On 11/30/2012 04:26 AM, Elaine Meng wrote:
Hi Antón, It sounds like you have already tried our suggested tricks for getting the molecular surface calculation to work. The only other thoughts on that are to try a different computer, or maybe even a different daily build, to avoid the numerical failure.
There is a famous computational geometry library (CGAL) that would not fail, whatever the input molecule is. http://www.cgal.org/Manual/latest/doc_html/cgal_manual/Skin_surface_3/Chapte...
Alternatives to molecular surface calculation, assuming it is the display and not the surface area that you need:
(a) Multiscale Models (as mentioned by Eric) although that would give a separate low-res surface blob for each chain, or the more detailed molecular surface for each chain if you set resolution to zero in that tool. <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multiscale/framemulti.html>
(b) if you need a single surface enclosing all the atoms, you could try generating a density map from those atoms using the "molmap" command, then showing the map as an isosurface. The contour level, smoothing, etc. can be controlled with Volume Viewer or various commands. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/molmap.html> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 29, 2012, at 3:00 AM, Anton Vila Sanjurjo wrote:
Hi,
I have seen posts regarding this problem before. Here is the log I got after attempting to render a surface representation of the 50S ribosomal subunit (rcsb ID: 3CPW).
#0, chain 0: 23S ribosomal rna #0, chain 1: L35E #0, chain 2: 50S ribosomal protein L44E #0, chain 4: 5'-R(*cp*cp*ap*(phe)*(aca))-3' #0, chain 9: 5S ribosomal rna #0, chain A: 50S ribosomal protein L2P #0, chain B: 50S ribosomal protein L3P #0, chain C: 50S ribosomal protein L4P #0, chain D: 50S ribosomal protein L5P #0, chain E: 50S ribosomal protein L6P #0, chain F: 50S ribosomal protein L7AE #0, chain G: HS6 #0, chain H: 50S ribosomal protein L10E #0, chain I: 50S ribosomal protein L13P #0, chain J: HMAL13 #0, chain K: 50S ribosomal protein L15P #0, chain L: 50S ribosomal protein L15E #0, chain M: 50S ribosomal protein LC12 #0, chain N: 50S ribosomal protein L18E #0, chain O: 50S ribosomal protein L19E #0, chain P: 50S ribosomal protein L21E #0, chain Q: HL31 #0, chain R: 50S ribosomal protein L23P #0, chain S: 50S ribosomal protein L24P #0, chain T: 50S ribosomal protein L24E #0, chain U: HL21/HL22 #0, chain V: 50S ribosomal protein L30P #0, chain W: 50S ribosomal protein L31E #0, chain X: 50S ribosomal protein L32E #0, chain Y: HL5 #0, chain Z: 50S ribosomal protein L37E C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 0 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags Surface calculation failed, mscalc returned code 5.
Surface calculation frequently fails for large, multi-chain structures. The calculation may be successful if the chains are treated individually, by using the "split" command before generating a surface. If splitting is not desired or the structure is already a single chain, changing molecular surface parameters in the Selection Inspector or (before surface creation) the New Surfaces category of Preferences may allow the calculation to succeed.
C:\Program Files\Chimera 1.7s\bin\mscalc.exe 1.400000 2.000000 1 MSMSLIB 1.3 started on Local PC Copyright M.F. Sanner (March 2000) Compilation flags
Surface 3CPW.pdb, category ligand, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 989.35 Total solvent accessible surface area = 1473.85
In this case, I am not interested in splitting the file into its individual chains. I have also unsuccessfully played with the probe-radius and vertex parameters. I should mention that I was able to get this to work with previous versions of Chimera (1.5.something) and that small proteins can be successfully rendered with the latest versions.
best,
Antón
-- Antón Vila-Sanjurjo, PhD Marie Curie fellow Grupo QOSBIOS, Dept. Química Fundamental Facultade de Ciencias Universidade de A Coruña (UDC) Campus Zapateira, s/n 15.071 - A Coruña - España (Spain).
tlf: (34) 981-167000 ext:2659 e-mail: antonvila.s@gmail.com _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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