Dear all,
thanks to everybody who offered their experience and hints.
The most convenient way of preparing a packing diagramme, at least for
me, was via PyMol as suggested by Michael Klein (see below).
One can do something similar with the CCP4 graphics package, but for
some reason the protocol suggested by the manual slows down the
computer too much to be practical.
Anyway, the challenge is out there: a programme for preparing a
packing diagramme with the protein represented by a reasonable
approximation of its real shape. It would make a good teaching tool as
well.
Thanks again,
Anita
I have made a few figures like the one you describe. I calculate
the center of mass of the domain using ccp4 program pdbset with the
command COM
#! /bin/csh -f
################### Take output from O into a form suitable for
refinement
pdbset xyzin domain.pdb xyzout junk.pdb << eof-1
#cell 132.02 115.21 96.20 90.00 90.00 90.00
NCODE 1
# New cell in junk.pdb, it is recommended that a spgrp is also given
#spacegroup P212121
COM
eof-1
#
then run pdbset.csh > pdbset.log
the center of mass is then listed in the pdbset.log
I then make a fake atom out of the center of mass X,Y,Z coordinates
using a pdb style format, name the atom O or whaterver. I then use
pymol to display the atom as a sphere.
Example:
ATOM 2 O TYR A 59 4.198 22.414 35.783 1.00
24.65 A O
replace 4.198 22.414 35.783 with the center of mass coordinates
from pdbset..
In pymol use command:
show spheres,
set sphere_scale=1.5
change the number to adjust the size
if the spheres do not show up try to ray the image..
if you want to show the symmetry of the atom/spere in pymol
symexp s,nameofyourobject,(all),50
change the number to adjust how big the symm operators are..
sorry if it seems complex, it really is'nt too bad and will work!
HTH,
michael
--
Michael G. Klein Ph.D.
Project Research Scientist
Structural Genomics
DOE Joint Genome Institute
2800 Mitchell Drive
Walnut Creek, CA 94598
Phone: (925) 927-2556
[email protected]
