Hi Markus, I computed a molecular surface for the PDB file you gave me by changing the probe radius from 1.4 A to 1.399 A. I set the new probe radius using the "New Surface" category of the Preferences dialog (menu Favorites / Preferences). The "New Surface" category was added in Chimera 1.2430 (July 23, 2007) so you'll need the newest Chimera snapshot on Linux http://www.cgl.ucsf.edu/chimera/download.html#snapshots or a weekly Chimera build (very latest code) on other platforms (Mac, Windows) http://www.cgl.ucsf.edu/chimera/alpha-downloads.html New Chimera surface calculation code is still 6 months away. Tom Markus Voehler wrote:
Tom
I have switched from my SGI to a RHEL 5 machine and see the same behavior now on that computer as I have seen on the Mac. Some pdb files do not seem to allow me to show the surface plot. This leaves me with no option to display the surface for some pdb's. In the past I was just doing this work on the SGI, which worked fine. I have tried your suggestion about increasing the vdv radius again on the Linux box, but it did not help either on this computer. Has there been any resolution to the mentioned report 1295?
I have deposited the pdb online, in case you want to reproduce the problem on your cpu. The link is:
[deleted]
Any help is appreciated.
Markus