[Chimera-users] surface calculation

Conrad Huang conrad at cgl.ucsf.edu
Fri Nov 30 09:34:43 PST 2012


I believe the CGAL 3D triangulation and alpha shapes licenses are GPL 
and we want an LGPL package for inclusion with Chimera.

Conrad

On 11/29/2012 4:51 PM, Francois Berenger wrote:
> 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
>>> _______________________________________________
>>> Chimera-users mailing list
>>> Chimera-users at cgl.ucsf.edu
>>> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>>
>>
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