VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 06 2003 - 10:18:30 CST

Lubos,
  Since you're having trouble with Surf, have you had a chance
to try using MSMS instead? MSMS runs much faster and in my opinion
the output is a bit cleaner. The MSMS surfaces also display in VMD
much faster since they are turned into triangle strips which render
quite a bit faster than the discrete triangles produced by Surf.
In the mean time, I'll take a look at what's happening when you
run Surf on that structure. If you get a chance, I highly recommend
trying out MSMS.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 06, 2003 at 05:14:59PM +0100, Lubos Vrbka wrote:
> hi!
>
> > What platform are you running VMD/Surf on?
> i observed the same problems on netbsd (running linux/mesa 1.8 binary
> under emulation) and on irix 6.5 (native irix binary)
>
> >Surf does have some
> >bugs and though we didn't write it, I might be able to take a look
> >and see if there's anything I can do about it if you give me more
> >information. Do you have a structure that causes the problem
> >easily?
> one of the structures is attached. i removed waters as it would be very
> large (600k tgz'ed)... but i think it's general issue applicable to all
> structures...
>
> one more output:
>
> Reading 390 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 23212 Total constraints 12796
> Max Neighbors per atom 68 Average Neighbors per atom 32.8103
> Surface construction + writing time 0.89 seconds
> done
> Info) Reading Surf output file...
> Info) Read Surf output file, processing geometry...
> Info) Done.
>
> the same output for residue 1-14, 1-15, 1-16, ... 1-25; the wrong malloc
> doesn't look very well...
>
> hope this will help you...
> 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