single-component calculation
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
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
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
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@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@cgl.ucsf.edu] Sent: Mittwoch, 16. Dezember 2009 18:06 To: Bala subramanian Cc: chimera-users@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
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Dear Richard, You can turn off warning dialogs in the preferences (Favorites... Preferences): in category "Messages" you can specify that warning messages be sent to the "reply log only." You can also do that for error messages, but I believe that this particular surface message is a warning. Remember to click Save if you want the setting to propagate to later uses of Chimera. It may be that we didn't discuss these preferences on the list before, at least in connection with surface calculations. Best, 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 17, 2009, at 12:00 AM, Marhoefer, R (Richard) wrote:
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
participants (3)
-
Bala subramanian -
Elaine Meng -
Marhoefer, R (Richard)