VMD-L Mailing List

From: Vivek Sharma (vivek.viv.sharma_at_gmail.com)
Date: Fri Aug 01 2008 - 23:16:14 CDT

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