Hi Elaine, The problem does not happen all the time. Sometimes I can display surfaces from the pdbs that cause problems. However, after displaying surfaces from these files, running chimera (trying to rotate or move the molecules) becomes very slow. This is the error message I get when failing to display surfaces: 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. Thanks Hernando Elaine Meng wrote:
Hi Hernando, Well, lots of things related to surfaces have changed, but in general significantly reducing the failure rate from before - see "Surfaces" and "Major Bugs Fixed" in the release notes:
http://www.cgl.ucsf.edu/chimera/docs/relnotes/1.2540.html
There are also more messages than before, so perhaps the same errors occurred before but you didn't know about them. Sometimes the error is just in one component such as an interior bubble that you don't really care about. Is the surface that was displayed before not displayed now? Also, it is difficult to know what you mean without an example (you could just give a PDB ID) and your telling us exactly what error message you got.
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 14, 2008, at 11:56 AM, hsosa@aecom.yu.edu wrote:
Have something related to displaying surfaces changed in the last production release version of chimera ?.
I now get error messages when trying to display surfaces from some pdb files that used to work in the previous version.
-- ----------------------------------- Hernando Sosa Dept. of Physiology and Biophysics Albert Einstein College of Medicine 1300 Morris Park Av. Bronx NY 10461 phone (718) 430-3456 FAX (718) 430-8819 email hsosa@aecom.yu.edu -----------------------------------