[Chimera-users] single-component calculation

[Elaine Meng]

Hi Bala,
This is fairly common and represents a numerical failure of the MSMS  
code included with Chimera for calculating molecular surfaces.   
However, it is usually some inside bubble that causes the failure --  
the "single component" is the main outer surface, and if that is what  
you wanted to show anyway, and you can see it in Chimera, you can just  
ignore the message.

Where it might have an effect is surface area calculations (now you  
only have the outside surface and not the bubbles).  Also, in some  
cases the single component might fail too and you wouldn't have any  
surface shown.

Because of the MSMS problems, we have been working for many months on  
code to replace it, but that is not yet available.  In the meanwhile,  
if surface calculation failures are blocking your work, there are  
several previous posts on possible ways to avoid them:

<http://www.cgl.ucsf.edu/pipermail/chimera-users/2009-April/003816.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html 
 >
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html>
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/ 
002954.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 Dec 15, 2009, at 10:00 PM, Bala subramanian wrote:

> Friends,
> When i try to show the surface sometimes, i get a chimera warning  
> that ' calculation of some surface components failed, falling back  
> to single component calculation'.
> The message in reply log is as follows. Kindly enlighten me on what  
> is causing the problem.
>
> Calculation of some surface components failed.
> Falling back to single-component calculation.
> /home/cbala/chimera/bin/mscalc 1.400000 2.000000 0
> MSMSLIB 1.3 started on RAMANA
> Copyright M.F. Sanner (March 2000)
> Compilation flags
> WARNING: check_SES_edge: weird case, 1 probe full1 and not full2
> WARNING: class_arete2: warning hole in a reentrant face 2119
> WARNING: classe_aretes2: No cycle in face 3781 (nba=-6)
>
> WARNING: classe_aretes2: No cycle in face 11830 (nba=-4)
>
> WARNING: classe_aretes2: No cycle in face 19652 (nba=4)
>
> WARNING: classe_aretes2: No cycle in face 19653 (nba=-1)
>
> WARNING: classe_aretes2: No cycle in face 19663 (nba=-3)
>
> RESTART FROM SES: 1
> radius of atom 1220 goes from 1.625000 to 1.725000
> radius of atom 1221 goes from 1.000000 to 1.100000
> radius of atom 1665 goes from 1.700000 to 1.800000
> radius of atom 1666 goes from 1.000000 to 1.100000
> radius of atom 3490 goes from 1.500000 to 1.600000
> radius of atom 3618 goes from 1.000000 to 1.100000
> radius of atom 3620 goes from 1.500000 to 1.600000
> radius of atom 3621 goes from 1.000000 to 1.100000
> radius of atom 5103 goes from 1.625000 to 1.725000
> radius of atom 5106 goes from 1.000000 to 1.100000
> Partial mode
> WARNING: class_arete2: warning hole in a reentrant face 2119
> RESTART FROM TRI: 2
> radius of atom 470 goes from 1.700000 to 1.800000
> radius of atom 4231 goes from 1.700000 to 1.800000
> radius of atom 4250 goes from 1.480000 to 1.580000
> Partial mode
>
> Surface black.pdb, category main, probe radius 1.4, vertex density 2
>   1 connected surface components
>   Total solvent excluded surface area = 16352.1
>   Total solvent accessible surface area = 17959.3
>
>
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