[Chimera-users] (no subject)

[Elaine Meng]

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
>
>