VMD-L Mailing List

From: Thomas Evangelidis (te8624_at_mbg.duth.gr)
Date: Thu Nov 29 2007 - 18:50:42 CST

Αρχικό μήνυμα από John Stone <johns_at_ks.uiuc.edu>:
Hi,
I may sound boring because I wrote the same things again last week. Are you
interested in reducing the size of your trajectories by keeping only the
atoms that are within a cuttof distance (you can define this) from your
macromolecule/s - instead of the x, y and z bounds determined by the minmax of
protein. I have written a tcl script that does this job automatically, if
you're interested let me know and I'll send it to you.
regards,
Thomas

>
> Hi,
> There isn't a selection keyword that performs an axis-aligned bounding
> box comparison, just the 'within' selection that's a radial distance. You
> could write a script that does this, but a selection by itself won't do the
> job unless your protein remains essentially fixed and the axis-aligned
> bounding
> box doesn't move or change size during the simulation.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Nov 29, 2007 at 10:17:51AM -0500, Pavan Ghatty wrote:
> > Hello All,
> >
> > I was wondering if there is an easy way to select water within the x, y and
> > z bounds determined by the minmax of protien for every timestep in VMD.
> >
> > Thank you,
> > Pavan Ghatty
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>