VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Oct 25 2004 - 13:25:50 CDT

Amarda,
  You said that VMD crashed on you when attempting to write out
atom coordinates from a selection? Can you send me the sequence of
commands or operations you performed that caused this to occur? I've
never seen this behavior before, so I'd be very curious to see what is
causing your problem! To save a selection via text commands you should
be able to do something like this:
  set sel [atomselect top "my selection"]
  $sel writecrd /tmp/my.crd

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Oct 23, 2004 at 02:58:21PM -0500, Amarda Shehu wrote:
>
> Does anyone know the command to output the xyz coordinates of a selection
> in crd format? I know how to get the selection and even get the xyz
> coordinates, but cannot find the command to write these out to a crd file.
>
> I even tried writepdb to output them to a pdb format file, but vmd crashes
> on me.
>
> -Amarda
>
>
> On Fri, 15 Oct 2004, John Stone wrote:
>
> >
> > Hi,
> > It depends greatly on how you want to select the residues as to how you
> > would proceed with coloring them. If you want all ALA residues to be a
> > different color, you can simply do something like:
> > color Resname ALA red
> >
> > If you want to color a certain group of residues a particular way, it is
> > often best to use atom selections to select that group of residues, and
> > then set the color via the ColorID coloring method:
> > mol modselect 0 0 "resid 1 to 10"
> > mol modcolor 0 0 ColorID 0
> >
> > There's more information about all of this in the User's Guide.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Wed, Oct 13, 2004 at 01:27:06PM +0400, S.G.Falkovich wrote:
> > > Sir,
> > >
> > > I need to change color and representation of some residues automatically, from script.
> > >
> > > Can anybody help me?
> >
> > --
> > 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
> > 

-- 
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