VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sat Oct 20 2007 - 15:44:39 CDT

On Sat, 20 Oct 2007, Jeffry D Madura wrote:

JM> Hi Everyone,

hi jeffry,

JM>
JM> I am using VMD 1.8.6 and trying to color a molecular surface by mapping
JM> electrostatics results from an APBS calculation. I am using the dataset
JM> from the colorbypot VMD tutorial to make sure I understand how to do this.
JM> When I select Color Method as Volume and Drawing Method as Surf VMD produces
JM> a "dotted" representation of the molecular surface. It does not produce the

you could try using the volmap tool to get an atom radius based density
map instead and use an isosurface representation instead.

JM> nice smooth Opaque surface I get when I change Color Method to Charge. The
JM> graphics card is an Intel 945GM. Has anyone run into this problem and if so
JM> is their a work around?

those intel chipset are a big problem. i have not yet seen one
that works fully with VMD on texture mapped surfaces.

can you post the vmd startup info from the vmd console?
here is what i get on my laptop with intel graphics decelerator
using the latest intel drivers on linux fedora (test3 of fedora 8).
the 3-D (128x128x1) is the killer for me. this turns 3d textures
into 2d and is pretty pointless. it had been worse before, tho.

Info) Multithreading available, 1 CPU detected.
Info) Free system memory: 463MB (74%)
Info) OpenGL renderer: Mesa DRI Intel(R) 852GM/855GM 20061017 x86/MMX/SSE2
Info) Features: STENCIL MDE CVA MTX PP
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), 3-D (128x128x1), Multitexture (4)

cheers,
    axel.

JM>
JM>
JM>
JM> Best Regards,
JM>
JM>
JM>
JM> Jeffry
JM>
JM>
JM>
JM> Jeffry D. Madura
JM>
JM> Professor & Chair
JM>
JM> Department of Chemistry & Biochemistry
JM>
JM> Duquesne University
JM>
JM> 600 Forbes Avenue
JM>
JM> Pittsburgh, PA 15282
JM>
JM>
JM>
JM> voice 412-396-6341
JM>
JM> voice 412-396-4129
JM>
JM> FAX 412-396-5683
JM>
JM>
JM>
JM> e-mail: madura_at_duq.edu
JM>
JM>
JM>
JM> 

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