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


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.

         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
                          SET_GUESS inte 6*real
                          FLAGS 6* inte
         PAIR         FORCE real
                      DISTANCE real
         BY  TOPOLOGY
             ATOMS   x*atom-numb
         SELECT ... END
         NEIGHBOR  string
         SYMBOL  string
         RESIDUE   string


... 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.



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



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.



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 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 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 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 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



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.


... PAIR FORCE       real
         DISTANCE    real

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   4*atom-numb real real   COPY
                 INTERACTION  SELECT ... END  SELECT ... END
                 MAP inte SELECT ... END
                 NCS  SELECT ... END
                      FORCE real
                      B-FORCE real
                      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   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.



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 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).


         FORCE real
         B-FORCE real
         SET_GUESS inte 6*real
         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 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 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.


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 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 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.