Hi Anna, That bug has actually been around since time immemorial -- we finally remembered to add it to the release notes. It is a behavior of the underlying MSMS library for certain particular geometries. We are working on a replacement library but it isn't ready yet. So there really isn't any version you can change to that won't have the problem. There are some workarounds. Because the problem depends on the exact geometry of the structure, changing that geometry only slightly will frequently allow surfacing to start working. So for example if your structure lack hydrogens, adding hydrogens (the AddH tool) will often allow the surface to work. Keep in mind that once surfacing fails, it won't work again in that same instance of Chimera -- you will have to quit and start Chimera again to try the workaround. Another way to slightly change the geometry is to modify the VDW radii slightly. Using the command line (Favorites->Command Line), the command "vdwdefine * * +0.01" will increase all vdw radii by 0.01 angstroms -- you could try other values also. Sorry we don't have a good solution yet. --Eric Eric Pettersen UCSF Computer Graphics Lab pett@cgl.ucsf.edu http://www.cgl.ucsf.edu On Feb 13, 2006, at 7:35 AM, Anna Feldman-Salit wrote:

Hello,

I have noticed that for 1.2199 version there is a "know bug" of surface failure. We have been working with 1.2176 version (which is probably even not release version). Apparently, I have the same problem with some of molecules (working with 1.2176). Is it occasionally or there is a "known bug" for 1.2176 too? Can you maybe recommend some version that has not such a problem?

Thank you in advance!

Sincerely,

Anna. _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users