VMD-L Mailing List

From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Mon Jun 05 2006 - 16:14:27 CDT

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