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.
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
CALCULATE BONDS INITIALIZE
[APPEND]
SELECT ... END [SELE ALL END]
NEIGHBOR
RESIDUE
DISULFIDE
DISTANCE [1.75]
Calculates covalent BONDS from interatomic distances.
... 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
Before calculating the bond list, the bond list is INITIALIZED.
... SELECT ... END
The calculation will be done on the SELECTED atom set. SELECT ALL END is the default.
... DISULFIDE
Only sulphur atoms from the selection will be considered by the DISULFIDE bonds calculation.
... RESIDUE
Only interatomic distances of selected atoms for each separate RESIDUE will be calculated and then checked to form the BONDING list.
... NEIGHBOR
Only interatomic distances for each two consecutive residues will be calculated and then checked to form the bonding list.
... 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.
CALCULATE HBONDS INITIALIZE
[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
The calculated hydrogen bonds will be appended to existing ones. APPEND is the default.
... INITIALIZE
Before CALCULATING the hydrogen BOND list, the program deletes all present hydrogen bonds.
... 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 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
Sets the HYDROGEN flag, which means, that the HYDROGEN atoms are present in the atom list and should be used in the calculation.
... 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 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.
CALCULATE PAIRS (
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
... (
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 )
... CALCULATE INTERNAL SELECT ... END
Calculates INTERNAL coordinates from cartesian coordinates and Z-mat-table (ZTABLE) for the selected atoms.
... COORDINATES SELECT ... END INITIALIZE X-AX (X-AX Y-AX)
( SELECT ALL END ) APPEND Y-AX
Z-AX
Calculates cartesian COORDINATES from INTERNAL coordinates
and z-mat-table for selected atoms. INITIALIZE is the
default. That means that all selected atom coordinates are
calculated from internal coordinate values. When APPEND is
used, only coordinates of nondefined atom centers (having
for x, y, and z absolute coordinate value) are
CALCULATE POTENTIAL SELECT ... END SELECT ... END
( 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.
CALCULATE PLANE SELECT ... END
Calculates the RMS fit plane of the SELECTED atomic set. Not implemented yet. See SET PLANE instead.