[Chimera-users] Molecular surface crash

Thomas Goddard goddard at cgl.ucsf.edu
Thu Sep 13 15:42:09 PDT 2007

Hi Markus,

   I computed a molecular surface for the PDB file you gave me by 
changing the probe radius from 1.4 A to 1.399 A.  I set the new probe 
radius using the "New Surface" category of the Preferences dialog (menu 
Favorites / Preferences).  The "New Surface" category was added in 
Chimera 1.2430 (July 23, 2007) so you'll need the newest Chimera 
snapshot on Linux


or a weekly Chimera build (very latest code) on other platforms (Mac, 


   New Chimera surface calculation code is still 6 months away.


Markus Voehler wrote:
> Tom
> I have switched from my SGI to a RHEL 5 machine and see the same 
> behavior now on that computer as I have seen on the Mac. Some pdb files 
> do not seem to allow me to show the surface plot. This leaves me with no 
> option to display the surface for some pdb's. In the past I was just 
> doing this work on the SGI, which worked fine. I have tried your 
> suggestion about increasing the vdv radius again on the Linux box, but 
> it did not help either on this computer. Has there been any resolution 
> to the mentioned report 1295?
> I have deposited the pdb online, in case you want to reproduce the 
> problem on your cpu. The link is:
> [deleted]
> Any help is appreciated.
> Markus

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