VECTORS (CCP4: Supported Program)
NAME
vectors - generates Patterson vectors from atomic coordinatesSYNOPSIS
vectors [ MAPIN foo_in.map ] XYZOUT foo_out.pdb[Keyworded input]
DESCRIPTION
Generate all Patterson vectors from a list of input atoms, and produce a list of all vectors which fall within the volume of the Patterson calculated (optionally reads Patterson map header to find this out) suitable for plotting into the Patterson map.
INPUT AND OUTPUT FILES
Input
- MAPIN
- Patterson map: the header from this file is used to define
the volume of space into which the vectors will be put. The program
assumes that the symmetry stored in the map header is the Patterson
symmetry for the true Patterson space-group. This is used to move
vectors into the volume of the map, but may be overridden by the
PSYMMETRY command.
If the command XYZLIM is present, a map will not be read, and the volume, cell & symmetry will be taken from the command input: in this case, XYZLIM, CELL and PSYMMETRY commands must be present.
Output
- XYZOUT
- The vectors are written to a standard PDB file as orthogonal coordinates with atom name "VAB" where A & B are the atomnames of the 2 atoms involved. This file may be plotted on the Patterson using NPO, with only the identity symmetry operation defined there. Duplicate vectors are removed, but all equivalent vectors in the map volume should be present.
KEYWORDED INPUT
The available keywords are:
ATOM, CELL, END, GRID, NCODE, PSYMMETRY, SYMMETRY, TITLE, XYZLIM.
TITLE <title>
Title for the run, written to the output vector file.
SYMMETRY <sg name> | <sg number> | <symmetry operation>
Space-group symmetry for the atoms (NOT the Patterson). This may be given in 3 ways:-
- space-group name
- space-group number
- symmetry operations as in International Tables, separated by '*', on a series of SYMMETRY lines if necessary.
For options 1 and 2, symmetry operations are read from the library file SYMOP.
PSYMMETRY <sg name> | <sg number> | <symmetry operation>
Space-group symmetry for the Patterson: by default this is taken from the Patterson header, but may overridden by this command This may be given in 3 ways, as for SYMMETRY. PSYMMETRY P1 will give the unique set of vectors, provided they lie within the cell volume given.
NCODE <orthogonalization code>
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 Patterson volume in fractions of the unit cell. If this command is present, a Patterson map file will not be read, and CELL, PSYMMETRY commands must be present; a GRID command is optional.
CELL <a> <b> <c> <alpha> <beta> <gamma>
Unit cell, by default taken from map header. This command is compulsory if no map is given (i.e. if XYZLIM is present).
GRID <nx> <ny> <nz>
Map grid used to convert vectors to grid coordinates. By default, taken from map header. Optional if no map is given (else set to 100 100 100).
ATOM <atomname> <x> <y> <z>
Input an atom to be used to predict vectors. <atomname> is a 1-character unique identifier for this site, x,y,z are the FRACTIONAL coordinates.
END
End of input, also end-of-file will do.
EXAMPLES
Unix example script found in $CEXAM/unix/runnable/
VMS example script found in $CEXAM/vms/
AUTHOR
Phil Evans, MRC Laboratory of Molecular Biology, Cambridge
(pre@mrc-lmb.cam.ac.uk)
July 1990