VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 11 2004 - 10:06:48 CDT

Dieter,
  This sounds like a problem with the 'Surf' application.
I'm trying a modified version of Surf locally and may have a new
version for you to try on your machine. We didn't write it, but over
the years we've found/fixed a few bugs in it anyway. The ideal solution
would be to use MSMS for a large structure like that, but the Windows
version of MSMS doesn't support socket connections and thus doesn't work
with VMD presently. Even MSMS occasionally has problems with very large
structures. One way to avoid these problems is to make separate surface
representations for each subunit of the virus, if there are subunits.
(look to see if they have different segnames, chains, etc and write a
 Tcl script to generate a Surf rep for each one rather than for the
 entire structure)

I've been somewhat frustrated with the behavior of the surface calculation
tools on large structures, but as they are outside of my area of expertise
I doubt I'd be able to write one that performs better than the existing ones.
If anyone knows of other solvent accessible/excluded surface calculation
tools that work better, I'd be glad to hear about them.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 11, 2004 at 02:10:36PM +0200, dieter blaas wrote:
> When trying to make a surface representation of a virus with ~ 250 000
> coordinates I only get a piece of surface that does not look like anything
> it shoud.
> It reads like this:
> .......
> Info) Determining bond structure from distance search ...
> Info) Analyzing structure ...
> Info) Atoms: 362827
> Info) Residues: 45360
> Info) Waters: 0
> Info) Segments: 1
> Info) Fragments: 180 Protein: 182 Nucleic: 0
> Info) Finished with coordinate file F:/all_60_h2.pdb.
> Reading 362827 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!!
> .....................
> and after an awful lot of time I get an error message something like
> "program has made a violation....."
> and the PC freezes and does not react any more until I push "reset".
> What can I do?
> Thanx for help, Dieter 

-- 
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