VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jun 07 2006 - 11:11:23 CDT

Hi,
  This sort of thing can be done by running VMD in text mode if you like:
http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.4/ug/node192.html

vmd -dispdev text -eofexit < input.tcl > output.log

In your script, you'd do something like:

mol new myfile.parm7
mol addfile myrestart.rst7
set sel [atomselect top "same residue as within 3 of chain X"]
set outfile [open "myresidues.txt" w]
puts $outfile [lsort -unique [$sel get resid]]
close $outfile

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jun 07, 2006 at 11:56:02AM -0400, Gustavo Seabra wrote:
> Hi,
>
> I was wondering if any of you experts could help me with a simple command.
>
> I'd like to be able to get, from an Amber restart file, all the waters
> within a distance (say, 3A) from a central molecule. I know how to do
> thins in the GUI, byt using, for example, "same residue as within..."
> .But, ideally, I want to do this without raising the whole VMD: maybe
> just a shell script or even a one liner that can print out the residue
> numbers to a separate file. Is that possible?
>
> Thanks.
>
> --
> ---------------------------------------------------------------------------------------------
> Gustavo Seabra Postdoctoral Associate
> Quantum Theory Project University of Florida
> Registered Linux user number 381680
> Say NO! to software patents: http://www.nosoftwarepatents.com
> ---------------------------------------------------------------------------------------------
> If at first you don't succeed...
> ...skydiving is not for you. 

-- 
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