From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 01 2008 - 23:28:04 CDT

Hi,
  The issue you're having with Surf is independent of the
OpenGL renderer issue. If Surf gives you a bad surface, then
I would suggest that you try using MSMS instead. You'll need
to download and install MSMS separately from VMD.
Regarding the OpenGL renderer issue, this is normally solved by
installing a vendor-provided driver for your video card/chipset.
I don't know what video card you have, but you should be looking
for a driver for your system.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Aug 02, 2008 at 09:46:14AM +0530, Vivek Sharma wrote:
> Hello John,
>
> I am using 'surf' over a small molecule to generate the surface with probe
> radii 1.4Angs. However, it seems to run, but fails to generate and show a
> complete surface. The surface is broken and incomplete, as I see in
> graphical window. The comments appeared in the console-window are pasted
> below:
>
> #####
> Reading 38 atoms..done
> Probe radius = 1.400
> Constructing solvent-accessible surface ..
> Max edge length = 1.200
> Malloc of zero or illegal length!!
> length = 0
> Malloc of zero or illegal length!!
> length = 0
> .
> Total Triangles 3478 Total constraints 832
> Max Neighbors per atom 34 Average Neighbors per atom 21.8947
> Surface construction + writing time 0.11 seconds
> done
> Info) This surface is made with SURF from UNC-Chapel Hill. The reference
> is:
> Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable Computation
> Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,
> Info) v. 14 (1994) pp. 19-25.
> Info) Reading Surf geometry output file...
> Info) Read Surf output file, processing geometry...
> Info) Done.
> #####
>
> Does it has to do anything with Malloc of ILLEGAL LENGTH?
>
> And, then searching the mailing list archives gave me some hints that there
> can be some problem in RENDERING. The INFO messages appeared in
> console-window during VMD start-up are pasted below as well.
>
> #####
> 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, 2 CPUs detected.
> Info) Free system memory: 2674MB (88%)
> Info) OpenGL renderer: Mesa GLX Indirect
> Info) Features: STENCIL MDE MTX NPOT PP PS
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), Multitexture (8)
>
> #####
>
>
> In one of the mails on mailing list (
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5650.html) the Mesa
> GLX Indirect was suggested to be the problem. Do you think, its the same
> problem here? Any suggestions please in this concern. If there are more data
> needed, please let me know as well.
>
> thanks for help,
>
> regards,
>
> Vivek

-- 
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