VMD-L Mailing List

From: hl332_at_drexel.edu
Date: Thu Mar 29 2007 - 16:04:02 CDT

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