[Chimera-users] single-component calculation
Marhoefer, R (Richard)
richard.marhoefer at sp.intervet.com
Thu Dec 17 00:00:25 PST 2009
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
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
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:
> 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 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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