[Chimera-users] (no subject)

Eric Pettersen pett at cgl.ucsf.edu
Thu Mar 5 16:51:02 PST 2009

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:


	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 Pettersen
                         UCSF Computer Graphics Lab

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.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 at 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 at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20090305/38bffd84/attachment.html>

More information about the Chimera-users mailing list