On Thu, Jul 3, 2014 at 10:21 AM, Jason Swails <jason.swails.gmail.com>
wrote:
>
> Perhaps a mask that selects based on a distance criteria will work?
>
> Something like "(:4.CG<.5.0)" will select all atoms within 5 angstroms of
> the CG atom of residue 4. Replacing .5.0 with :5.0 will select all
> residues within 5 Angstroms of the CG atom of residue 4.
>
> You can use the "mask" command in cpptraj to write a list of atoms that
> satisfy the criteria. In general, masks are evaluated once at the
> beginning (on the reference structure or first frame), but I think the
> "mask" command is different in this regard and evaluates the mask for every
> frame. Dan can correct me if I'm wrong here.
>
Jason is correct - the 'mask' command in cpptraj will update a
distance-based selection each frame, and print out which atoms are selected
and/or a PDB containing only selected atoms.
-Dan
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Thu Jul 03 2014 - 10:00:02 PDT
