VMD-L Mailing List

From: Chang, Christopher (Christopher_Chang_at_nrel.gov)
Date: Tue Oct 04 2005 - 20:05:48 CDT

Sam,

   You could do a compound selection by residue index and atom index. If
it were Met 97 and the errant carbon atom number 1170 (indexed from 1 in
the PDB), something like

set sel [atomselect top "resid 97 or index 1169"]
$sel writepdb example.pdb

should include both the Met residue and the carbon. Atom indexing is
from 0, so it would be 1169 rather than 1170.

Chris

Christopher H. Chang, Ph.D.
Research Associate
National Renewable Energy Laboratory
1617 Cole Blvd., Mail Stop 1608
Golden, CO 80401
Phone (303) 275-3751
Fax (303) 275-4007

> -----Original Message-----
> From: owner-vmd-l_at_ks.uiuc.edu
> [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Samuel Flores
> Sent: Tuesday, October 04, 2005 5:32 PM
> To: 'John Stone'
> Cc: 'mashaojie163'; 'vmd'
> Subject: RE: vmd-l: VMD removing slightly misplaced atoms
>
> 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
>
>
>