VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 04 2005 - 14:27:18 CDT

Sam,
  VMD won't remove any atoms... If you're missing the atom it's because
the atom wasn't part of the atom selection you saved with "$sel writepdb" or
however you chose to do it. If you saved an atom selection that was
specified like this:
  set sel [atomselect top "all"]
  $sel writepdb my.pdb

Then you should not be missing any atoms.
If you had some selection other than "all", then you may have made a
mistake and excluded the atom of interest unintentionally.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 04, 2005 at 03:03:46PM -0400, Samuel Flores wrote:
> Hi guys,
>
> I have a CE atom in a methionine residue that is a little distant from its
> corresponding sulfur. When I open the molecule using VMD, make some minor
> rotations and then save the protein, the saved protein is missing this atom.
> Presumably it was too far away to be recognized as part of the MET residue
> (in fact no bond is displayed in the viewer) and was truncated. I'd rather
> not have this truncated (I'll do an energy minimization later, hopefully fix
> the problem that way). Can anyone tell me how to instruct VMD to not remove
> atoms?
>
> Many thanks
>
> Sam
>
> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of
> mashaojie163
> Sent: Monday, October 03, 2005 9:16 PM
> To: vmd; John Stone
> Subject: Re: vmd-l: How can I compile win32-vmd
>
> Thank you
> Maybe you just provide the current windows vmd for me. I have
> compiled plugins successfully by use of cygwin and was compiling vmd by use
> of MSVC and now meeting some errors. Please send me the new vmd in windows .
> I will compile it when I have spare time.
> Best Regards
>
> Ma shaojie
>
>
> ----- Original Message -----
> From: "John Stone" <johns_at_ks.uiuc.edu>
> To: "mashaojie163" <mashao_jie_at_163.com>
> Cc: "vmd" <vmd-l_at_ks.uiuc.edu>
> Sent: Tuesday, October 04, 2005 12:15 AM
> Subject: Re: vmd-l: How can I compile win32-vmd
>
>
> >
> > Hi,
> > If you need a current build of VMD on Windows, I can provide one for
> you.
> > If you really want to build from source, you should be warned that the
> build
> > requires you to use MSVC and if you plan to build the plugins from source,
>
> > you'll also need cygwin to get the 'make' and other utilities we're using
> > there. Let me know what you're trying to do and I can help you solve
> this.
> >
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Sun, Oct 02, 2005 at 01:18:11PM +0800, mashaojie163 wrote:
> > >
> > >
> > >
> > > Dear Sir:
> > > I get the source code by vmd-cvs and by use of make command to
> compile linux vmd. But can you tell me how I should compile window vmd. I do
> not know make command in windows
> > --
> > 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