VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 14 2003 - 11:09:15 CST

Lubos,
  I think I have just found the reason you've been having problems
with Surf. I'll have a new set of VMD binaries for Unix available
today which contain a fix. Let me know if you're interested in testing
them. This should cure the problems a few people have found with Surf
lately.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 06, 2003 at 05:00:38PM +0100, Lubos Vrbka wrote:
> hi!
>
> i'm probably asking on the wrong place, but maybe... i've got following
> problem: if i select some part of the protein (let's say 1 residue) and
> want to change the representation to Surf, it doesn't display anything
> except following output:
>
> Malloc of zero or illegal length!!
> length = 0
> Reading 0 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
> Malloc of zero or illegal length!!
> length = 0
> Total Triangles 0 Total constraints 0
> Max Neighbors per atom 0 Average Neighbors per atom nan
> Surface construction + writing time 0.00 seconds
> done
>
> this repeats for fragments <14 residues (this number differs among
> different structures). what more it seems that the output for 14 - 25
> residues fragment remains all the time the same, it changes for fragment
> of 1 - 26 residues (the numbers vary again among different structures) -
> it reports
> reading xxx atoms
> done
>
> where xxx is same for fragments of (for example) 14 - 25 residues.
>
> could anyone tell me what i'm doing bad?
>
> tia,
> lubos
>
> --
> -
> #################################################
> Lubos Vrbka
> National Centre for Biomolecular Research
> Masaryk university, Brno, Czech Republic
>
> shnek_at_chemi.muni.cz
> http://www.chemi.muni.cz/~shnek
> tel. +420 541 129 508
> #################################################
> 

-- 
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