VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Fri Jul 31 2009 - 07:44:29 CDT

On Fri, 2009-07-31 at 14:58 +1200, Srikanth Dhondi wrote:
> Hi there,
>

> I am using VMD 1.8.6 on Ubuntu 8.04. I have difficulty visualizing 2D
> simulations with Graphical representation option as Points. When I
> load the xyz file with the above mentioned options when the point size
> is 1 some of the particles just don't appear on the visualization
> window (Screenshot 1). As I increase the size the particles take

srikanth,
there are no screenshots attached to the mail.

have you checked that the atoms were not colored black?

> squarish shape rather than circular (Screenshot 2). I have used VMD
> before on other Linux OS didn't had this problem. CPK style works fine
> again. If anyone can give any suggestions on this I would be grateful.

hard to say, but the Points representation uses only elementary
functionality, so it would work about everywhere. without seeing
the screenshots and any details about your hardware, it is impossible
to even guess. most linux related visualization problems seem to
be related to broken or incomplete drivers.

please have a look at the vmd linux release notes and the
instructions on how to report problems properly. thanks.

cheers,
   axel.

>
>
> Srikanth 

-- 
=======================================================================
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.