The commands in this section are primarily used for manipulating atoms. There is a wide range of commands and options. All of the commands except for the HBUILD command and the unit cell commands may be used on either the main coordinate set, or the comparison set. Some commands require both sets of coordinates.
COORdinates { INITialize } [COMP] [atom-selection]
{ COPY }
{ SWAP }
{ AVERage [ FACT real ] }
{ TRANslate vector-spec [DIST real] }
{ ROTAte { vector-spec } PHI real }
{ { byatom-spec } }
{ ORIEnt [MASS] [RMS] [SAVE name] }
{ RMS [MASS] }
{ RANDOM random-options }
{ DIFF [ FACT real ] }
{ XFORm name }
{ XINVert name }
{ SCALE real }
{ CONV real real real real real real}
{ EQUI }
random-options ::= [UNIForm] [SEED int] [SD real]
[NORMal ]
name ::= word
COORdinate { TRAF-translate-unit-cell } you-better-look-at-the-source
HBUILD hbond-spec
vector-spec ::= [XDIR real] [YDIR real] [ZDIR real]
byatom-spec ::= BYATom segid resid iupac segid resid iupac END
The syntax of the atom-selection is given in section Atom Selection. The syntax of the hbond-spec is given in section Syntax of the Hydrogen Bond Command.
All of these commands (except the unit cell and HBUILD commands) allow either the main coordinate set (default), or the comparison set (COMP keyword) to be modified. The other coordinate set is only changed by the SWAP command and the ORIEnt RMS command when the specified atoms are not centered about the origin.
Each of these commands may also operate on a subset of the full atom space (except the ORIEnt and unit cell commands). The selection specification should be at the end of the command. The default atom selection includes all atoms.
The INITIALIZE command returns the coordinate values of
the specified atoms to their start up values (the parameter, ANUM
which is currently 9999.0). The main use of this command is in connection
with the BUILD BILD command, which may only find coordinates
for atoms with the initial value.
The COPY command will copy the coordinate values into the specified set FROM the other coordinate set.
The SWAP command will cause the coordinate values of the specified atoms to be swapped with the comparison set.
The AVERAGE command will generate a new coordinate set at a point along the displacement vector between the present coordinate set and the other set. The FACTOR value determines the relative step along this vecor. Its default value is 0.5 (a true average). A FACTOR value of 1.0 is equivalent to the COPY command. Negative or greater than unit positive values are also allowed.
The TRANSLATE command will cause the coordinate values of the specified atoms to be translated. The translation step may be specified by either X, Y, and Z displacements, or by a distance along the specified vector. When no distance is specified, The XDIR, YDIR, and ZDIR values will be the step vector.
The ROTATE command will cause the specified atoms to be rotated about the specified axis vector through the origin. The vector can specified either in terms of its Cartesian components, using the XDIR, YDIR, and ZDIR options, or by the vector between two atoms using the BYATOM option. The vector need not be normalized, but it must have a non zero length. The PHI value gives the amount of rotation about this axis in degrees (in the right handed sense). Only the atoms specified will be rotated.
The ORIENT command will modify the coordinate values of all of the atoms. The select set of atoms is first centered about the origin, and then rotated to either align with the axis, or the other coordinate set. The RMS keyword will use the other coordinate set as a rotation reference. The MASS keyword cause a mass weighting to be done. This will align the specified atoms along their moments of inertia. When the RMS keyword is not used, then the structure is rotated so that its principle geometric axis coincides with the X-axis and the next largest coincides with the Y-axis. The SAVE option will result in the coordinate transformation being saved under the given name, and it can be used by XFORM option described below. This command is used for preparing a structure for graphics and viewing, for finding RMS differences, for model building, and in conjunction with the vibrational analysis.
The RMS command will compute the Root Mean Square (RMS) or mass weighted RMS coordinate differences between the selected set of atoms just as they lie. This differences from the COOR ORIENT RMS command in that no coordinate modifications are made and no translation is done.
The RANDOM command will randomize the selected set of atoms around their current coordinates. Two probability distributions are provided, normal (Gaussian) and uniform. For the normal distribution, the SD option specified the standard deviation of the distribution. For the uniform distribution, the SD option specifies the range of possible variation in both directions, i.e., new coordinates will have values anywhere between -SD and +SD. The default distribution is normal. The SEED option specifies the random number seed used to initialize the random number generator. It defaults to 1234.
The DIFF command will compute the differences between the main and comparison set (or the reverse) and store this difference in the coordinate displacement arrays, also referred to as the normal mode arrays (see section Normal Modes). Each difference is scaled by the FACT keyword value. The differences are not appended onto current values. The differences may then be printed, etc...
The XFORM command will apply a stored coordinate transformation to a set of atoms. The coordinate transformation is specifed by name, and can be created by the ORIENT option above or by a analysis comparison command, see section Comparisons. This command is useful when you want to move a set of atoms onto a position that is determined by another set of atoms.
The XINVERT command will invert a stored coordinate transformation. The transformation is specified by the given name. No coordinates are affected by this command. For example, this command may be used to invert the transformation to orient a set of atoms, so that one set of atoms could be placed in the space occupied by another set. E.g.
COOR ORIE SAVE A CLEAR ATOM 1 * * ! Get transform for moving
! first segment to x axis.
COOR XINV A ! Invert the transform
COOR ORIE CLEAR ATOM 2 * * ! Put second set on x axis
COOR XFORM A CLEAR ATOM 2 * * ! Move second set onto position
! of first segment.
The SCALE command will multiply the selected coordinates in the system by the given scale factor.
The CONVERT command will convert from fractional coordinates to Cartesian coordinates. This command requires six real numbers; A, B, C, ALPHA, BETA, GAMMA; which are the unit cell parameters for the crystal. It assumes the current coordinates are in the fractional cell system, and it converts the selected atoms to Cartesian coordinates.
The EQUIVALENCE command will generate symmetry related coordinates of the molecule. To use this command, you must first create a PSF which has multiple copies of the structure you wish to replicate by symmetry, and you must have read in the coordinates for the first assymetric unit. The EQUIVALENCE will first read a line containing just the number of transformations. Then it will read that number of transformations in the following format:
ROTxx ROTxy ROTxz TRANSx ROTyx ROTyy ROTyz TRANSy ROTzx ROTzy ROTzz TRANSz
Each of the symbols above is parsed as a real number. The first transformation is expected to be the identity transformation and is not applied.
The coordinates are divided into blocks whose number equals the number of transformations. New coordinates for every block after the first are generated by multiplying the rotation matrix (ROTxx) by the coordinates (as a column matrix) of the first block and then adding the translation vector (TRANSx). Blank lines in this input are ignored.
The following input to CONGEN illustrates an example of generating coordinates for the alanines in a crystal of P4_1 symmetry.
READ SEQUENCE CARD A94P UNIT 5 Alanine 1 ALA GENERATE A READ SEQUENCE CARD A94P UNIT 5 Alanine 1 ALA open unit 11 name ala.crd form read read coor card unit 11 GENERATE B READ SEQUENCE CARD A94P UNIT 5 Alanine 1 ALA GENERATE C READ SEQUENCE CARD A94P UNIT 5 Alanine 1 ALA GENERATE D COOR EQUI 4 1 0 0 0 0 1 0 0 0 0 1 0 -1 0 0 0 0 -1 0 0 0 0 1 0.5 0 -1 0 0 1 0 0 0 0 0 1 0.25 0 1 0 0 -1 0 0 0 0 0 1 0.75
The command COOR TRAN is a relic of the old code in CHARMM. There are no other keywords, but all of these commands require further input in formatted, fixed field form.
TRAFAC in the file `CORMAN.FLX' for details.The HBUILD command is used to construct positions for hydrogens. Generally, x-ray crystallography cannot resolve the position of hydrogens. However, the position of many of the hydrogens can be determined from the local geometry, e.g. the peptide hydrogen is easy to construct. In other cases, one must examine the local environment to find the best position for a hydrogen, e.g. the position of the gamma hydrogen in serine.
The HBUILD command is a variant of the HBOND command in that it performs a complete determination of all the possible hydrogen bonds with a given set of options, and it uses this set to determine how best to place ambiguous hydrogen positions. This code depends on the current protein topology and parameter files, and will break if the parameter type codes are changed. It will not work with DNA or other molecules.
After using the HBUILD command, it is a good idea to minimize the hydrogen positions only. A sample input follows:
CONS FIX CLEAR ATOM * * H* NOT MINI ABNR NSTEP 250 INBFRQ 25 IHBFRQ 25 CUTNB 8.0 CTONNB 98.0 CTOFNB 99.0
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