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 consumption. 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. Best, Elaine ----- Elaine C. Meng, Ph.D. meng@cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html 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