On May 28, 2012, at 9:57 AM, Ryan Doherty wrote:

Hello,

I'm trying to create a chimera script and am stumped. I'm trying to iterate through a series of PDB entries that contain a specific protein-protein interaction (some are NMR ensembles) to create a list of residues that within specific distances of the binding interface.

I am able to successfully iterate through pdb files and residues, but am having difficulty iterating through chains of NMR ensembles. Is there a variable like m.chains or is the number of chains accessible through chimera.openModels.list? Also, do you have any example scripts that could help me?

Hi Ryan, Do you really mean the chains, like chain A, chain B, etc.? Or do you mean the separate MODEL entries in the NMR ensemble? I'm guessing the latter (if it's the former just say so and I can fill you in on that too). chimera.openModels.list() returns a list. If you have a non-NMR PDB file open, that list has exactly one element. For NMR ensembles, it has one element for every MODEL in the PDB file. So you would just iterate through that list. I'm guessing you're just using the first element of the list in your script right now? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu