GENSYM (CCP4: Supported Program)
- generate sites by symmetry
Generate 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:
Title for the run, written to the output file as a REMARK record.
SYMMETRY <space-group-name | space-group-number | symmetry operation>
Space-group symmetry for the atoms (NOT the Patterson).
This may be given in 3 ways:-
symmetry operations as in International Tables, separated
by '*', on a series of SYMMETRY lines if necessary, e.g.
SYMMETRY -X,Y,-Z * 1/2+X,1/2+Y,Z
For options (a) and (b), symmetry operations are read from the
library file SYMOP (see SYMLIB).
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 Radius
Define 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
Write Brookhaven file to logical name XYZOUT.
Default: do not write file.
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
Read coordinates from PDB file (containing orthogonal coordinates), instead of
from ATOM commands. The file is read from XYZIN.
Don't print list of sites to output log.
SORT SYMMETRY | CHAIN
This determines the order in which the symmetry-generated positions are listed
in the output. The options are:
This 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.
- the positions generated from a single target position by different symmetry
operations will be grouped together. This means that the sequence of positions
in the input file will be lost.
- all the positions from a single symmetry operation are listed together,
followed by all those from the next symmetry operation etc. This preserves
the sequence of positions from the original file.
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.
End 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
XYZLIM 0 0.5 0 0.5 0 0.25
CELL 148.13 148.13 148.13
GRID 144 144 144
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
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
ATOM A 0.3959 0.1636 0.1751
ATOM B 0.2648 0.3357 0.0835
ATOM A 0.3713 0.1320 0.2208
ATOM B 0.2175 0.3570 0.1147
Phil Evans, MRC LMB Cambridge, August 1990