VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 21 2008 - 11:34:53 CST

Hi,
  I forgot to mention, that if you have atom coordinates stored in the wrong
units (e.g. not Angstroms), you could end up with a wildly out-of-scale
molecule. This may actually be contributing to your trouble. Check this
by measuring the distance between two of the atoms in VMD and see if it
makes sense or not. (VMD uses Angstroms internally)

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 16, 2008 at 05:51:04PM -0600, Arnab Chakrabarty wrote:
> Hi,
> Thanks John and Axel for your valuable suggestions. I looked into the
> radius of the atoms and found it non-zero. I mapped atom types to different
> elements through console and had similar experience. However after changing
> the sphere scaling resolution and bond scaling and radius to high values in
> CPK i was able to see the bonds. I was wondering does this thing relate to
> the system size i am trying to view (It's in the order of 10 nm X 10nm X
> 10nm with ~ 75000 atoms) and/or the hardware,
>
> Thanks
> Arnab
>
> On Feb 15, 2008 4:51 PM, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
>
> > On Fri, 15 Feb 2008, Arnab Chakrabarty wrote:
> >
> > AC> Hi,
> > AC> I am using a LAMMPS dump file in VMD 1.8.6 version in Mac
> > AC> 10.4.11version. While the Lines representation works ok, when i try to
> > AC> change it to
> > AC> VDW or CPK representation it just shows some dots. I am not sure why
> > AC> this is happening. The console gave the following message
> >
> > AC>
> > AC> 'RCNE SendEventToEventTarget (suom Moved ) failed, -50'
> >
> > this seems to be harmless and X-server related.
> >
> > AC> I looked through the some of the messages in mailing list which for
> > AC> similar error messages with a different action seems not to do with
> > AC> file format. Any help is appreciated.
> >
> > the problem is with the LAMMPS dump file format not containing
> > any useful information about the atom types (just numbers 1,2,3
> > and so on). so you have no elements and thus no radius.
> >
> > if you have a .pdb/.psf of the system (or can create one)
> > you could load that file first and then the lammps dump
> > (but in that case you would also be better off with .dcd
> > or .xtc as they are binary and thus smaller and faster to read).
> >
> > what i usually do is to load one frame of the lammps dump,
> > and then create a selection for each atom type and then
> > set the relevant properties. for model systems, that do
> > not related to any real atoms, i actually have a small
> > script that i do execute after loading the parses that
> > information from a lammps data file and assigns it automatically.
> >
> > cheers,
> > axel.
> >
> >
> >
> > AC>
> > AC> Thanks
> > AC> Arnab
> > AC>
> >
> > --
> > =======================================================================
> > Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> > =======================================================================
> > If you make something idiot-proof, the universe creates a better idiot.
> >
>
> On Feb 15, 2008 4:42 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > If you're getting dots when you try displaying in VDW, I would
> > guess that your atoms got assigned a radius of 0.0. You can check
> > this for sure by doing this in the text console:
> > set sel [atomselect top all]
> > $sel get radius
> >
> > If you get a list of zeroes, then that's what's going on. If not,
> > then I would be happy to examine your dump file and see what might be
> > happening there.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >
> > On Fri, Feb 15, 2008 at 04:25:23PM -0600, Arnab Chakrabarty wrote:
> > > Hi,
> > > I am using a LAMMPS dump file in VMD 1.8.6 version in Mac
> > > 10.4.11version. While the Lines representation works ok, when i try to
> > > change it to
> > > VDW or CPK representation it just shows some dots. I am not sure why
> > this is
> > > happening. The console gave the following message
> > >
> > > 'RCNE SendEventToEventTarget (suom Moved ) failed, -50'
> > >
> > > I looked through the some of the messages in mailing list which for
> > similar
> > > error messages with a different action seems not to do with file format.
> > Any
> > > help is appreciated.
> > >
> > > Thanks
> > > Arnab
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> >
>
>
> --
> Arnab Chakrabarty
> Graduate Student
> Texas A & M University 

-- 
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