[PyMOL] why is PyMOL renaming my residues?

[michael l. <ml...@um...>]

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