oops .. two problems with my last message:
1) i said "residue" a few times when i meant "atom" .. it should be
obvious from the context of the message.
2) my email program seems to have messed up some of the formatting in
the last message .. the original PDB file should look like this
(assuming i can format it correctly this time):
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
in case that's still not formatted correctly, each line should begin
with HETATM, and the point is that the atoms are named "OA22", "OA23",
"ABCD", "XYZ " and " LMN" respectively.
also, i noticed that PyMOL is changing the atom ID (OA22 was 1313 in the
first file, but 1 in the second). that's not actually causing me any
trouble, but i'm curious: is there a way to make PyMOL leave the IDs alone?
thanks,
-michael
michael lerner wrote:
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
