Irida,
> I am looking for a free program
> or script that can calculate all sulfur-sulfur distances in
> pdb files from the Protein Data Bank.
This is the kind of problem you can solve in PyMOL with just a few lines
of Python code. For example:
from pymol import cmd
from glob import glob
for file in glob("*.pdb"):
print file
cmd.load(file,'prot')
for a in cmd.index("elem s and bound_to elem s"):
if cmd.select("s1","%s`%d"%a) and \
cmd.select("s2","elem s and bound_to %s`%d"%a):
if cmd.select("(s1|s2) and not ?skip"):
cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")
print ' ',round(cmd.dist("tmp","s1","s2"),3)
cmd.select("skip","s1|s2|?skip")
cmd.delete("all")
Would generate the following output in a directory with pdb files:
1alk.pdb
A CYS 168 SG
A CYS 178 SG
1.975
A CYS 286 SG
A CYS 336 SG
1.995
B CYS 168 SG
B CYS 178 SG
1.996
B CYS 286 SG
B CYS 336 SG
2.032
1btu.pdb
CYS 42 SG
CYS 58 SG
2.039
CYS 136 SG
CYS 201 SG
2.031
CYS 168 SG
CYS 182 SG
2.001
CYS 191 SG
CYS 220 SG
2.019
...
Note that the above is for bonded sulfurs in disulfides. For all
intra-cysteine gamma sulfur distances, you'd want to do something more
like:
from pymol import cmd
from glob import glob
for file in glob("*.pdb"):
print file
cmd.load(file,'prot')
for a in cmd.index("CYS/SG"):
for b in cmd.index("CYS/SG"):
if a[1]<b[1]:
cmd.select("s1","%s`%d"%a)
cmd.select("s2","%s`%d"%b)
if cmd.select("(s1|s2) and not ?skip"):
cmd.iterate("s1|s2","print '
',chain,resn,resi,name")
print ' ',round(cmd.dist("tmp","s1","s2"),3)
cmd.select("skip","s1|s2|?skip")
cmd.delete("all")
1alk.pdb
A CYS 168 SG
A CYS 178 SG
1.975
A CYS 168 SG
A CYS 286 SG
35.845
A CYS 168 SG
A CYS 336 SG
35.029
A CYS 168 SG
B CYS 168 SG
63.64
A CYS 168 SG
B CYS 178 SG
63.775
A CYS 168 SG
B CYS 286 SG
39.02
A CYS 168 SG
B CYS 336 SG
39.314
1btu.pdb
CYS 42 SG
CYS 58 SG
2.039
CYS 42 SG
CYS 136 SG
...
http://delsci.com/pymol
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
. DeLano Scientific LLC
. 400 Oyster Point Blvd., Suite 213
. South San Francisco, CA 94080 USA
. Biz:(650)-872-0942 Tech:(650)-872-0834
. Fax:(650)-872-0273 Cell:(650)-346-1154
. mailto:war...@delsci.com
> -----Original Message-----
> From: owner-chemis...@ccl.net [mailto:owner-chemis...@ccl.net]
> Sent: Wednesday, January 18, 2006 6:03 PM
> To: Warren DeLano
> Subject: CCL: Program or Script to Calculate Atom-Atom
> Distances in pdb files
>
> Sent to CCL by: "Irida Kastrati" [ikastr2[a]uic.edu]
> Hello CCLers,
> Because of some excellent feedback I received when I asked
> for help about a year ago, I thought of using the CCL members
> expertise again this time. I am looking for a free program
> or script that can calculate all sulfur-sulfur distances in
> pdb files from the Protein Data Bank. The program or script
> should be able to read the massive database of protein
> structures from the Protein Data Bank, or a local copy of PDB
> files. Then, pinpoint S-S distances within a certain value,
> or calculate the actual distance. I have access to SYBYL.
> Any suggestion is very welcome!
> Thank you in advance for your time and help.
>
> Sincerely,
> Irida Kastrati
> e-mail: ikastr2{=}uic.edu
> University of IL at Chicago
> College of Pharmacy, Medicinal Chemistry
>
>
>
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