From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 16 2007 - 09:20:37 CDT

Hi,
  Thew new versions of MSMS no longer support the "all" or "selected"
feature, so the behavior you're witnessing is expected for current versions
of MSMS. I plan to reimplement the VMD MSMS interface to allow this
feature to work by having VMD do the post-processing of the triangles
returned by MSMS, emulating the behavior of the older versions of
MSMS. For the time being, you'll have to either use an old version
of MSMS, or stick to using the "selected" option.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 16, 2007 at 12:33:07PM +0000, Ezequiel Quintana Morales wrote:
> Hi,
>
> I'm trying to draw a MSMS surface of a set of small organic molecules
> I'm working with and I'm seen what it seems to me a strange behaviour of
> MSMS.
>
> I'm using VMD 1.8.6 (x86_64) and MSMS (x86_64) from inside VMD.
>
> In short, the problem is: I can draw a msms surface of several atoms of
> the whole set of molecules when i select 'Which Atoms: Selected and
> Probe Radius: 1.5' but the surface disappears when I change 'Which
> Atoms: All and Probe Radius: 1.5'. The surface is visible again when
> 'Which Atoms: All and Probe Radius: 2.0'. Of course, the group of atoms
> and not buried and they are in a inner open surface.
>
> I think that if I'm able to obtain the surface with a probe radius of
> 2.0, at a value of 1.5 should make it also be visible ...
>
> Any help will be appreciated
>
> Thanks
> Ezequiel
>
> PS. This is the output of MSMS for each calculation:
>
> Surface obtained using 'Which Atoms: Selected'
> 'Sample Density: 12.6'
> 'Probe Radius: 1.5'
>
> Info) Starting MSMS with: '/usr/local/msms/msms -no_area -socketPort
> 1357 &'
> INPUT 72 spheres 0 collision only, radii 1.000 to 1.500
> PARAM Probe_radius 1.500 density 12.600 hdensity 0.000
> REDUCED SURFACE ...
> RS component 0 identified 9 65 6
> 0 free edge(s) found in component 0
> RS component #faces #edges #free_edges #vertices genus
> 0 200 300 0 72 15
> Time Reduced Surface real: 0.00 user: 0.00 sys: 0.00
> ANALYTICAL SOLVENT EXCLUDED SURFACE...
> Component 0
> Time Surface real: 0.01 user: 0.00 sys: 0.00
> ordonne_arete: warning hole in a reentrant face 233
> Time Singularities real: 0.00 user: 0.00 sys: 0.00
> SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
> 0 622 1269 41 644 38 1 0 3
> TRIANGULATION...
> Component 0
> component#, vertices, edges, faces, genus, density
> 0 10116 30360 20240 3 0.000
> Time Triangulation real: 0.09 user: 0.09 sys: 0.00
> MSMS terminated normally
> Total Time real: 0.12 user: 0.10 sys: 0.00
> MSMS END
> Info) Done with MSMS surface.
> Info) Performing ACTC Triangle Consolidation...
> Info) ACTC: Created 2634 triangle strips
> Info) ACTC: Average vertices per strip = 9
>
>
> No surface obtained using switching to 'Which Atoms: All'
> with the same 'Sample Density: 12.6' and 'Probe Radius: 1.5'
>
> Info) Starting MSMS with: '/usr/local/msms/msms -no_area -socketPort
> 1361 &'
> INPUT 510 spheres 438 collision only, radii 1.000 to 1.900
> PARAM Probe_radius 1.500 density 12.600 hdensity 0.000
> REDUCED SURFACE ...
> RS component 0 identified 14 12 13
> 0 free edge(s) found in component 0
> RS component #faces #edges #free_edges #vertices genus
> 0 750 1125 0 338 19.5
> Time Reduced Surface real: 0.04 user: 0.04 sys: 0.00
> ANALYTICAL SOLVENT EXCLUDED SURFACE...
> Component 0
> Time Surface real: 0.00 user: 0.01 sys: 0.00
> ERROR) No data from MSMS.. giving up.
> Info) Done with MSMS surface.
>
> Surface obtained again using 'Which Atoms: All'and 'Sample Density:
> 12.6'
> but switching to 'Probe Radius: 2.0'
>
> Info) Starting MSMS with: '/usr/local/msms/msms -no_area -socketPort
> 1364 &'
> INPUT 510 spheres 438 collision only, radii 1.000 to 1.900
> PARAM Probe_radius 2.000 density 12.600 hdensity 0.000
> REDUCED SURFACE ...
> RS component 0 identified 14 12 7
> 0 free edge(s) found in component 0
> RS component #faces #edges #free_edges #vertices genus
> 0 686 1029 0 310 17.5
> Time Reduced Surface real: 0.05 user: 0.04 sys: 0.00
> ANALYTICAL SOLVENT EXCLUDED SURFACE...
> Component 0
> Time Surface real: 0.00 user: 0.01 sys: 0.00
> ordonne_aretes: No cycle in face 61 (nba=-3)
> ordonne_aretes: No cycle in face 64 (nba=-3)
> ordonne_aretes: No cycle in face 570 (nba=-2)
> ordonne_aretes: No cycle in face 571 (nba=-3)
> 4 faces with problems
> radius of atom 30 goes from 1.500000 to 1.600000
> radius of atom 31 goes from 1.000000 to 1.100000
> radius of atom 112 goes from 1.500000 to 1.600000
> radius of atom 113 goes from 1.000000 to 1.100000
> radius of atom 121 goes from 1.000000 to 1.100000
> Failed to compute level 0 surface, try again 2
> REDUCED SURFACE ...
> RS component 0 identified 14 12 7
> 0 free edge(s) found in component 0
> RS component #faces #edges #free_edges #vertices genus
> 0 686m 1029 0 310 17.5
> Time Reduced Surface real: 0.04 user: 0.04 sys: 0.00
> Component 0
> Time Surface real: 0.00 user: 0.00 sys: 0.00
> Time Singularities real: 0.01 user: 0.00 sys: 0.00
> SES comp. #fac. #edg. #s_edg. #vert. #s_vert. R_h C_h genus
> 0 568 1230 52 662 74 0 0 1
> TRIANGULATION...
> Component 0
> component#, vertices, edges, faces, genus, density
> 0 6818 19882 13255 -94.5 0.000
> WARNING: Genus mismatch (ana = 1.0, tri = -94.5 )
> Time Triangulation real: 0.09 user: 0.09 sys: 0.00
> MSMS terminated normally
> Total Time real: 0.21 user: 0.20 sys: 0.00
> MSMS END
> Info) Done with MSMS surface.
> Info) Performing ACTC Triangle Consolidation...
> Info) ACTC: Created 1860 triangle strips
> Info) ACTC: Average vertices per strip = 9
>
>

-- 
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