[Chimera-users] code 5 error

Elaine Meng meng at cgl.ucsf.edu
Thu Sep 18 10:58:13 PDT 2008

Hi Steve,
This is a common problem reflecting the numerical failure of the MSMS  
code on some fraction of structures (it is in the "Known Bugs" section  
of the release notes).  The MSMS code was developed elsewhere, and we  
are working on our own code to replace it, but it is not done yet.   
Sometimes you can avoid the numerical failure by changing something  
slightly, such as VDW radii, probe radius, and sometimes even just the  
orientation of the molecule, but it is unpredictable and different for  
every different structure as to what might work.

Previous post with workaround suggestions:

The most recent post, mentions recent changes we made in Chimera to  
decrease the problem severity:

I hope this helps,
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 Sep 17, 2008, at 1:47 PM, steve field wrote:

> Hello'
> I am trying to render a surface depiction on various fluorescent  
> protein molecules. The program seems to work with some  but not  
> others. A code 5 error message displays. Any insight into what is  
> causing this? PyMol is  able to depict the surface from the same PDB  
> file and Chimera works with other molecules, but not the one I need.  
> Any thoughts would be appreciated.
> Thank you,
> steve field

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