Hi,
If I load up a PDB file that looks like this:
HETATM 1313 OA22 NAP 164 28.315 61.969 12.250
31.54 O
HETATM 1314 OA23 NAP 164 26.554 62.174 14.275
21.05 O
HETATM 1314 ABCD NAP 164 28.554 64.174 16.275
11.05 O
HETATM 1314 XYZ NAP 164 30.554 66.174 18.275
1.05 O
HETATM 1314 LMN NAP 164 32.554 68.174 20.275
41.05 O
and then save it from PyMOL, the resulting PDB file looks like this:
HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00
31.54 O
HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00
21.05 O
HETATM 3 DABC NAP 164 28.554 64.174 16.275 0.00
11.05 O
HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00
41.05 O
HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00
1.05 O
END
You'll note that OA22 has been renamed to 2OA2, OA23 has been renamed to
3OA2 and ABCD has been renamed to DABC. It looks to me like residue
with a four-letter name is getting renamed.
No .. wait .. it's a little stranger than that .. if I open up the
second file (the one with DABC) and save *it*, I get this:
HETATM 1 2OA2 NAP 164 28.315 61.969 12.250 0.00
31.54 O
HETATM 2 3OA2 NAP 164 26.554 62.174 14.275 0.00
21.05 O
HETATM 3 CDAB NAP 164 28.554 64.174 16.275 0.00
11.05 O
HETATM 4 LMN NAP 164 32.554 68.174 20.275 0.00
41.05 O
HETATM 5 XYZ NAP 164 30.554 66.174 18.275 0.00
1.05 O
END
Note that ABCD went to DABC which went to CDAB, but OA22 went to 2OA2
and stayed there. LMN and XYZ weren't touched.
Is there a way to supress this behavior? It causes me a bit of trouble
when, e.g., my AMBER parameter files expect residues to have certain names.
I'm not sure exactly when PyMOL decides to rename things .. if I
shift-left-click on one of the residues in the first file (either before
or after saving), PyMOL says "You clicked NAP: /test1///164/OA23" (i.e.
it gives me the original name).
thanks,
-michael
--
michael lerner
