GENSYM (CCP4: Supported Program)
NAMEgensym - generate sites by symmetry
SYNOPSISgensym [ XYZIN foo_in.pdb ] [ XYZOUT foo_out.pdb ]
DESCRIPTIONGenerate all symmetry-related sites from a list of input atoms, entered either explicitly (e.g. for heavy atom sites) or from a PDB file.
GENSYM may not be suitable for applications where symmetry-related protein chains are required, since the program constrains the generated coordinates to lie within a volume which can be no larger than the unit cell. The SYMGEN option of PDBSET is the preferred method for generating symmetry-related protein chains.
Available keywords are:
ATOM, BROOKHAVEN, CELL, CHAIN END, GRID, NOPRINT, ORTHOGONALIZATION, READ, RESIDUE, SORT, SPHERE, SYMMETRY, TITLE, XYZLIM
TITLE <title>Title for the run, written to the output file as a REMARK record.
SYMMETRY <space-group-name | space-group-number | symmetry operation>[COMPULSORY]
Space-group symmetry for the atoms (NOT the Patterson). This may be given in 3 ways:-
For options (a) and (b), symmetry operations are read from the library file SYMOP (see SYMLIB).
ORTHOGONALIZATION <ncode>Vectors are written out to a PDB file in an orthogonal frame defined by this code. The default is <ncode> = 1, which is the usual frame for Brookhaven files, so normally this command can be omitted.
XYZLIM <Xmin> <Xmax> <Ymin> <Ymax> <Zmin> <Zmax>Limits of volume, in fractional or grid coordinates. If the limits are supplied in grid units then the GRID keyword must also be supplied, to set the grid sampling.
The alternative to XYZLIM is SPHERE.
Default: 0.0 1.0 0.0 1.0 0.0 1.0
SPHERE [ORTHOGONAL] Xcen Ycen Zcen RadiusDefine spherical volume (alternative to XYZLIM). The coordinates of the centre of the sphere are Xcen Ycen Zcen, and are in fractional coordinates unless the keyword ORTHOGONAL is present. The radius of the sphere is in Å.
CELL <a> <b> <c> <alpha> <beta> <gamma>Cell dimensions for orthogonalization (for Brookhaven file). If XYZIN is assigned then the default is to read the cell dimensions from the CRYST1 record.
GRID <NX> <NY> <NZ>Sampling intervals along x,y,z, for grid coordinates (used only for output listing). The GRID keyword is required by XYZLIM, if the volume limits have been supplied in grid units.
Default: 100 100 100
BROOKHAVENWrite Brookhaven file to logical name XYZOUT.
Default: do not write file.
RESIDUE <residue_name>Input a residue name for following atoms, until changed, for labelling output.
ATOM <atomname> <x> <y> <z>Input an atom. <atomname> is a 1-character unique identifier for this site; <x> <y> <z> are the FRACTIONAL coordinates.
READ [<file_name>]Read coordinates from PDB file (containing orthogonal coordinates), instead of from ATOM commands. The file is read from XYZIN.
NOPRINTDon't print list of sites to output log.
SORT SYMMETRY | CHAINThis determines the order in which the symmetry-generated positions are listed in the output. The options are:
CHAIN SYMMETRY Nsym [orig_chn] new_chThis allows symmetry generated atoms from an input pdb file to be assigned chain names on output. It is based on the CHAIN option of PDBSET.
Positions generated by symmetry operation Nsym (and optionally from an original position with chain id orig_chn) will be assigned a chain id of new_ch. If orig_chn is not present then all positions generated from the specified symmetry operation will be assigned the requested chain name.
ENDEnd of input, also end-of-file will do
$! $! Convert heavy atom coordinates to Brookhaven file $! $! $ gensym xyzout hasites.pdb TITLE A95 sites for X16, X17, X18, X19 BROOKHAVEN SYMMETRY 1 XYZLIM 0 0.5 0 0.5 0 0.25 CELL 148.13 148.13 148.13 GRID 144 144 144 RESIDUE X16 ATOM A 0.2617 0.2671 0.1936 ATOM B 0.2383 0.2778 0.1908 ATOM C 0.2027 0.2760 0.2161 ATOM D 0.2217 0.2856 0.2043 RESIDUE X17 ATOM A 0.2368 0.1373 0.1435 ATOM B 0.3362 0.3478 0.2257 ATOM C 0.2483 0.1403 0.1189 ATOM D 0.3140 0.3428 0.2415 RESIDUE X18 ATOM A 0.3959 0.1636 0.1751 ATOM B 0.2648 0.3357 0.0835 RESIDUE X19 ATOM A 0.3713 0.1320 0.2208 ATOM B 0.2175 0.3570 0.1147
AUTHORPhil Evans, MRC LMB Cambridge, August 1990