VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Sep 23 2014 - 22:02:31 CDT
Please read these pages of the documentation as a starting point:
You want to use a combination of coordinate based selections and
"same residue as", e.g.:
set seltext "same residue as (x > 0 and x < 30 and y > 0 and y < 30 and z > 0)"
set sel [atomselect top $seltext]
$sel writepdb box.pdb
On Wed, Sep 24, 2014 at 02:49:32AM +0000, Parker de Waal wrote:
> Hi John,
> Thanks for the tip. Unfortunately after looking for about 30 minutes or so
> minutes Išve been unable to find any previous mailings or any guides
> online regarding similar tasks.
> If you could point me in a more specific direction I would greatly
> appreciate it.
> On 9/23/14, 10:00 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
> >You can use VMD atom selections based on the atom coordinates along
> >with "same residue as" to achieve what you're looking for. There are
> >many examples in the user's guide and past mailing list discussions that
> >will likely prove useful.
> > John Stone
> > vmd_at_ks.uiuc.edu
> >On Wed, Sep 24, 2014 at 01:27:08AM +0000, Parker de Waal wrote:
> >> Hello everyone,
> >> I?ve recently been working with membrane protein simulations, generated
> >>by the CHARMM-GUI membrane builder and simulated in AMBER, and am trying
> >>to figure out a way to trim down on excess system padding (resulting
> >>from the unoptimized GUI).
> >> What I would like to do is be able to take the generated
> >>protein/membrane PDB, select a rectangular region with origin x,y,z and
> >>dimensions a,b,c, and then delete everything else that doesn?t fall
> >>within that selection. This way I can reduce my atom count and help get
> >>more ns/day for the simulation.
> >> Does anyone know if this is possible in VMD, or perhaps another tool?
> >> Best,
> >> Parker
> >NIH Center for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Phone: 217-244-3349
-- NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349 http://www.ks.uiuc.edu/Research/vmd/