[Chimera-users] surface calculation

Francois Berenger berenger at riken.jp
Sun Dec 2 17:31:49 PST 2012


On 12/01/2012 02:34 AM, Conrad Huang wrote:
> I believe the CGAL 3D triangulation and alpha shapes licenses are GPL
> and we want an LGPL package for inclusion with Chimera.

It is also possible to buy a commercial license:
http://www.cgal.org/license.html

> 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
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>>>
>>>
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>>
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