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