VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 04 2007 - 16:38:59 CST

Hi,
  You can select a boxes, spheres, and other shapes with
the position based selection operators such as:
  not (water and (x > 5) and (x < 10)))

  John

On Thu, Jan 04, 2007 at 07:13:49PM -0300, Cesar Luis Avila wrote:
> No. I have an equilibrated membrane/water/ions system which I want to
> combine with an equilibrated protein/water/ion system. I do not want to
> lose all the water from both systems. So I want to make a hole to
> accomodate the protein box. I know this may sound a little strange but I
> think it is the best way for my system.
> Regards
> Cesar
>
> nunolf_at_ci.uc.pt escribió:
> >Hi Cesar
> >
> >Quoting Cesar Luis Avila <cavila_at_fbqf.unt.edu.ar>:
> >
> >>Dear all,
> >>I would like to remove water molecules in a box. The number of water
> >>molecules is huge and they are spread among several segments which
> >>may also contain ions. Does anyone have an efficient tcl script for
> >>doing this under vmd /psfgen ?
> >>Thanks in advance
> >>Cesar
> >>
> >>
> >
> >Supposing that your box has protein+water+ions.
> >On the VMD console, if you type:
> >
> >set sel [atomselect top protein]
> >$sel writepdb only_protein.pdb
> >
> >You will get a pdb file with only protein atoms.
> >Is this what you want?
> >
> >Cheers,
> >Nuno
> >
> >
> > 

-- 
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