VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 27 2008 - 16:13:41 CDT

Hi,
  You can increase the atom radii to prevent pockets and cavities
from creating internal surfaces like the ones shown in your rendering,
you can also use a different isovalue for the rendered surfaces to avoid
such things.

  John

On Tue, May 27, 2008 at 05:10:05PM -0400, Yinglong Miao wrote:
> Hi, John,
>
> Thanks for your reply.
>
> I tried volmap and used blue transparent for a small system, but it seems
> there are some deep blue bands wrapping around the system in the result
> image (see the attached). Tachyon Internal was used for the rendering. Can I
> adjust some parameters to remove those bands?
>
> Thanks,
> Yinglong
>
> On Tue, May 27, 2008 at 4:12 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> >
> > Hi,
> > Niether the MSMS program nor Surf can really handle huge water boxes,
> > these are limitations of these two programs. The authors of those packages
> > never intended them to be used on structures of the size that you're
> > working with.
> >
> > If you want to make a water box like the ones you've seen on our web site,
> > use the "volmap tool" plugin that's in the Extensions->Analysis menu.
> > You'll want to use "all" as the selection, and you'll want to adjust
> > the resolution down to something more like 2.0 or 3.0. Give that a try.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, May 27, 2008 at 03:53:54PM -0400, Yinglong Miao wrote:
> > > Dear VMDers,
> > >
> > > I have been trying to apply transparent surf or MSMS representation for
> > > water in a large system (2336817 atoms), but keep getting error messages
> > as
> > > pasted below. I am wondering whether there is a size limit for these two
> > > representations. I did see nice images with these two presentations used
> > for
> > > water in VMD gallery like:
> > >
> > http://www.ks.uiuc.edu/Gallery/Science/Structure/tn/Fig1-new2_st.jpg.html.
> > > How do you get around for large systems? Any help will be greatly
> > > appreciated.
> > >
> > > Thanks,
> > > Yinglong
> > >
> > >
> > > *Error messages for "surf":*
> > > vmd > Reading 2336817 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
> > > compute_tri_plane_int(): denom close to zero 0.000000
> > > find_sol_cons() warning: sol is somewhat away from vertex (0.002365).
> > > .find_sol_cons() warning: sol is somewhat away from vertex (0.001152).
> > > ..find_sol_cons() warning: sol is somewhat away from vertex (0.001434).
> > > .compute_tri_plane_int(): denom close to zero 0.000000
> > > compute_tri_plane_int(): denom close to zero 0.000000
> > > find_sol_cons() warning: sol is somewhat away from vertex (0.003361).
> > > ...find_sol_cons() warning: sol is somewhat away from vertex (0.003765).
> > > ..find_ray_sphere_int(): disc = -0.042826 sqrt probs for atom center
> > > -128.998001
> > > -156.473999 3.010000
> > > Stop here
> > > Stop here
> > > Stop here
> > > Stop here
> > > ...
> > > Stop here
> > > Segmentation fault (core dumped)
> > > 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.
> > >
> > > *Error messages for "MSMS":*
> > > Info) Starting MSMS with: 'msms -no_area -socketPort 1357 &'
> > > INPUT 2336817 spheres 0 collision only, radii 1.000 to 1.520
> > > PARAM Probe_radius 1.500 density 1.500 hdensity 0.000
> > > REDUCED SURFACE ...
> > > RS component 0 identified 71133 73188 93825
> > > 2 free edge(s) found in component 0
> > > RS component #faces #edges #free_edges #vertices genus
> > > 0 196596 294894 2 90806 3748
> > > Time Reduced Surface real: 9.15 user: 8.97 sys: 0.17
> > > ANALYTICAL SOLVENT EXCLUDED SURFACE...
> > > Component 0
> > > ERROR) No data from MSMS.. giving up.
> > > Info) Done with MSMS surface.
> > >
> > >
> > > --
> > > Yinglong Miao
> > > Ph.D. Candidate
> > > Center for Cell and Virus Theory
> > > Chemistry Department, Indiana University
> > > 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> > > Tel: 1-812-856-0981
> >
> > --
> > 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> > Fax: 217-244-6078
> >
>
>
>
> --
> Yinglong Miao
> Ph.D. Candidate
> Center for Cell and Virus Theory
> Chemistry Department, Indiana University
> 800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
> Tel: 1-812-856-0981 

-- 
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