[Chimera-users] printing "zone" search
pett at cgl.ucsf.edu
Fri Dec 14 11:26:53 PST 2007
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
> 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.
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