From: Ahmet Bakan (lordnapi_at_gmail.com)
Date: Mon Sep 28 2009 - 16:22:36 CDT

Hi All,

I am having a problem with VMD representations for a while now. I checked
the VMD-l archive, but couldn't find a similar posting.
I have uploaded some pictures to show the problem:

http://a.imagehost.org/0126/cartoon.jpg
http://a.imagehost.org/0084/cartoon2.jpg
http://a.imagehost.org/0989/msms.jpg
http://a.imagehost.org/0895/msms2.jpg

I have this problem particularly with NewCartoon and MSMS representations.
I had the same problem with VMD versions older than 1.8.7.
I currently use 64bit Ubuntu 9.04. Previously, I used OpenSUSE 10.3, and
still had the problem.
My graphics card is NVIDIA 7900 GTX. I always install the latest drivers
from NVIDIA site, and compile them for the kernel that I have.

For the MSMS example that I show above:
When only the molecule with MSMS representation is displayed, I
rotate/scale/translate the view with no problems.
When another molecule with cartoon representation is also displayed, gives
that weird representation problem.

This is not the general trend though. In the cartoon example, I have the
problem always.
This problem comes up usually after I load a couple of molecules and play
around for a while, but it also sometimes come up at the very beginning of a
session. In MSMS exmaple, I loaded the two molecules using a TCL script, and
generated all representations automatically. As soon as I rotate, the
representations are distorted.

Below is what VMD outputs, when I run it. Please also note that I have the
same problem when I turn of the X11 Composite extension.

Does this information help anyone to figure out what is wrong with my
system/configuration? Thanks in advance for any suggestions.
Best wishes,
Ahmet

Info) VMD for LINUXAMD64, version 1.8.7 (August 1, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 6900MB (87%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce 7900 GTX/PCI/SSE2
Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (512x512x512), Multitexture (4)