Failed surface calculation
Dear Chimera, I¹m trying to calculate the surface for a protein but I get an error ²Surface calculation failed, mscalc returned code 5². I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I¹m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don¹t have this problem. I¹m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim
Dear Ibrahim, This is common and represents a numerical failure of the MSMS code included with Chimera for calculating molecular surfaces. The first thing to do is make sure you have a fairly recent version of Chimera, say 1.4 from Dec 2009 or newer. Although we have not eliminated the failures, we have made some improvements that reduce their frequency. Sometimes when there is an error, it can still fall back to a "single component" calculation. The problem may be in some inside bubble, whereas the "single component" is the main outer surface. If that's what happened, but it still looks like you got the surface you want, you can ignore the message. If you didn't get any surface, however, there are several things to try, as mentioned in several previous posts (links below). Unfortunately none is a magic bullet that works in all situations. <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> Because of the MSMS problems, we have been working for many months on code to replace it, but it is not yet available. 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 Jan 22, 2010, at 4:10 PM, Ibrahim Moustafa wrote:
Dear Chimera, I’m trying to calculate the surface for a protein but I get an error ”Surface calculation failed, mscalc returned code 5”. I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I’m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don’t have this problem. I’m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim
Thanks Elaine for the reply. The trick of changing the vdw radius (vdwdef +0.05) worked; then I got the default back by "~vdwdef". I'm not sure whether this affect the accuracy of the calculation. Because, I noticed by increasing the vdw radius by "+0.05" the value of the volume got increased from 111.0e3 to 113.6e3 (2.3%), which is expected. However, the measured area decreased from 36.73e3 to 36.2e3, which does not make sense to me (please correct me if I am missing something here). Do you have any comment?! Thanks, Ibrahim On 1/22/10 7:32 PM, "Elaine Meng" <meng@cgl.ucsf.edu> wrote:
Dear Ibrahim, This is common and represents a numerical failure of the MSMS code included with Chimera for calculating molecular surfaces.
The first thing to do is make sure you have a fairly recent version of Chimera, say 1.4 from Dec 2009 or newer. Although we have not eliminated the failures, we have made some improvements that reduce their frequency.
Sometimes when there is an error, it can still fall back to a "single component" calculation. The problem may be in some inside bubble, whereas the "single component" is the main outer surface. If that's what happened, but it still looks like you got the surface you want, you can ignore the message.
If you didn't get any surface, however, there are several things to try, as mentioned in several previous posts (links below). Unfortunately none is a magic bullet that works in all situations.
<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>
Because of the MSMS problems, we have been working for many months on code to replace it, but it is not yet available.
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 Jan 22, 2010, at 4:10 PM, Ibrahim Moustafa wrote:
Dear Chimera, I¹m trying to calculate the surface for a protein but I get an error ²Surface calculation failed, mscalc returned code 5². I tried to change the probe size from 1.4 to 1.5 or 1.7 but still getting the same error. I know there is some issue with The code that calculates the surface (if I¹m not wrong) but I wonder if there is a way to get around this. For some smaller pdb files I don¹t have this problem. I¹m not sure if the size of the protein is a factor here. The protein having the problem is a single chain protein with 880 amino acids. Any advice? Thanks for help. Ibrahim
Hi Ibrahim, Wow, I'm surprised that it worked after the radii were decreased back to the default! But anyway, yes, it could make sense for the *total* surface area to get smaller when radii are larger, because the increase in radii could make interior bubbles shrink or even disappear. For example, with structure 1zik with default settings, there are two surface components, the one around the outside and one inside bubble. If I increase all radii by 0.05, the inside bubble goes away and there is only one surface component, and the total solvent-excluded surface area decreases. Here is the info from the reply log for 1zik with default and then increased radii: [...] Surface 1zik, category main, probe radius 1.4, vertex density 2 2 connected surface components Total solvent excluded surface area = 3701.55 component areas = 3668.52, 33.0338 Total solvent accessible surface area = 4639.4 component areas = 4639.21, 0.19492 [...] Surface 1zik, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 3683.55 Total solvent accessible surface area = 4648.53 If you don't want any inside bubbles in an existing surface, you can use the command: setattr s allComponents false <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> and for surfaces to be created in the future, you can specify that in the Preferences, category New Surfaces, by setting "show disjoint surfaces" to false (remember to click Save if you want it to apply to later uses of Chimera). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Surfaces> 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 Jan 22, 2010, at 5:44 PM, Ibrahim Moustafa wrote:
Thanks Elaine for the reply. The trick of changing the vdw radius (vdwdef +0.05) worked; then I got the default back by "~vdwdef". I'm not sure whether this affect the accuracy of the calculation. Because, I noticed by increasing the vdw radius by "+0.05" the value of the volume got increased from 111.0e3 to 113.6e3 (2.3%), which is expected. However, the measured area decreased from 36.73e3 to 36.2e3, which does not make sense to me (please correct me if I am missing something here). Do you have any comment?! Thanks, Ibrahim
Thanks Elaine for your reply. But, in my case I set "show disjoint surfaces to false". Does your answer still apply? Thanks, Ibrahim ---------------------------------------------------------------------------- ---------------------------------------------- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927 -----Original Message----- From: Elaine Meng [mailto:meng@cgl.ucsf.edu] Sent: Friday, January 22, 2010 10:20 PM To: Ibrahim Moustafa Cc: UCSF Chimera Mailing List Subject: Re: [Chimera-users] Failed surface calculation Hi Ibrahim, Wow, I'm surprised that it worked after the radii were decreased back to the default! But anyway, yes, it could make sense for the *total* surface area to get smaller when radii are larger, because the increase in radii could make interior bubbles shrink or even disappear. For example, with structure 1zik with default settings, there are two surface components, the one around the outside and one inside bubble. If I increase all radii by 0.05, the inside bubble goes away and there is only one surface component, and the total solvent-excluded surface area decreases. Here is the info from the reply log for 1zik with default and then increased radii: [...] Surface 1zik, category main, probe radius 1.4, vertex density 2 2 connected surface components Total solvent excluded surface area = 3701.55 component areas = 3668.52, 33.0338 Total solvent accessible surface area = 4639.4 component areas = 4639.21, 0.19492 [...] Surface 1zik, category main, probe radius 1.4, vertex density 2 1 connected surface components Total solvent excluded surface area = 3683.55 Total solvent accessible surface area = 4648.53 If you don't want any inside bubbles in an existing surface, you can use the command: setattr s allComponents false <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html> and for surfaces to be created in the future, you can specify that in the Preferences, category New Surfaces, by setting "show disjoint surfaces" to false (remember to click Save if you want it to apply to later uses of Chimera). <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New% 20Surfaces> 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 Jan 22, 2010, at 5:44 PM, Ibrahim Moustafa wrote:
Thanks Elaine for the reply. The trick of changing the vdw radius (vdwdef +0.05) worked; then I got the default back by "~vdwdef". I'm not sure whether this affect the accuracy of the calculation. Because, I noticed by increasing the vdw radius by "+0.05" the value of the volume got increased from 111.0e3 to 113.6e3 (2.3%), which is expected. However, the measured area decreased from 36.73e3 to 36.2e3, which does not make sense to me (please correct me if I am missing something here). Do you have any comment?! Thanks, Ibrahim
participants (2)
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Elaine Meng -
Ibrahim Moustafa