[Chimera-users] Issue with surface modelling using Chimera

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 5 16:52:12 PST 2009

Dear Leiah,
It is hard to tell without looking at your data file.  However, here  
is my best guess:  maybe your file has long "bonds" that shouldn't be  
there at all (maybe there should be TER lines in your file, or maybe  
it has incorrect CONECT lines).  When you show the surface it doesn't  
enclose the lines because there are no atoms there.  However, I can't  
get this to happen in Chimera in my tests, so maybe your file is  
incorrect in some way that makes it different from my missing segment  
test case 1www (taken from the PDB, so it has correct format).
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 5, 2009, at 2:03 PM, Leiah Luoma wrote:

> Hi there,
> I'm in the middle of using Chimera to analyze my protein model and  
> want to look at the predicted surface. I cannot get it to show the  
> whole surface: a few tracts of ribbon structure pepper the model.
> I selected all from the drop down menu, and waited until the whole  
> model was highlighted, and then set it to show surface.  When I  
> select the regions which are not showing up, and try to surface  
> model them individually, it does not work either.
> Is there any solution, or some reason why this would happen?  The  
> tracts are between 2 and 5 amino acids long.  Attached is an image  
> (jpg) of the problem I'm describing.
> Thanks for your help in advance,
> Leiah Luoma

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