Hi Steve, This is a common problem reflecting the numerical failure of the MSMS code on some fraction of structures (it is in the "Known Bugs" section of the release notes). The MSMS code was developed elsewhere, and we are working on our own code to replace it, but it is not done yet. Sometimes you can avoid the numerical failure by changing something slightly, such as VDW radii, probe radius, and sometimes even just the orientation of the molecule, but it is unpredictable and different for every different structure as to what might work. Previous post with workaround suggestions: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html> The most recent post, mentions recent changes we made in Chimera to decrease the problem severity: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-August/ 002954.html> I hope this helps, 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 Sep 17, 2008, at 1:47 PM, steve field wrote:
Hello' I am trying to render a surface depiction on various fluorescent protein molecules. The program seems to work with some but not others. A code 5 error message displays. Any insight into what is causing this? PyMol is able to depict the surface from the same PDB file and Chimera works with other molecules, but not the one I need. Any thoughts would be appreciated. Thank you, steve field