[Chimera-users] surface calculation

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 29 11:26:03 PST 2012

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.

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.

(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.

I hope this helps,
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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