VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 29 2007 - 16:10:43 CDT

Hi,
  Have you tried using MSMS instead? MSMS is much newer than Surf
and is supported by the people at Scripps. Surf hasn't been maintained
for many years now and the version we provide with VMD just has various
bug fixes that we've added ourselves. Give MSMS a try and let us know
if you still need help.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 29, 2007 at 05:04:02PM -0400, hl332_at_drexel.edu wrote:
> Hi,
> I have been trying to draw my protein and several of its residues using surface representation 'SURF' but for some reason it displays only a small portion as surf not the whole protein. The following commands are executed in vmd console:
> =================================
>
> vmd > Reading 4716 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
> ...........compute_tri_plane_int(): denom close to zero 0.000000
> .....................................
> Total Triangles 255214 Total constraints 228706
> Max Neighbors per atom 90 Average Neighbors per atom 48.4958
> Surface construction + writing time 4.94 seconds
> done
> Info) This surface is made with SURF from UNC-Chapel Hill. The reference is:
> Info) A. Varshney, F. P. Brooks, W. V. Wright, Linearly Scalable Computation
> Info) of Smooth Molecular Surfaces, IEEE Comp. Graphics and Applications,
> Info) v. 14 (1994) pp. 19-25.
> Info) Reading Surf geometry output file...
> Info) Read Surf output file, processing geometry...
> Info) Done.
> ========================================
>
> regards
> Harish
>
> -------------------------------------------------
> Harish Vashisth (Ph.D Candidate)
> CAT-361,Chemical & Biological Engg.
> Drexel University, Philadelphia, PA
> office: 215-895-5823 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078