Dear Sean, Unfortunately it is a very common problem relating to numerical failure of the MSMS code on certain structures, and is listed in our known bugs. We have been working on our own code to replace MSMS, but it is not available yet. There are many possible things to try to avoid the problem, but it is very trial-and-error and different for each structure. It is helpful when reporting a problem to say what version of Chimera you are using, since there have been some improvements throughout time (although not eliminating the problem completely). It might help to get a newer version of Chimera, or it might not. Please see these previous posts for more information and workaround suggestions: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.html

http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html <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 Mar 5, 2009, at 2:08 PM, Du, Sean wrote:

Dear Chimera developers and sophisticated users,

I have trouble to show the surfaces of serveral crystal structures, including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would get pop-up error window and the following message in my Reply Log:

C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5

Since I don't have problem with other pdb files, such as 3dnn, I wonder if this problem is simply associated with some particular pdb files? If anyone out there knows a few tricks to overcome this, I'd really appreciate it.

Many thanks in advance,

Sean

Elaine and Eric Thanks very much for such a quick response. To Elaine, the version I was using should be pretty recent. I downloaded about a month ago. To Eric, you suggestion to split/surf worked out beautifully. I haven't done anything with these surfaces yet, but I will let you know if I encounter any new problems. Cheers! Sean ________________________________ From: Eric Pettersen [mailto:pett@cgl.ucsf.edu] Sent: Thursday, March 05, 2009 4:51 PM To: Du, Sean Cc: chimera-users@cgl.ucsf.edu BB Subject: Re: [Chimera-users] (no subject) Hi Sean, I find that these structures surface on my Mac, but do fail on the Windows machine I tried. There is a workaround I recently found that isn't mentioned in the messages Elaine listed and that is to split the model into separate models on a per-chain basis and then surface those models. This works for both the structures your mentioned, but of course might be awkward to work with depending on what you intend to do after surfacing. Anyway, to do the splitting/surfacing open the command line (Favorites->Command Line) and type: split surf We intend to replace our current surfacing library (MSMS) with our own custom library in our next release, but that won't be until the middle of this year. --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu On Mar 5, 2009, at 4:34 PM, Elaine Meng wrote: Dear Sean, Unfortunately it is a very common problem relating to numerical failure of the MSMS code on certain structures, and is listed in our known bugs. We have been working on our own code to replace MSMS, but it is not available yet. There are many possible things to try to avoid the problem, but it is very trial-and-error and different for each structure. It is helpful when reporting a problem to say what version of Chimera you are using, since there have been some improvements throughout time (although not eliminating the problem completely). It might help to get a newer version of Chimera, or it might not. Please see these previous posts for more information and workaround suggestions: <http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-September/003096.h tml http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html <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 Mar 5, 2009, at 2:08 PM, Du, Sean wrote: Dear Chimera developers and sophisticated users, I have trouble to show the surfaces of serveral crystal structures, including 1rzk and 2b4c. Whenever I select: Action/Surface/Show, I would get pop-up error window and the following message in my Reply Log: C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 C:\Program Files\Chimera\bin\mscalc.exe 1.400000 2.000000 0 Surface calculation failed, mscalc returned code 5 Since I don't have problem with other pdb files, such as 3dnn, I wonder if this problem is simply associated with some particular pdb files? If anyone out there knows a few tricks to overcome this, I'd really appreciate it. Many thanks in advance, Sean _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users This email message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any review, use, disclosure or distribution of this email (or any attachment thereto) by others is prohibited. If you are not the intended recipient, please contact the sender immediately by reply email and destroy all copies of the original message and any attachments thereto.