HAVECS (CCP4: Unsupported Program)
NAME
havecs - Generate heavy atom vectorsSYNOPSIS
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 coordinatesXYZOUT 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 assymetric unit of real cell
0 39 0 39 0 59
MAP GRID 40 80 60
GRID LIMITS OF ASSYMETRIC UNIT OF REAL CELL
0 39 0 39 0 59
FRAC LIMITS OF ASSYMETRIC 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