[Chimera-users] surface failures

Julian Marzi julian.marzi at googlemail.com
Tue Mar 11 08:25:33 PDT 2014


Dear Elaine Meng,

I tryed the surface option in different pdb files (also the 50S of E.coli) and always the same error (code 11- see attached). I also tried the different option of the webpage (Surface calculation failures and workaround).
I would like to have the surface structure of the chain 1 (25S of the yeast ribosome). Now I use the pdb file 3U5E and 3U5D. Please can you help me. Chimera is such a beautiful program and it always looks good, but in the most publication the surface structure is built up. 

Thank you

Best regards

Julian 





Am 06.03.2014 um 19:20 schrieb Elaine Meng <meng at cgl.ucsf.edu>:

> Dear Julian,
> The surface failure is a numerical thing that may differ on different machines, and there is not a consistent recipe for how to solve the problem.  Please see this page on possible solutions, including showing some alternative types of surface instead of a "molecular" surface:
> 
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/surfprobs.html>
> 
> 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 Mar 4, 2014, at 3:31 AM, Julian Marzi <julian.marzi at googlemail.com> wrote:
> 
>> Dear Chimera,
>> I try to show the surface of the 60S in yeast (PDB: 3O5H), but it doesn't work. Mscalc returned code 11 is shown. If I split the 60S every chain show the surface except the first strain (25S). How can I show the surface from the first chain?
>> Thank you very much
>> Best regards
>> Julian Marzi
> 

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