VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 18 2012 - 11:01:13 CST

Hi,
  As Axel already pointed out, the "Surf" representation has not been
changed at all for some time. The new surface algorithm in VMD 1.9.1
is named "QuickSurf". If you're having trouble with "Surf", you may
a structure that causes some kind of internal algorithm failure in Surf
and/or triggers some other problem when VMD reads the output that Surf
produces. If you can send me the structure file(s) that are causing you
trouble, I would be happy to investigate. In the mean time, I would
strongly recommend that you try using MSMS or the new QuickSurf representation
as alternatives for the case that is causing you trouble with Surf.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 18, 2012 at 01:12:08PM +0100, FX wrote:
> Hi all,
>
> I have a strange problem with the "Surf" representation (molecular surfaces). I have a PDB file of a porous material, which when loaded into VMD and switched to "surf" representation:
>
> -- on my Mac OS 10.7.2, with VMD 1.9 (not the latest beta), works fine
> -- on our x86_64 linux boxes (without CUDA), alternatively does not work (display seemingly random triangles) or crashes VMD as a whole, depending on probe size used; this happens with both versions 1.9 and 1.9.1
> -- on our Windows 7 64-bit box (which has CUDA accelerators), same thing as Linux, both with 1.9 and 1.9.1
>
> I cannot make any sense of that. I know that the "surf" code is not the most stable algorithm, but that's very impressive crashing rate. Moreover, I thought there was a new CUDA-based code for calculation of molecular surfaces (the "surf" representation) in 1.9.1, and so I expected it to work fine on the Windows system (which detects the graphic card fine, and states that CUDA accelerators are present).
>
> So, how do I debug this? Are any of my assumptions wrong? How could I get the CUDA version of the code to run on Windows (hoping it is more stable that the external SURF program)?
>
> Many thanks in advance,
> FX Coudert 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078