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