[Chimera-users] Surfaces

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 15 10:40:18 PDT 2008

Hi Hernando, Dave, et al.
Those messages are common and expected.  Although the error messages  
themselves are new, the success rate in surface calculation is  
actually improved from previous versions.

Surface calculation failures in MSMS on some proportion of structures  
are a known and long-standing problem, possibly the most commonly  
reported problem.  We have been working for some time to write our  
own code to replace MSMS, but it is not yet ready for public  

Changes in this most recent release separated the MSMS part from the  
rest of Chimera (so it wouldn't crash Chimera), fixed at least one  
bug in the MSMS library, and increased messages and fallback  
procedures.  In our tests this significantly decreased failures,  
prevented crashes, and allowed calculation of some components when  
some other components failed.  By components I mean disconnected  
blobs or pieces.  Now I frequently see those messages but still get  
the desired main/outer surface, whereas the component that failed was  
a small internal cavity.  There will still be instances of complete  
MSMS failures, where you do not get any surface, but in our tests  
much fewer than before.
> see "Surfaces" and "Major Bugs Fixed" in the release notes:
> http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html

MSMS will still fail on some structures, and we are still working on  
replacement code.

I cannot easily explain cases of where you get a surface successfully  
in the old version but not the new, but it is a numerical failure and  
it is possible if anything about the computing environment changed  
(sometimes even the position of the molecule!).  The error messages  
are new, however, so might be alerting you to failures on minor  
components (small internal bubbles) that you might have been  
blissfully unaware of in earlier versions.

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 Aug 15, 2008, at 9:28 AM, David Konerding wrote:
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 1
> Calculation of some surface components failed (code 5).
> Falling back to single-component calculation.
> C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0
> Surface calculation failed, mscalc returned code 5
> Two pdb files that I've been having problems with are 1JFF and 2P4N.
> I see this error frequently myself - for example, 1ffk on Windows  
> XP with Chimera
> build 2450.
> Dave

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