[Chimera-users] Residue Numbers vs. Residue Codes

[Korbin West]

Hi all,


I'm trying to determine uncommon ligands in pdb files using a python code, but have run into an odd dilemma.


In my code, I open a pdb in Chimera, select the ligand, and write out the residue list.  However, the formatting of this list changes depending on how I run the program.


If I run the program through xterm, it will print out only residue numbers. If I run the program though Chimera's Idle, however, I will get the residue codes and the residue numbers.


For example, I ran this with 3VKG, you can see the results in the attached files, where I show a sample code of what I'm using, the xterm results and the Chimera results.


I want to do this for a large number of pdbs, so I'd like to do this --nogui through xterm, but I need the residue codes. Has anyone else ran into this problem or know of a work-around? Thanks in advance.


Best,


Korbin West

Wabash College
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