[PyMOL] Re: why is PyMOL renaming my residues?

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
>