Re: [Chimera-users] surface display
Hi Markus, This is a problem with the surface calculation library MSMS used by Chimera. It crashes on specific PDB files. It is described more in this post: http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-February/000685.html which suggest you use Chimera command vdwdefine * * +0.01 to make the atom radii 1/100 Angstrom bigger which may circumvent the crash. Trying to surfce fewer residues generally does not fix the problem because Chimera still computes the whole surface and then just limits the display to the few residues you selected. Here is the Chimera bug report about this problem. http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl?cmd=view&pr=1295&database=chimer... Tom Markus Voehler wrote:
Tom
I have installed the new version and the same thing happens. Here is what I do: 1) open pdb (3003 atoms) 2) display round ribbon, hide atoms/bonds 3) action --> surface --> show also tried it on a smaller selection of a few residues.
I have submitted the chimera error report and have attached the crash report. Any ideas would be appreciated.
Markus
On Mar 9, 2007, at 1:43 PM, Tom Goddard wrote:
Hi Markus,
Is your problem with molecular surfaces (menu Actions / Surface / show) or contour surfaces of volume data?
In either case you should first try a newer version of Chimera. I recommend trying the snapshot 1.2352 released this week (scroll down the Chimera download page a little).
http://www.cgl.ucsf.edu/chimera/download.html
Tom
A few additional comments: 1) We _are_ working on a replacement library. Really. It's just has proven very tricky to get the geometry right in all cases. 2) Aside from changing the VDW radii, adding hydrogens to your structure (or deleting them if you have them already) may also do the trick. Tools->Structure Editing->AddH. That's also in the post that Tom references but he only mentioned the vdwdefine method. 3) In recent versions of Chimera, the vdwdefine syntax would be "vdwdefine +0.01" rather than "vdwdefine * * +0.01" 4) Once surfacing fails in an instance of Chimera, it won't work again no matter what you try. You have to quit and restart in order to try the "tricks". --Eric On Mar 9, 2007, at 12:39 PM, Tom Goddard wrote:
Hi Markus,
This is a problem with the surface calculation library MSMS used by Chimera. It crashes on specific PDB files. It is described more in this post:
http://www.cgl.ucsf.edu/pipermail/chimera-users/2006-February/ 000685.html
which suggest you use Chimera command
vdwdefine * * +0.01
to make the atom radii 1/100 Angstrom bigger which may circumvent the crash. Trying to surfce fewer residues generally does not fix the problem because Chimera still computes the whole surface and then just limits the display to the few residues you selected.
Here is the Chimera bug report about this problem.
http://www.cgl.ucsf.edu/cgi-bin/gnatsweb.pl? cmd=view&pr=1295&database=chimera
Tom
Markus Voehler wrote:
Tom
I have installed the new version and the same thing happens. Here is what I do: 1) open pdb (3003 atoms) 2) display round ribbon, hide atoms/bonds 3) action --> surface --> show also tried it on a smaller selection of a few residues.
I have submitted the chimera error report and have attached the crash report. Any ideas would be appreciated.
Markus
On Mar 9, 2007, at 1:43 PM, Tom Goddard wrote:
Hi Markus,
Is your problem with molecular surfaces (menu Actions / Surface / show) or contour surfaces of volume data?
In either case you should first try a newer version of Chimera. I recommend trying the snapshot 1.2352 released this week (scroll down the Chimera download page a little).
http://www.cgl.ucsf.edu/chimera/download.html
Tom
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (2)
-
Eric Pettersen -
Tom Goddard