[Chimera-users] segmentation fault - surface rendering

Eric Pettersen pett at cgl.ucsf.edu
Thu Mar 13 15:47:51 PDT 2008

One further caveat is that once surfacing fails in Chimera it won't  
work again in that Chimera -- you'll have to restart to try the  


                         Eric Pettersen
                         UCSF Computer Graphics Lab

On Mar 13, 2008, at 3:43 PM, Elaine Meng wrote:

> Hi Mike,
> Rather than a memory issue, it is likely a failure of the surface
> calculation.  Chimera uses MSMS for surface calculations, and we (and
> many bug reporters) have noted that it fails on a significant
> proportion of structures.  The developers have been working very hard
> to write code to replace MSMS, but it is not yet available.
> The MSMS problems appear to be numerical instabilities sensitive to
> small changes in atomic radii, coordinates, surface vertex positions,
> and sometimes even the orientation of the molecule.  Thus for each
> structure you can generally experiment and find some change(s) that
> will allow successful surface calculation.  Unfortunately, there is
> no fix that necessarily works for all of the problem structures, and
> no way to tell beforehand which adjustment will be successful for a
> given structure!
> If the surface calculation is failing, here are a few things to try:
> (1) increase all atomic radii by some small amount, for example with
> the command:
> vdwdefine +0.01
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html
> (2) change surface calculation parameters in the "New Surfaces"
> preferences (Favorites... Preferences, change to "New Surfaces"
> category).  For example, in one recent case, it was necessary to
> increase the probe radius to 1.5 and set "show disjoint surfaces" to
> false.  Remember to click Save if you want the settings to apply to
> your next use of Chimera.
> http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/preferences.html#New%
> 20Surfaces
> (3) add hydrogens  (Tools... Structure Editing... AddH) or command
> "addh" - I prefer (1) or (2), however, as adding hydrogens will make
> the surface bumpier
> I don't know if you are calculating surfaces in some high-throughput
> fashion or concentrating on a few structures.  If the latter and you
> are having trouble finding a tweak that will allow surface
> calculation, I could take a look at the structure for you (let me
> know the pdb ID, if any, or send the structure).
> I also don't know why splitting up your structure into multiple files
> might help, unless opening parts of the structure separately changed
> the surface geometry by making the surface enclose the individual
> parts rather than the entire thing  (that can also be controlled with
> the "surfcat" command rather than splitting the file).
> Sorry for the difficulties.  We are all looking forward to the new
> surface calculation code!
> Elaine
> -----
> Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
> UCSF Computer Graphics Lab and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>                       http://www.cgl.ucsf.edu/home/meng/index.html
> On Mar 13, 2008, at 11:37 AM, Michael DiMattia wrote:
>> Hello, I am trying to surface render a few different proteins
>> within the same Chimera session and I keep encountering a
>> segmentation faullt.  I imagine this is due to a memory limit being
>> reached, although I do not know if it is a Chimera parameter that
>> can be increased/overriden.  Instead of having the different
>> macromolecules in the same pdb, I have actually split it up into
>> many pdbs and opened them one at a time, surface rendering one at a
>> time.  This worked for awhile but it seems I can't even get that
>> far now.
>> Any advice or tips on what I can do?
>> I realize surface rendering is very computationally intensive but I
>> would love to get this to work!
>> Thanks
>> Mike DiMattia
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