[Chimera-users] single-component calculation

[Marhoefer, R (Richard)]

Dear Elaine,

I get the error most of the times when I run a surface calculation. However, in more than 99.9% of all cases I run so far the outer surface was ok. However, the popup window reporting the error caused me some trouble sometimes. When I try to record a movie the window sometimes pops in front of the chimera graphics window and is therefore also rendered into the movie, which does not look very nice ;-)

Is it possible to switch off the popup window? It would be sufficient for me if the error message would be written to the reply log.

I beg your pardon if you mentioned the answer in any of the previous posts you mentioned. I read through all of them but couldn't find a solution.

Mit freundlichen Grüßen / With kind regards
 
Dr. Richard Marhoefer
Senior Scientist BioChemInformatics
Intervet Innovation GmbH
Zur Propstei
55270 Schwabenheim, Germany
 
E-Mail: richard.marhoefer at sp.intervet.com
Phone:  +49 (6130) 948 204
Fax:    +49 (6130) 948 517
Mobile: +49175 723 081 4
Home    http://www.intervet.com
 
Sitz der Gesellschaft: Schwabenheim 	     Amtsgericht Mainz, HRB 23 166	  Geschäftsführer: Dr. Peter Schmid
 

> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: Mittwoch, 16. Dezember 2009 18:06
> To: Bala subramanian
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] single-component calculation
> 
> 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/00
3816.html>
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-Septembe
r/003096.html
>  >
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/00
2417.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
> >
> >
> > _______________________________________________
> > Chimera-users mailing list
> > Chimera-users at cgl.ucsf.edu
> > http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 
> 
> 
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