VECTORS (CCP4: Supported Program)

NAME

vectors - generates Patterson vectors from atomic coordinates

SYNOPSIS

vectors [ XYZIN foo_in.pdb ] [ MAPIN foo_in.map ] XYZOUT foo_out.pdb
[Keyworded input]

DESCRIPTION

Generate all Patterson vectors from a list of input atoms, and produce either a list of all vectors within the Patterson asymmetric unit, (XYZLIM ASU or a complete list of all which fall within some specified volume of the Patterson map. This can be taken from the Patterson map header, or defined on XYZLIM. The unique set for the Patterson asymmetric unit can be plotted into the Patterson map without duplication.

INPUT AND OUTPUT FILES

Input

XYZIN
This optional input file contains orthogonal coordinates for heavy atom sites in PDB format. The file MUST have a CRYST1 and optionally SCALEi cards, which will be used to convert the orthogonal coordinates to fractional ones. If XYZIN is given there is no need to input the CELL. If the CRYST1 record includes the space group name, there is no need to give SYMMETRY. The atoms are each given a one-character alphabetical name with first upper-case then lower case identifiers; A B ..Z a b ..z. If there are more than 52 input atoms the identifiers are repeated.
MAPIN
Optional - Patterson map: the header from this file is used to define the XYZLIM. The program assumes that the symmetry stored in the map header is the Patterson symmetry for the true Patterson space-group.

If the command XYZLIM is present, these limits override those in the Patterson map.

Output

XYZOUT
The vectors are written to a standard PDB file as orthogonal coordinates with for example, atom name "VAB" if A & B are the atomnames of the 2 atoms involved. For plotting using NPO it is best to only output a unique set of vectors. Duplicate vectors are always removed, but there is an option to list all equivalent vectors in the map volume.

All vectors at origin omitted The file contains a unique set of vectors AB_Sym1_Sym1 AC_Sym1_Sym1 AD_Sym1_Sym1 ... AA_Sym1_Sym2 AB_Sym1_Sym2 AC_Sym1_Sym2 AD_Sym1_Sym2 ... AA_Sym1_Sym3 AB_Sym1_Sym3 AC_Sym1_Sym3 AD_Sym1_Sym3 ... AA_Sym1_Sym4 AB_Sym1_Sym4 AC_Sym1_Sym4 AD_Sym1_Sym4 ... ...... BC_Sym1_Sym1 BD_Sym1_Sym1 BB_Sym1_Sym2 BC_Sym1_Sym2 BD_Sym1_Sym2 ... ..... ... All AA_Sym1_Sym1 = BB_Sym1_Sym1 = ... = (0,0,0) omitted

XXX It would be better to call this file UVWOUT XXX

KEYWORDED INPUT

The available keywords are:

ATOM, CELL, END, GRID, SYMMETRY, TITLE, XYZLIM,

ATOM <atomname> <x> <y> <z>

An atom site can be input on the command line in fractional coordinates . <atomname> is a 1-character unique identifier for this site, Here x,y,z are the FRACTIONAL coordinates. If XYZIN has been input these ATOM sites are appended to those input from XYZIN. BEWARE - if you have also read in atoms from a PDB file they will already have been identified as A B C etc - you will need to select other identifiers.

CELL <a> <b> <c> <alpha> <beta> <gamma>

Unit cell, by default taken from the XYZIN or the map header. This command is compulsory if neither XYZIN nor MAPIN is assigned.

GRID <nx> <ny> <nz>

Map grid used to convert vectors to grid coordinates. By default, the values are taken from map header. Optional; if no map is given set to 100 100 100.

SYMMETRY <sg name> | <sg number> | <symmetry operation>

Space-group symmetry for the atoms (NOT the Patterson). The program must know the crystal symmetry and this command is compulsory if the space group is not given in the XYZIN CRYST1 record. The Patterson symmetry is derived from the crystal symmetry.

This may be given in 3 ways:-

  1. space-group name
  2. space-group number
  3. 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.

TITLE <title>

Title for the run, written to the output vector file.

XYZLIM [ASU] [<xmin> <xmax> <ymin> <ymax> <zmin> <zmax>]

Limits of Patterson volume in fractions of the unit cell. It is possible to automatically extend to the CCP4 default Patterson asymmetric unit by specifying `XYZLIM ASU' If this command is present, a Patterson map file will not be read, and CELL, and SYMMETRY information must be present; a GRID command is optional.

END

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

EXAMPLES

Unix example script found in $CEXAM/unix/runnable/

AUTHOR

Phil Evans, MRC Laboratory of Molecular Biology, Cambridge (pre@mrc-lmb.cam.ac.uk)
July 1990

SEE ALSO

fft, npo

Example 1
5 sites in PDB format read from ha.pdb
CELL and Space group name both read from the CRYST1 record.
 Program deduces the Patterson symmetry.

.../vectors1 xyzin ha.pdb XYZOUT $CCP4_SCR/ha-vectors.pdb
xyzlim asu
end

==================================================================
ha.pdb
CRYST1  134.690  134.690  148.674  90.00  90.00 120.00 P 63 2 2    
SCALE1      0.007424  0.004286  0.000000        0.00000
SCALE2      0.000000  0.008573  0.000000        0.00000
SCALE3      0.000000  0.000000  0.006726        0.00000
ATOM      1  A   UNK     1       5.118  20.530  16.651  1.00  1.00              
ATOM      2  B   UNK     2      16.500  29.745  14.867  1.00  1.00              
ATOM      3  C   UNK     3       8.688  23.679   1.784  1.00  1.00              
ATOM      4  D   UNK     4      36.501  52.024  35.682  1.00  1.00              
ATOM      5  E   UNK     5      26.399   6.532   6.393  1.00  1.00              
==================================================================


==================================================================
$CCP4_SCR/ha-vectors.pdb
==================================================================

REMARK  Patterson vectors                                                       
CRYST1  134.690  134.690  148.674  90.00  90.00 120.00            
SCALE1      0.007424  0.004286  0.000000        0.00000
SCALE2      0.000000  0.008573  0.000000        0.00000
SCALE3      0.000000  0.000000  0.006726        0.00000
ATOM      1 VAB  VEC     1      55.963 107.430   1.784  1.00  1.00              
ATOM      2 VAC  VEC     1      63.775 113.496  14.867  1.00  1.00              
ATOM      3 VAD  VEC     1      35.962  85.151 129.643  1.00  1.00              
.....
ATOM     12 VAA  VEC     1     134.689   0.001 148.673  1.00  1.00              
ATOM     13 VAB  VEC     2     -53.674 111.396   1.784  1.00  1.00              
ATOM     14 VAC  VEC     2     -62.833 115.128  14.867  1.00  1.00              

ATOM     15 VAA  VEC     2      25.456  26.363   0.000  1.00  1.00              
ATOM     16 VAB  VEC     3      39.128  21.113   1.784  1.00  1.00              
ATOM     17 VAC  VEC     3      29.969  24.845  14.867  1.00  1.00              
.....
==================================================================

.../vectors1 xyzin ha.pdb XYZOUT $CCP4_SCR/ha-vectors.pdb mapin $CCP4_SCR/patterson.map
end

Vector limits taken from patterson.
Fractional coordinates input in body of command file
 No XYZIN or MAPIN assigned so  CELL and SYMM must be supplied.


.../vectors1  XYZOUT $CCP4_SCR/ha-vectors.pdb mapin $CCP4_SCR/patterson.map
SYMMETRY P6322
CELL 134.690  134.690  148.674  90.00  90.00 120.00   
ATOM A 0.126 0.176 0.112
ATOM B 0.250 0.255 0.100
ATOM C 0.166 0.203 0.012
ATOM D 0.494 0.446 0.240
ATOM E 0.224 0.056 0.043
ATOM F 0.553 0.429 0.152
ATOM G 0.457 0.444 0.140
ATOM H 0.660 0.023 0.000
ATOM I 0.037 0.217 0.151
ATOM J 0.072 0.350 0.076
ATOM K 0.596 0.237 0.246
ATOM L -0.005 0.359 0.196
end