[Chimera-users] Failed surface calculation

Ibrahim Moustafa I.moustafa at psu.edu
Sat Jan 23 09:15:08 PST 2010

Thanks Elaine for your reply. But, in my case I set "show disjoint surfaces
to false".
Does your answer still apply?


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 at 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


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).


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 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

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