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@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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