VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 05 2006 - 17:02:21 CDT

Hi,
  Yes, I know of at least reason for this to happen, if you send
me your structure I'll have a look.

  John

On Mon, Jun 05, 2006 at 04:14:27PM -0500, Leonardo G. Trabuco wrote:
> I assume the problem is that the 'nucleic' macro is not recognizing your
> last residue for some reason. I remember seing some problem like this
> before, but I didn't find any structure now that reproduced this
> problem.
>
> The 'solvent' stuff is not surprising. It is just a macro defined as:
> atomselect macro solvent {not (protein or sugar or nucleic or lipid)}
>
> Therefore, 'nucleic not solvent' and 'all not solvent' are going to give
> you the same error if the problem is with the 'nucleic' macro.
>
> You should probably send your problematic file to John Stone to take a
> look at.
>
> Best,
> Leo
>
> On Sun, Jun 04, 2006 at 04:53:18PM +0200, Vineet Pande wrote:
> > Hi,
> > Now I notice that if I load the same trajectoty [but] without solvent
> > (solvent removed already from a CHARMM trajectory), VMD shows the display of
> > solute correctly. Still its strange that display is incomplete with a
> > trajectory containing solvent.
> >
> > Vineet,
> >
> > ---
> > Vineet Pande, Ph.D.
> > Karolinska Institute, Stockholm
> >
> >
> > On 6/3/06, Vineet Pande <pande.vin_at_gmail.com> wrote:
> > >
> > > Yes. even if use "nucleic not solvent" or "all not solvent" selection
> > >while displaying in *default display*; VMD does not show the molecule
> > >completely.
> > >
> > >Vineet
> > >
> > >---
> > >Vineet Pande, Ph.D.
> > >Karolinska Institute, Stockholm
> > >
> > >
> > > On 6/2/06, Leonardo G. Trabuco <ltrabuco_at_ks.uiuc.edu> wrote:
> > >>
> > >> On Fri, Jun 02, 2006 at 04:17:51PM +0200, Vineet Pande wrote:
> > >> > Hi,
> > >> > I am using VMD for WIN32, version 1.8.4b10 to display a simple CHARMM
> > >> > trajectory of a nucleic acid duplex. However, in the graphics, I can't
> > >> see
> > >> > one of the terminal nucleotides in both the strands; the MD movie runs
> > >> fine
> > >> > however. What could be the problem?
> > >>
> > >> Are you using the keyword 'nucleic' in your atom selection? Which
> > >> representation are you using?
> > >>
> > >> Leo
> > >>
> > >> --
> > >> Leonardo Giantini Trabuco
> > >> Ph.D. candidate
> > >> Center for Biophysics and Computational Biology
> > >> University of Illinois at Urbana-Champaign
> > >>
> > >
> > >
>
> --
> Leonardo Giantini Trabuco
> Ph.D. candidate
> Center for Biophysics and Computational Biology
> University of Illinois at Urbana-Champaign 

-- 
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