On Dec 14, 2007, at 8:23 AM, Ryan wrote:

I am actually currently interested in doing something similar to Francesco's previous question about writing out a list of residue names within a certain zone of a ligand -- however i would like to do this from a Python script.

I tried to find the zone selection command to use in a script, but could not. Would it be easiest to just use the runCommand('z<') function to select a zone?

Using runCommand() would be by far the easiest and is what I would recommend. Nonetheless, there are alternatives. I've appended a script that finds all NZ atoms of lysines that are within 8 angstroms of an NZ of a different lysine. It calls into the underlying chimera.specifier.zone() function since it needs to do additional processing to exclude each lysine's own NZ atom when examining the zones for NZs within 8 angstroms. If efficiency is important (and it doesn't sound like it really is from your description) you would want to consider using the _closepoints module to quickly eliminate most atoms that aren't in the zone, but then you have to process the remainder to ensure that they meet the zone criteria (some remaining ones won't). Look at the start of the detectClash() function in DetectClash/__init__.py for an example.

Also, when the zone is selected, are the selected residue names stored in a list? If so, how can i access this list to print out the residue names into an output file of my own?

chimera.selection.currentResidues() returns such a list. --Eric