[Chimera-users] surface display

Tom Goddard goddard at cgl.ucsf.edu
Fri Mar 9 12:39:46 PST 2007

Hi Markus,

  This is a problem with the surface calculation library MSMS used by 
Chimera.  It crashes on specific PDB files.  It is described more in 
this post:


which suggest you use Chimera command

    vdwdefine * * +0.01

to make the atom radii 1/100 Angstrom bigger which may circumvent the 
crash. Trying to surfce fewer residues generally does not fix the 
problem because Chimera still computes the whole surface and then just 
limits the display to the few residues you selected.

  Here is the Chimera bug report about this problem.



Markus Voehler wrote:
> Tom
> I have installed the new version and the same thing happens. Here is 
> what I do:
> 1) open pdb (3003 atoms)
> 2) display round ribbon, hide atoms/bonds
> 3) action --> surface --> show also tried it on a smaller selection of 
> a few residues.
> I have submitted the chimera error report and have attached the crash 
> report. Any ideas would be appreciated.
> Markus
> On Mar 9, 2007, at 1:43 PM, Tom Goddard wrote:
>> Hi Markus,
>>  Is your problem with molecular surfaces (menu Actions / Surface / 
>> show) or contour surfaces of volume data?
>>  In either case you should first try a newer version of Chimera.  I 
>> recommend trying the snapshot 1.2352 released this week (scroll down 
>> the Chimera download page a little).
>>  http://www.cgl.ucsf.edu/chimera/download.html
>>    Tom

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