> "Find me the distance between atom1 and atom2 in state 4"
print cmd.get_distance("atom1","atom2",4)
> "select all waters that are within 5.0 angstroms of residue
> 15 during state 7"
Hmm...not easily done. The problem is that distance-based selection
criteria apply to all states, giving you a superset of what you actually
want. To perform a selection operation on a single state, you must first
copy all the content into a single-state object:
Assuming trajectory object "traj"...
create tmp_obj, (traj///15/ & polymer) or ((traj and solvent) within 5 of
(traj///15/ & polymer),7,1
select tmp_near, (tmp_obj and solvent) within 5 of (tmp_obj///15/)
select traj_near, traj in tmp_sele
dele tmp_*
Ugly!
Cheers,
Warren
> -----Original Message-----
> From: pymol-users-boun...@lists.sourceforge.net
> [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
> Of Michael Lerner
> Sent: Tuesday, April 17, 2007 12:29 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] distances and selections within states?
>
> Hi,
>
> I feel like I'm missing something obvious here. How do I say
>
> "Find me the distance between atom1 and atom2 in state 4"
>
> or
>
> "select all waters that are within 5.0 angstroms of residue
> 15 during state 7"
>
> I'm trying to analyze various properties throughout the
> course of a trajectory.
>
> I made an el cheapo hack that loads up a chunk of the
> trajectory, calls split_states, calculates things for the
> individual states, deletes everything, loads up the next
> chunk, etc. It's really slow, though. It's even slower (or
> blows up) if I load the whole thing up and call split_states
> for my many-nanosecond trajectory.
>
> Thanks,
>
> -Michael
>
> --
> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner http://lernerclan.net
>
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