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Process All Files In Directory - Revision history
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Bell
https://wiki.pymol.org/index.php?title=Process_All_Files_In_Directory&diff=8450&oldid=prev
Cowsandmilk at 12:54, 2 February 2010
2010-02-02T12:54:19Z
<p></p>
<p><b>New page</b></p><div>=Explanation=<br />
For a given directory with PDB files in it, the following code will output, for each PDB, the bound disulfide bond lengths like this:<br />
<pre><br />
1alk.pdb<br />
A CYS 168 SG<br />
A CYS 178 SG<br />
1.975<br />
A CYS 286 SG<br />
A CYS 336 SG<br />
1.995<br />
B CYS 168 SG<br />
B CYS 178 SG<br />
1.996<br />
B CYS 286 SG<br />
B CYS 336 SG<br />
2.032<br />
1btu.pdb<br />
CYS 42 SG<br />
CYS 58 SG<br />
2.039<br />
CYS 136 SG<br />
CYS 201 SG<br />
2.031<br />
CYS 168 SG<br />
CYS 182 SG<br />
2.001<br />
CYS 191 SG<br />
CYS 220 SG<br />
2.019<br />
...<br />
</pre><br />
<br />
=Bound Disulfides=<br />
<source lang="python"><br />
from pymol import cmd<br />
from glob import glob<br />
<br />
for file in glob("*.pdb"):<br />
print file<br />
cmd.load(file,'prot')<br />
for a in cmd.index("elem s and bound_to elem s"):<br />
if cmd.select("s1","%s`%d"%a) and \<br />
cmd.select("s2","elem s and bound_to %s`%d"%a):<br />
if cmd.select("(s1|s2) and not ?skip"):<br />
cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")<br />
print ' ',round(cmd.dist("tmp","s1","s2"),3)<br />
cmd.select("skip","s1|s2|?skip")<br />
cmd.delete("all")<br />
</source><br />
<br />
=All Sulfur Distances=<br />
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:<br />
<pre><br />
1alk.pdb<br />
A CYS 168 SG<br />
A CYS 178 SG<br />
1.975<br />
A CYS 168 SG<br />
A CYS 286 SG<br />
35.845<br />
A CYS 168 SG<br />
A CYS 336 SG<br />
35.029<br />
A CYS 168 SG<br />
B CYS 168 SG<br />
63.64<br />
A CYS 168 SG<br />
B CYS 178 SG<br />
63.775<br />
A CYS 168 SG<br />
B CYS 286 SG<br />
39.02<br />
A CYS 168 SG<br />
B CYS 336 SG<br />
39.314<br />
1btu.pdb<br />
CYS 42 SG<br />
CYS 58 SG<br />
2.039<br />
CYS 42 SG<br />
CYS 136 SG<br />
</pre><br />
<br />
<source lang="python"><br />
from pymol import cmd<br />
from glob import glob<br />
<br />
for file in glob("*.pdb"):<br />
print file<br />
cmd.load(file,'prot')<br />
for a in cmd.index("CYS/SG"):<br />
for b in cmd.index("CYS/SG"):<br />
if a[1]<b[1]:<br />
cmd.select("s1","%s`%d"%a)<br />
cmd.select("s2","%s`%d"%b)<br />
if cmd.select("(s1|s2) and not ?skip"):<br />
cmd.iterate("s1|s2","print ' ',chain,resn,resi,name")<br />
print ' ',round(cmd.dist("tmp","s1","s2"),3)<br />
cmd.select("skip","s1|s2|?skip")<br />
cmd.delete("all")<br />
</source><br />
<br />
[[Category:Script_Library|Processing All File in Directory]]<br />
[[Category:System_Scripts]]</div>
Cowsandmilk