GENSYM (CCP4: Supported Program)

NAME

gensym - generate sites by symmetry

SYNOPSIS

gensym [ XYZIN foo_in.pdb ] [ XYZOUT foo_out.pdb ]
[Keyworded input]

DESCRIPTION

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.

KEYWORDED INPUT

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:-

(a): space-group name
(b): space-group number
(c): 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).

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 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

BROOKHAVEN

Write 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.

NOPRINT

Don't print list of sites to output log.
Default: do.

SORT SYMMETRY | CHAIN

This determines the order in which the symmetry-generated positions are listed in the output. The options are:

SYMMETRY: 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.
CHAIN: 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.

Default: SYMMETRY

CHAIN SYMMETRY Nsym [orig_chn] new_ch

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.

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

End of input, also end-of-file will do

EXAMPLES


$!
$! 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

AUTHOR

Phil Evans, MRC LMB Cambridge, August 1990