[Chimera-users] Failed surface calculation

Elaine Meng meng at cgl.ucsf.edu
Sat Jan 23 12:03:19 PST 2010

Hi Ibrahim,
First, make sure you set the New Surfaces preference value before  
showing the surface for the first time -- it would not affect a  
surface that already exists (even if it is hidden when you set the  
preference).  If the surface already exists, you could change it to  
single-component by changing its attributes, such as with the command  
given in my previous message.

However, if the Reply Log says there is only one component of the  
surface in both sets of parameters, I think it is still possible for  
a surface area to decrease when the VDW radii increase.  I'm  
imagining a case where there is a lot of concavity.  Similar to the  
situation of an inside bubble shrinking or disappearing, a concave  
part of the surface could become shallower or much less extensive as  
the VDW radii are increased.

This is just a case I'm imagining.  If you feel there is an error,  
please use "Help... Report a Bug" in the Chimera menu and be sure to  
describe exactly what you did to get the two area measurements, what  
two values you are comparing, and attach the PDB file of the  
structure (or just include the PDB ID in your description if it is  
taken directly from the Protein Databank).
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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