VMD-L Mailing List

From: Arnab Chakrabarty (r.arnab_at_gmail.com)
Date: Sat Feb 16 2008 - 17:51:04 CST

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