HAVECS (CCP4: Unsupported Program)

NAME

havecs - Generate heavy atom vectors

SYNOPSIS

havecs XYZIN foo_in.xyz XYZOUT foo_out.xyz UVWOUT foo_out.uvw
[Online Input]

DESCRIPTION

The program generates Patterson vectors from atomic coordinates and writes them to UVWOUT.

XYZOUT contains the original coordinates, reduced to the asymmetric unit, if necessary, and the symmetry related positions.

The program runs interactively - see example below.

INPUT AND OUTPUT FILES

XYZIN Input coordinates

XYZOUT Output coordinates

UVWOUT Output Patterson vectors

INPUT CONTROL CARDS

The input control lines must be given in the correct order.

line 1   ...   spgrpnum             space group number.



line 2   ...   FRC | PHARE | PDB    format of XYZIN. There must be no
                                    spaces before the keyword.


               if the format is PHARE or FRC then

line 2a  ...   cell ncode           this line is read in free format
                                    but alpha, beta, gamma must be 
                                    included.


               if the input format is FRC then

line 2b  ...   atomname             derivative atom type (AU, HG etc.)



line 3   ...   nx ny nz             map grid. This is so that vectors 
                                    can be given in grid coordinates.
                                    Read in free format.



line 4   ...   xlim ylim zlim       The limits that define the 
                                    asymmetric unit of the real space 
                                    group.

AUTHORS

Originator : ?

Availability : Fortran 77

Contact : this program is unsupported

EXAMPLES

The following is an example of an interactive session (on Unix):

havecs xyzin heavy.brk xyzout heavy.out uvwout vectors.out


 **** Generate Heavy atom vectors ***
 **** Coordinates output in PDB format to xyzout ***
 **** Vectors output in PDB format to uvwout ***


 FORMATTED      OLD     file opened on unit  14
 Logical name: XYZIN, Full name: /Throb1/Wojtek/scratch/heavy.brk


 FORMATTED      UNKNOWN file opened on unit  22
 Logical name: XYZOUT, Full name: /Throb1/Wojtek/scratch/heavy.out


 FORMATTED      UNKNOWN file opened on unit  23
 Logical name: UVWOUT, Full name: /Throb1/Wojtek/scratch/vectors.out

   Input spacegroup no
4

 FORMATTED      OLD     file opened on unit  20
 Logical name: SYMOP, Full name: /Tara2/public/xtal/ccp4/lib/data/symop.lib

 NO OF SYM OPS RETURNED     2

  Are input coords in FRC PHARE PDB format? Give word
PDB

   PDB file should be assigned to xyzin
   ** Beware - uvwout will NOT have CRYST and SCALE cards ***


  input grid : nx ny nz
40 80 60

   Input GRID limits of asymmetric unit of real cell
0 39 0 39 0 59



  MAP GRID    40   80   60

  GRID LIMITS OF ASYMMETRIC UNIT OF REAL CELL
         0    39         0    39         0    59

  FRAC LIMITS OF ASYMMETRIC UNIT OF REAL CELL
     0.000 0.975     0.000 0.488     0.000 0.983


       1565  Pb  PB  A 225      -7.378  35.339   8.859

 atom   1 symm 1
 Fractional coordinates    0.86145   0.52054   0.23326
 Grid       coordinates     34.458    41.643    13.995
 Angstrom (PDB) coords.     25.922    35.339     8.859

 atom   1 symm 2
 Fractional coordinates    0.13855   0.02054   0.76674
 Grid       coordinates      5.542     1.643    46.005
 Angstrom (PDB) coords.     -4.472     1.395    29.120

       1571  Pb  PB  A 225      -9.388  33.156   7.259

 atom   2 symm 1
 Fractional coordinates    0.78610   0.48839   0.19113
 Grid       coordinates     31.444    39.071    11.468
 Angstrom (PDB) coords.     23.912    33.156     7.259

 atom   2 symm 2
 Fractional coordinates    0.21390   0.98839   0.80887
 Grid       coordinates      8.556    79.071    48.532
 Angstrom (PDB) coords.     -2.462    67.100    30.720


 VECTORS FOR ATOM     1  Grid then fractional
 TO  ATOM   1 SYMM EQUIV   1
 Grid  Vector    0.0   0.0   0.0   Fractional Vector   0.000  0.000  0.000
 TO  ATOM   1 SYMM EQUIV   1
 Grid  Vector   40.0  80.0  60.0   Fractional Vector   1.000  1.000  1.000
 TO  ATOM   1 SYMM EQUIV   2
 Grid  Vector   11.1  40.0  32.0   Fractional Vector   0.277  0.500  0.533
 TO  ATOM   1 SYMM EQUIV   2
 Grid  Vector   28.9  40.0  28.0   Fractional Vector   0.723  0.500  0.467
 TO  ATOM   2 SYMM EQUIV   1
 Grid  Vector   37.0  77.4  57.5   Fractional Vector   0.925  0.968  0.958
 TO  ATOM   2 SYMM EQUIV   1
 Grid  Vector    3.0   2.6   2.5   Fractional Vector   0.075  0.032  0.042
 TO  ATOM   2 SYMM EQUIV   2
 Grid  Vector   14.1  37.4  34.5   Fractional Vector   0.352  0.468  0.576
 TO  ATOM   2 SYMM EQUIV   2
 Grid  Vector   25.9  42.6  25.5   Fractional Vector   0.648  0.532  0.424


 VECTORS FOR ATOM     2  Grid then fractional
 TO  ATOM   2 SYMM EQUIV   1
 Grid  Vector    0.0   0.0   0.0   Fractional Vector   0.000  0.000  0.000
 TO  ATOM   2 SYMM EQUIV   1
 Grid  Vector   40.0  80.0  60.0   Fractional Vector   1.000  1.000  1.000
 TO  ATOM   2 SYMM EQUIV   2
 Grid  Vector   17.1  40.0  37.1   Fractional Vector   0.428  0.500  0.618
 TO  ATOM   2 SYMM EQUIV   2
 Grid  Vector   22.9  40.0  22.9   Fractional Vector   0.572  0.500  0.382
  Normal Termination of havecs.for
User: 0.40s System: 0.52s Elapsed: 01:45.00s


Date: 10 Mar 1993
From: WOJTEK@de.EMBL-Hamburg