VMD-L Mailing List

From: Samuel Flores (samuel.flores_at_yale.edu)
Date: Tue Oct 04 2005 - 18:32:25 CDT

Hi John,

I selected by residue number. I think the atom was too far away and VMD
didn't recognize it as part of that residue, therefore didn't include it in
the selection set. The question is, how to counter this problem? I can't
select all, and then deselect the unwanted residues, because then the extra
atoms would end up in ALL selections, not just the intended one.

Sam

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Tuesday, October 04, 2005 3:27 PM
To: Samuel Flores
Cc: 'mashaojie163'; 'vmd'
Subject: Re: vmd-l: VMD removing slightly misplaced atoms

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