
      ANGLE atom-num   atom-num   atom-num
      DIHEDRAL atom-num   atom-num   atom-num   atom-num
      INTERNAL  atom-num   atom-num   atom-num   atom-num






UNIT



... UNIT int




Redirects the SHOW output to the logical UNIT number int.



FILE



... FILE string




Redirects the SHOW output to the specified FILE.



IMAGE


AUTO_DIA
BALL
CENTER
CLIPPING
COLOR
CONTRAST
DIALS
FONT
HISTORY
LIGHTS
LIST
MATRIX
RATIO
REFLECTI
SCALE
SCREEN
STEREO
STICK
TRANSLAT
VIEW_CEN
WINDOW



 ... ALL
     (
     )
     AUTO_DIA
     BALL
     CENTER
     CLIPPING
     COLOR
     CONTRAST
     DIALS
     FONT
     HISTORY
     LIGHTS
     LIST
     MATRIX
     RATIO
     REFLECTI
     SCALE
     SCREEN
     STEREO
     STICK
     TRANSLAT
     VIEW_CEN
     WINDOW




Shows image parameters.  ALL shows all of them, whereas use
of "( ... )" enables you to specify a list.



AUTO_DIA



Automatic generation of dial events.



BALL



The shown parameters are the current plygonal approximations
applied for ATOM BALL generation.


Use "POINT BALL" commands to modify them.



CENTER



Shows the current image CENTER in X, Y, Z.


Use "IMAGE CENTER" commands or dials to change it.



CLIPPING



Shows the current clipping planes.



COLOR




CONTRAST



Shows image contrast value.



DIALS




FONT




HISTORY



Shows HISTORY display label flags and, when requested, the
list of picked atoms.


Use "IMAGE HISTORY" commands or pick the atoms using a mouse
to create the list and edit it (menu block "HISTORY"), and
menu block "HISTORY_FLAGS" to change the label definitions.



LIGHTS



Shows current light sources status and parameters.


Use "IMAGE LIGHT" commands and SET DIAL nn LIGHT commands
together with dials to modify them.



LIST



Lists all deposited image objects, their on / off status and
color.



MATRIX



Shows the current view matrix.


Use dials and "IMAGE MATRIX" commands to modify it.



RATIO



Shows ratio number. The number is used ofr control the size
of ATOM CROSSES etc...


Use "IMAGE RATIO" commands to spefify it.  Default is 0.2.



REFLECTI



Shows reflectance coefficients.



SCALE



Scale of image,



SCREEN



SCREEN to eye (viewwer) distance.



STEREO



Stereo projection parameters, mode and status.



STICK



Shows parameters applied for BOND STICK generation.


Use SET STICK commands to define them.



TRANSLAT



The current translation of the image, apart from the center
of rotation.


Use "IMAGE TRANSLATE" commands to change the translation.



VIEW_CEN



Shows viewer to center of the obect distance.



WINDOW



Shows the current size of image window in pixels.



ATOM



... ATOMS




SHOWS the number of present ATOMS.



BOX



... BOX SELECT ... END




SHOWS the BOX limits of the SELECTED atomic coordinates.



RESIDUE



... RESIDUE




SHOWS the number of present RESIDUES.



SEGMENT



... SEGMENT




SHOWS the number of present SEGMENTS and lists their names
and counts the atoms inside each one.



SIZES



Shows sizes of most important data arrays (atoms, points,
refelctions, maps).



PLANES



... PLANE  LIST
           ANGLE int int
           DISTANCE atom-num int




LISTS currently present planes with their PLANE equations,
SHOWS ANGLE between the two specified planes and the
DISTANCE of an atom from the plane (int denotes the PLANE
number and atom-num an ATOM NUMBER).



POINTS



...  POINTS   (SELECT ... END)
               SURFACE ALL                 RESIDUE
                       CONTACT            RANGE  real real
                       REENTRANT           STEP   real
                       ACCESSIBLE






               VOLUME  ALL
                       ATOM
                       ACCESSIBLE






               DENSITY






               POTENTIAL




Each point belongs to an atom, so that SELECT statement can
be applied. The default SELECTION are ALL atoms.


The 4 kinds of points (SURFACE, VOLUME, map DENSITY,
electrostatic POTENTIAL) can be checked and some statistics
can be done with their values.  The SURFACE points are
divided also further in CONTACT, REENTRANT, ACCESSIBLE
points and VOLUME points into ATOM and ACCESSIBLE points.


When nothing else is required only the range, sum, average
value per point and number of SELECTED atom points are
displayed.  With RESIDUE, the same data are displayed for
each RESIDUE separately and per an averaged ATOM in the
residue.  With RANGE the points with their values in the
specified RANGE are counted. When the STEP is defined, then
they are counted for each STEP interval in the specified
RANGE.



MATRIX



... MATRIX




Shows all (8) 3*3 MATRICES used for rotation
transformations.



KEY



... KEY / SELECTION




Displays the list of KEYED SELECTIONS with the number of
atoms included in each one.



SELECTION



... KEY / SELECTION




Displays the list of KEYED SELECTIONS with the number of
atoms included in each one.



CHAIN



... CHAIN  SELECT ... END




Shows a summary of residue and atom numbers included
in each chain.



VARIABLES



... VARIABLES string []
                     NUMBER




Displays the list of to the 'string' matching integer, real
and character VARIABLES with their values. With no further
argument the usual long description is used. With the NUMBER
only the variable values without variable names are SHOWN.



TOPOLOGY



...   TOPOLOGY LIST
               RESIDUE string1
                           ATOM string2 []
                                        CHARGE
                                        CLASS
                                        COORDINATES
                                        ALL
                           INTERNAL string2
                           ZTABLE string2
                           VARIABLE string2
                           GROUP string2
                           BOND string2
                           DIHEDRAL string2
                           IMPROPER string2




The SHOW TOPOLOGY gives insight into the TOPOLOGY library.
With LIST all present RESIDUE names can be listed.  With the
RESIDUE 'string', only the matching residues are listed.  To
get the list of ATOMS, INTERNAL coordinates, ZTABLE, BONDS,
DIHEDRAL and IMPROPER angles ... of the chosen 'string2'
atoms. The ATOM list, can include besides the atom names
(without a further argument), also partial atomic CHARGES,
atom CLASSES and initial COORDINATES. ALL lists CHARGES,
CLASSES and COORDINATES.



PARAMETERS



...   PARAMETERS    BOND  string
                    ANGLE string
                    DIHEDRAL string
                    IMPROPER string


!                    VdW    string


The SHOW PARAMETER ... lists all force field parameters
including the particular atom CLASS.



ENERGY



... ENERGY




Displays the currently turned on ENERGY terms with the last
calculated ENERGIES.



FORCES



... FORCES SELECT ... END




SHOWS the list of last calculated forces acting on the
SELECTED atoms.



DENSITY



...   DENSITY       SELECT ... END
                    RESIDUES




Calculates the DENSITY energy of the SELECTION.  With
RESIDUES, it prepares a list of the density energy for each
SELECTED RESIDUE and calculates an averaged atom
contribution to it.  With different weighting factors and
density energy options several lists can be prepared (see
MAIN$EXA:[DENSITY]).



OBJECTS



... OBJECTS




Shows the list of the current active OBJECTS with their
definitions and their values.



COLOR



... COLOR        SELECT ... END




Lists COLORS of the SELECTED atoms.



CHARGE



... CHARGE        SELECT ... END




Lists partial atomic CHARGES of the SELECTED atoms.



CLASS



... CLASS         SELECT ... END




Lists CLASS of the SELECTED atoms.



RADII



... RADII         SELECT ... END




Lists atomic RADII of the SELECTED atoms.



WEIGHT



... WEIGHT        SELECT ... END




Lists crystallographic WEIGHTS of the SELECTED atoms.



TEMPERATURE



... TEMPERATURE   SELECT ... END []
                                 LIST
                                 RESIDUE
                                 RANGE  real real
                                 STEP real




With no argument [] calculates the average TEMPERATURE
factor of the SELECTION. With the LIST writes the list of
temperature factors. Per RESIDUE calculates average
temperature factor for each RESIDUE and with the RANGE and
STEPS it counts all atoms that are in the specified RANGE
for each STEP size separately.



DISTANCE



... DISTANCE  2*atom-num




SHOWS the DISTANCE between the 2 atoms in Angstroems.



ANGLE



... ANGLE  3*atom-num




SHOWS the ANGLE defined by the 3 specified atoms in degrees.



DIHEDRAL



... DIHEDRAL 4*atom-num




SHOWS the DIHEDRAL angle defined by the 4 atoms in degrees.



INTERNAL



... INTERNAL 4*atom-num




SHOWS INTERNAL coordinates as defined by the 4 atoms
(DISTANCE, ANGLE and DIHEDRAL angle).



Examples





MAIN> show image all
MAIN> show bond
MAIN> show color select symbol atom C* .and. number residue 1  5 end
MAIN> show topology residue GL%% atom C* internal ztable
MAIN> show internal 3 4 100 6789
MAIN> show keys





File: main/doc/spawn.txt

Last modified: 28-jan-96



SPAWN





 SPAWN string ....




Invokes any system functions by entering into a separated
process.


If you want to create a shell in UNIX environment you have
to specify it explicitly, while in VMS SPAWN with no
argument string, creates a user sub_process: Use exit or
logout to return to MAIN>.







SYMMETRY


Syntax
SELECT
CELL
NEIGHBOUR
RESIDUE
DISTANCE
CUT
MATRIX
TRANSLATE
AROUND
DELETE
EXAMPLES

SYMMET.TEX     4-JUL-1990


SYMMETRY applies crystal SYMMETRY operations on given
SELECTIONS of atoms.  The cell constants and symmetry
operations in the form of international tables or from a
density map should be read before.  Each additional SYMMETRY
operation applied results in a new segment which name begins
with '#'.



Syntax



SYMMETRY     SELECT  ... END
             NEIGHBOUR  inte
             RESIDUE
             DISTANCE  real (15.0)
             CUT     real
             MATRIX inte
             TRANSLATION inte inte inte
             CELL
             AROUND   SELECT ... END
                      CENTER *
             DELETE ON / TRUE
                    OFF / FALSE





SELECT



... SELECT ... END ...





CELL



... CELL ...




CELL applies each SYMMETRY operation only once. The atomic
coordinates are afterwards converted so, that they are
placed into 1 cell only.  (Their fractional coordinates can
only have values between 0.0 and 1.0.)  However, the
resulting coordinates are, as by other options, in cartesian
coordinate system.




NEIGHBOUR



... NEIGHBOUR inte




NEIGHBOUR integer specifies how many neighbour layers (inte)
of molecules should be created from each crystal symmetry
molecule.  Each molecule is translated for inte times for a
cell length in the crystal lattice in all 6 directions.  All
together 26 additional structures are created when integer
is 1. Do not use more than 1 for proteins unless you really
know what you are doing.




RESIDUE



... RESIDUE




The RESIDUE command word turns a flag, that disables copying
of RESIDUE structure into the newly created SEGMENT, so that
each newly created segment is a single RESIDUE only.  It
should be used for crystal packing studies, otherwise the
residue number goes quickly over the array boundaries.



DISTANCE



... DISTANCE real




The 'DISTANCE real' specifies how close should some the
box inside which by symmetry operations generated molecules
comes to the AROUND boundaries. When CUT is turned on, then
the DISTANCE is explicitly checked for each particular atom.
The default value is 15.0A.



CUT



... CUT real




CUT is a flag, that enables the DISTANCE checking of each
particular atom. Each generated atom should be closer than
the specified DISTANCE AROUND the CENTER or any atom in the
AROUND SELECTION.



MATRIX



... MATRIX inte




Applies only the specified crystal rotation MATRIX.



TRANSLATE



... TRANSLATE inte inte inte




Applies beside the crystal symmetry operation explicitly
only the specified TRANSLATION. The NEIGHBOUR option is
DISABLED.



AROUND



... AROUND  SELECT ... END
... CENTER  *   (see syntax at image center)




Creates symmetry related atoms from the first SELECTION
around the AROUND SELECTION of atoms.


Specifies the CENTER around which symmetry related atoms
will be generated.


The CENTER option defers from the SELECT option since it
automaticaly assumes the CUT and DELETE ON option.  It is
also computationally faster, however it can not generate
atoms AROUND a nonspherical shape.  The CENTER option is
supposed to be used during an interactive model building
session.  The RESIDUE information can not be suppressed
as well.




DELETE



...  DELETE ON
            OFF




DELETES when the DELETE flag is ON or TRUE, the symmetry
related atoms generated by the identity crystal symmetry
operation (X,Y,Z) with no additional translation. When the
DELETE flag is OFF or FALSE, the atoms are not deleted. OFF
is the default. It should be used for generation of symmetry
environment while building the residues in to the electron
density.



EXAMPLES





MAIN> symmetry select all end neigh 1 around select sequence 57 end -
MAIN> distance 20. cut delete on






MAIN> key old select all end
MAIN> symmetry select numb segment 1 end neigh 1 around select napa end -
MAIN> distance 20. cut delete on
MAIN> key sym1 select .not old end
MAIN> key old select all end
MAIN> symmetry select numb segment 2 end neigh 1 around select napa end -
MAIN> distance 20. cut delete on
MAIN> key sym2 select .not old end
MAIN> key old select all end
MAIN> symmetry select numb segment 3 end neigh 1 around select napa end -
MAIN> distance 20. cut delete on
MAIN> key sym3 select .not old end
MAIN> key old select all end






MAIN> symmetry select ca end neigh 1 around select ca end -
MAIN> distance 50.0 residue





File: temp.txt

Last modified: 2-feb-1999



TEMPERATURE


Syntax
=
ADD
COLOR
INITIALI
KICK
RESTORE
SELECT
SCALE
EXIT



Manipulates B-values of SELECTED atoms.



Syntax



> TEMPERATURE
        =     real
        ADD   real
        COLOR
        EXIT
        INITIALI
        KICK   real inte
        RESTORE
        SCALE   real
        SELECT ... END






=



... = real




Set B-values to the specified (real) number.



ADD



... ADD real




Adds the specified number (real) to the current B-values.




> set temperat sele segm name MY SEGMENTS end add 20.0





COLOR



... COLOR




Copies the value of current atomic color to the B-value
field.  May be useful for passing analysis information to
other programs via the B-value column in a PDB file.




> set temperat sele segm name ICGB end color





INITIALI



... INITIALI




Set B-values to zero.




> set temperat sele segm name MY SEGMENTS end init





KICK



... KICK   real [inte ]




Gives current atomick B-values a random shift (KICK)
with maximum deviation specified by the real argument.


The second argument (inte) is not necessary.  It provides
the seed for the random number generator.




> set temperat sele segm name MY SEGMENTS end kick 4.0





RESTORE



... RESTORE




RESTORES atomic B-values to the last saved value.  Saving is
automatic and can not be controlled by the user.  B-values
are saved before SCALE, KICK, ADD or MINIMIZE commands are
invoked on B-values.



SELECT



... SELECT ... END




SELECTs the atoms on which the consequent operations on
atomic B-values will be performed.  A "SELECT ... END"
command can be applied in combination with all other "SET
TEMPERATURE" commands except "RESTORE".



SCALE



... SCALE real




Scales the current B-values of the selected atoms by a
factor (real). "SCALE" and "ADD" can be applied
simoultaneously.  First "SCALE" is applied and then "ADD".




> set temperat sele segm name MY SEGMENTS end scale 20.0 add 4.





EXIT



If you have entered the TEMPERATURE module (similarly as COLOR)
without providing any arguments, you need and "EXIT" command to
come back to the "MAIN" prompt.


Command




> TEMPERATURE SELECT ALL END = 20.0




remains in 'MAIN>', whereas the command




> TEMPERATURE




enters the 'TEMP>' module. EXIT should be used to return
back to MAIN>.







TOPOLOGY

TOP.TXT        11-DEC-1991


Syntax
TOPOLOGY INITIALIZE


         APPEND  SELECT ... END
                 XPLOR





The TOPOLOGY command sentence INITIALIZES the topology
library (sets the number of TOPOLOGY residues to 0) or
APPENDS new reasidues to already existing ones.  If the name
of the APPENDING residue matches with the last one in the
library then the last one is replaced by the new one.


The newly created TOPOLOGY library residue(s) contain(s) the
complete residue description (ATOM NAME, CLASS, partial
atomic CHARGE, cartesian (shifted to origin) and INTERNAL
COORDINATES, the covalent BOND, DIHEDRAL and IMPROPER angle
lists). The required information is extracted form the
availabe data attached to the SELECTED residues.  More than
one residue can be APPENDED with a single TOPOLOGY APPEND
sentence.


The XPLOR turns on the XPLOR mode, so that the created
residues in the topology library will have no terms (BOND,
DIHEDRALS, IMPROPERS) relating to the previous residue in
the sequence.  By default, the XPLOR mode is turned off, so
that ATOM NAMES from the previous residue are preceeded by a
hyphen '-'.







TRANSLATE


Syntax

ATOM
POINTS
VECTOR
RMS
CENTER

Examples

TRANSL.TEX     19-OCT-91


TRANSLATE command sentence moves atom or point selection
by the specified vector.



Syntax


ATOM
POINTS
VECTOR
RMS
CENTER







TRANSLATE




          ATOMS
          POINTS    SURFACE
                    VOLUME
                    POTENTIAL
                    DENSITY






          SELECT ... END






          VECTOR    3*real   DISTANCE (abs(3*real))
                                           real
          RMS






          CENTER





ATOM



TRANSLATES selected atoms by adding the specified vector. This is the
default, it just makes the syntax easier to understand.



POINTS



TRANSLATES the specified kind of points of selected atoms.



VECTOR



The translational vector must be specified by its X Y and Z components.
When the DISTANCE is specified than the specified vector is
normalized to length 1.0 and each component is multiplied by the
specified distance.



RMS



The translational vector is taken from the last RMS fit calculation.



CENTER



The translational vector is calculated from the current image center and
the center (arithmetic middle) of the selected coordinates. The selected
atoms are translated into the center of the image.



Examples





MAIN> translate atom select all end vector 10.0 15. 3. distance 1.0






MAIN> translate select segment number 1 end vector 10.0 15. 3.






MAIN> translate atom select all end rms






MAIN> translate atom select all end center






MAIN> translate points density select all end vect 10. 0. 3.





File: VLTSET.TXT

Last modified:  4-NOV-87



VLT


Syntax:
BACK
CHANGE
COLOR
COPY inte1 inte2
ERASE
FIRST
INITIALIZE
MODUL inte
MOVE red 16 31 gre 128
RANGE
SCROLL
SHOW
VLT
Examples:



Within Video_Lookup_Table interpreter colors can be defined
according to red green and blue real values. 4 different
VLT`s can be loaded into the program.




Syntax:



 BACK inte
 CHANGE  RED inte inte     RED inte
         GREEN inte inte    ........
         BLUE inte inte    ......
         COLO inte inte    ......
 COLOR RED real    inte4 inte5
       GREEN real
       BLUE real






 COPY  inte inte






 ERASE






 FIRST inte






 INITIALIZE






 EXIT






 MODUL inte






 MOVE  RED inte inte     red inte
       GREEN inte inte    ........
       BLUE inte inte    ......
       COLO inte inte    ......






 RANGE inte inte






 SCROLL inte inte






 SHOW






 VLT  int





BACK



... BACK int




Defines the index of the background color. Default is usually 0.
Depth cuing - merging of image with the background - against a new
color takes place after you change the window size or specify a new
"IMAGE CONTRAST" value.



CHANGE



Changes two specified RGB colour in current VLT.



COLOR



... COLOR inte RED real
               GREEN real
               BLUE real




Sets RGB values into the current vlt and specified color entry.




COPY inte1 inte2



Copies form inte1 vlt to the inte2 vlt..



ERASE



Erases the shown colour table rectangle.
Fills it with bacground colour.



FIRST



The first colour the first line in shown colour table to start.



INITIALIZE



Copies the values from the first VLT to the current one.



MODUL inte



The length of line in the shown colour table.



MOVE red 16 31 gre 128



Moves one colour into another (RGB) in the current vlt.



RANGE



Specifies the minimum and maximim colour addres.


 0 255 for tektronix 4115,
 0 3 for VISUAL 240
 0 15 for TRIGLAV ...





SCROLL



Rolles the lines of coloure numbers beginning with the first and second
integer for the third integer times. Takes the first ( top line ) and
rolls the rest for one line higher and puts the first into the last.
Leng of line is current modul.



SHOW



Shows an reactangle with terminal current coloures in small rectangles.
The number of small reactangles is defined with the modul command.
Because small rectangles are of the same size, changing modul valuse affects
the general shape of rectangle area where small rectangless are displayed.



VLT



Sets the new current vlt. (one of 4 possibilities).




Examples:





> color 0 255 red 255 -1 gre 0 1 blu 128
> change red 16 31 blu 80
> move red 16 31 gre 128
> range 0 255
> scrol 16 128 5
> show
> vlt 3







WEIGHT

WEIGHT.TEX     11-dec-1991


Syntax
WEIGHT


            SELECT ... END * real
            EXIT




Sets the crystallographic WEIGHT factors to the SELECTED
atoms.


The comand sentence:




MAIN> WEIGHT SELECT ... END 1.0




remains in MAIN>, while the:




MAIN> WEIGHT




enters the WEIGHT> module. EXIT should be used to return
back to MAIN>.







WRITE


Syntax
UNIT
FILE
APPEND
OVER
SELECT
Units
NUMBER
NAMES
COORDINATES
ATOMS
SCATTERI
ELEMENTS
INTERNAL
ZTABLE
BONDS
CTABLE

NAMES
FIRST

HBONDS
PAIRS
POINTS
MAP
SYMMETRY
CELL
Examples

WRITE.TEX            19-nov-91


The WRITE sentence is used to write data to files or to the
terminal. First the FILE or FORTRAN logical UNIT should be
specified, then the SELECTION and after that the write
object specification (COORDINATES, BONDS, INTERNAL, MAP),
format (PDB, DIAMOND ...)  and units (ANGSTROM, ATOMIC,
NANOMETERS).  The FILE, UNIT and SELECT are optional.  When
the FILE or UNIT are omitted the output comes to the
terminal (SYS$OUTOUT).  The default SELECTION are all atoms
and the default length UNIT is ANGSTROM.



Syntax



WRITE UNIT int
      FILE string
      OVER
      APPEND
      SELECT ... END
             ATOM
             NANOMETER
             NUMBER   (inte)
             NAMES






             COORDINATES     NORMAL
                             CARD
                             PDB        SEGMENT
                             XPLOR
                             DIAMOND
                             DISCOVER
                             GROMOS
                             GAUSSIAN
            BOND    []
                    NUMBER
            CTABLE  []
                    NUMBER
                    NAMES
                    FIRST SELECT ... END
            HBOND
            PAIR   []
                   NUMBER
                   RAMACHANDRAN
            ZTABLE
            INTERNAL  (GAUSSIAN)  VARIABLES
                      AMPAC






            POINT SURFACE   ALL            (CONNOLY)
                            REENTRANT      GAUSSIAN
                            ACCESSIBLE     G80
                  VOLUME    ALL
                            ATOM
                            ACCESSIBLE
                  POTENTIAL
                  DENSITY






            MAP inte   NUMBER
                       CHARACTER
                       ALPHA
                       FFT
                       XPLOR






            SYMMETRY






            CELL





UNIT

WRITE UNIT inte ...


WRITES the selected data to the FORTRAN logical UNIT number
inte.



FILE

WRITE FILE string ...


WRITES the selected data to the FILE string.



APPEND



... APPEND




Using APPEND it is possible to APPEND information to the end
of an already existing file.



OVER



... OVER




Using OVER it is possible to overwrite an already existing file.




SELECT



... SELECT ... END




When data related to atoms are WRITTEN a SELECTION can be
applied.  The SELECT ... END sentence should proceed the
command word that specifies the kind of data.  The default
SELECTION are all atoms.



Units



... []
    ATOMIC
    NANOMETER




The default length units are Angstroems. When COORDINATES
are to be written in NANOMETERS and ATOM units, then the
units should be explicitly specified.




NUMBER



... NUMBER   (inte)




The NUMBER flag is the opposite of the NAMES flag. In
common it means that the data are less descriptive and that
NAMES are replaced by NUMBERS.  In any case, the NAMES or
NUMBER specifier must follow the write object specification.
The meaning of NUMBER or NAMES has different meanings:


by COORDINATES:




NORMAL or GAUSSIAN format writes the atomic numbers for
the periodic system (this is the default).

PDB and XPLOR format replaces the SEQUENCE information by
the consecutive residue number. A value could however start
at the specified 'inte' and then rise by 1 for each next
residue.



by BONDS, PAIRS:


This is actually a format to write only the bond list
containing only the atomic NUMBERS.


by CTABLE, ZTABLE:


Writes atomic NUMBERS of the reference atoms.


by MAP:


It is the real*4 MAIN MAP format.



NAMES



... NAMES




The NAMES flag, is the opposite of the NUMBER flag and has
a bit ambiguous meaning. In common it means that the
description is more complete and that NUMBERS are replaced
by NAMES.  In any case, the NAMES or NUMBER specifier
must follow the write object specification.


by COORDINATES:


NORMAL or GAUSSIAN format writes the atom names

PDB and XPLOR format writes the SEQUENCE names
(this is the default).



by BONDS, PAIRS: This is the default form.


by CTABLE, ZTABLE: Writes atomic numbers of the reference atoms.


by MAP: It is the real*4 MAIN MAP format.



COORDINATES



See WRITE ATOMS.



ATOMS





... ATOMS  PLAIN
           CARD
           PDB        REORDER
           XPLOR
           DIAMOND
           DISCOVER
           GROMOS
           GAUSSIAN
           ATOM
           NANOMETER
           NUMBER   inte
           NAMES






The length units applied are Angstroems (default for all
formats except for GROMOS, where nanometers are used),
NANOMETERS and ATOM units.  The following formats are
available: NORMAL, CARD, PDB, XPLOR, DIAMOND, DISCOVER,
GROMOS, GAUSSIAN. The NUMBER and NAMES flag effect only PDB
and XPLOR format. The ATOM and NANOMETER units could be
applied anywhere.


The REORDER keyword is applied only with the PDB format.  It
reorders residues accoridng to their connectivities.



SCATTERI



Write SCATTERING factors tells you which atomic numbers have
their scattering factors defined and what are their Gaussian
coeficient values.



ELEMENTS



Writes ATOMIC NUMBERS with ELEMENT IDS.  The rule, what is
written can be also READ is obeyed.




INTERNAL



... INTERNAL  (GAUSSIAN)  VARIABLES
          AMPAC




INTERNAL coordinates can be written with VARIABLE names and
values too.  VARIABLES are used by GAUSSIAN geometry
optimization. The default format is the GAUSSIAN.



ZTABLE



... ZTABLE




WRITES the ZTABLE list either with atomic NUMBERS or names
(NAMES).



BONDS



... BOND    []
            NUMBER




WRITES the BOND list. The default format is NAMES. The
outout contains atom, residue, sequence and segment name of
each atom included in the covalent bond and its length.
When NUMBER is specified, then the BOND list contains only
atomic numbers.



CTABLE


NAMES
FIRST

WRITE       CTABLE  NAMES


                    NUMBER
                    FIRST SELECT ... END




WRITES the connectivity table. The CTABLE contains the
complete set of each atom names (atom, residue, sequence and
segment NAMES) and its neighbours.



NAMES



... NAMES




The neighbors are written with their atom NUMBER or atom
NAMES.  Atoms names are useful for debugging purposes only,
they can, however, give you a better idea, which are the
neighbours of a particular atom.  The NAMES file can not be
read again though.



FIRST



... SELECT ... END




FIRST command enables you to modify the atom number when it
is written to file.  This way you can save connectivity
tables of various molecules and later read them in a
different order, again using FIRST command in a READ CTABLE
sentence.



HBONDS

WRITE       HBOND


WRITES the hydrogen bond (HBOND) list. The list contains
the atom, residue, sequence and segment name of each atom
included in the hydrogen bond list, its length and angle.
Angle is written only when hydrogen atoms are present.



PAIRS

WRITE       PAIR   NAMES


                   NUMBER
                   RAMACHANDRAN




WRITES the PAIR list. NAMES is the default format. The
outout contains atom, residue, sequence and segment name of
both PAIRED atoms, the interatomic distance and when the
equilibrium distance and force constant are DEFINED also
these. With the NUMBER format only atomic NUMBERS are
written.


When the PAIR list is defined as the RAMACHANDARN PAIR list
then the PHI and PSI angles for each residue are written.



POINTS



... POINT SURFACE ALL    (CONNOLY)
                  REENTRANT       GAUSSIAN
                  ACCESSIBLE      G80
          VOLUME ALL
                 ATOM
                 ACCESSIBLE
          POTENTIAL
          DENSITY




Points can be chosen according to their kind (SURFACE,
VOLUME, DENSITY, POTENTIAL) written in 3 different formats
(CONNOLY, GAUSSIAN86, G80).  SURFACE and VOLUME points can
be also further divided into (REENTRANT, ACCESSIBLE and
ATOM, ACCESSIBLE) GAUSSIAN and G80 formats only write point
coordinates. G80 is in atom units.  So that appropriate
programs can read them. Units and NAMES/NUMBER flag have no
effect. The CONNOLY format is in Angstroems and the G80
format is in ATOM units.



MAP

WRITE MAP inte   NUMBER


                 CHARACTER
                 ALPHA
                 FFT
                 XPLOR




The 'inte' tells which MAP to write and is required. When no
format is specified the character*1 maps are written with
the CHARACTER format and the real*4 maps with the NUMBER
format.  MAP can be written in 5 different formats (NUMBER,
CHARACTER, ALPHA, FFT and XPLOR). The NUMBER, CHARACTER and
ALPHA are MAIN formats, while the FFT format is unformatted
and is the input for the FFT calculation using P1SF (Lyn Ten
Eyck program) or PROTEIN and the XPLOR map is a formatted
text file.



SYMMETRY



... SYMMETRY




WRITES the crystal SYMMETRY operations (matrices and
translation vector).



CELL



... CELL




WRITES the crystal CELL constants.



Examples





MAIN> write unit 3 select atom name CA end coordinates pdb






MAIN> write file int_coor.dat internal variable -
MAIN> first select number residue 2 end






MAIN> write select pro end point surface accessible






MAIN> write file cell.fft map 2 fft




Back to MAIN home.