[Chimera-users] surface calculation

Francois Berenger berenger at riken.jp
Thu Nov 29 16:51:09 PST 2012


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/Chapter_main.html

> 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 at gmail.com
>> _______________________________________________
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>> Chimera-users at cgl.ucsf.edu
>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>
>
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