VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Jul 26 2009 - 20:09:45 CDT

On Sun, 2009-07-26 at 19:19 -0500, Jehanzeb Hameed wrote:
> Thanks!
>
> Since I just started to use VMD today, please tell me if this is what you mean.
>
> Select "save coordinates" from the menu. In the dialog box, there is a
> field for "selected atoms". In that field, I should write "not water".
> Is this correct?

yes. if you are new to VMD, please have a look at the user's guide.
it contains a lot of useful information and also makes it easier to
understand some of the "slang" that experienced users are using.

cheers,
   axel.

p.s.: please keep the mailing list in cc. thanks.

>
> -Jehanzeb
>
> On Sun, Jul 26, 2009 at 6:47 PM, Axel
> Kohlmeyer<akohlmey_at_cmm.chem.upenn.edu> wrote:
> > On Sun, 2009-07-26 at 18:24 -0500, Jehanzeb Hameed wrote:
> >> Hello,
> >>
> >> I am trying to strip out water from pdb files downloaded from Protein
> >> Data Bank (rcsb.org). Can someone please tell me how to do this in
> >> vmd?
> >
> > load the file into VMD and then use an atom selection of
> > "not water" or "not resname XXX" (with XXX chosen according
> > to the name in your file) when writing out the file again.
> >
> > cheers,
> > axel.
> >
> >>
> >> Thanks,
> >> -Jehanzeb
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
> > 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.