[Chimera-users] chimera segmentation fault

[Elaine Meng]

Hello,
Chimera uses MSMS for surface calculations, and it is a known problem  
(very frequently reported!) that MSMS fails on many structures.   
These recent posts discuss possible ways to avoid the problem:

http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002417.html
http://www.cgl.ucsf.edu/pipermail/chimera-users/2008-March/002418.html

We are working very hard to write a new surface module that will  
replace MSMS.  In the meanwhile, in the most recent versions of  
Chimera (if you get a daily build) the surface calculation has been  
better separated from the rest of Chimera so that it will not crash  
Chimera.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html




On Mar 31, 2008, at 10:28 AM, Selami ERCAN wrote:
> hi. i'm using chimera-1.2470-linux_x86_64.exe on suse 10.3. in  
> addition
> to this my graphic card is nvidia geforce 8600m gt 512 mb and also i
> have installed mesa and xorg softwares.
> and here is problem: using 1EP4.pdb from rcsb.org causes
> problem.whenever i select structure-->main, then action-->surface-- 
> >show
> it crashes. and it gives the report shown below.
>
> Copyright M.F. Sanner (March 2000)
> Compilation flags
> WARNING: class_arete2: warning hole in a reentrant face 17081
> WARNING: class_arete2: warning hole in a reentrant face 22603
> WARNING: classe_aretes1: No cycle in face 25771 (nba=-4)
>
> WARNING: classe_aretes1: No cycle in face 25772 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25774 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25776 (nba=-3)
>
> WARNING: classe_aretes1: No cycle in face 25779 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25781 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25783 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25785 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25787 (nba=-1)
>
> WARNING: classe_aretes1: No cycle in face 25789 (nba=-1)
>
> RESTART FROM SES: 1
> radius of atom 2855 goes from 1.760000 to 1.860000
> radius of atom 2857 goes from 1.640000 to 1.740000
> radius of atom 2858 goes from 1.760000 to 1.860000
> radius of atom 2871 goes from 1.880000 to 1.980000
> radius of atom 6942 goes from 1.880000 to 1.980000
> radius of atom 6945 goes from 1.760000 to 1.860000
> radius of atom 6946 goes from 1.760000 to 1.860000
> radius of atom 6947 goes from 1.760000 to 1.860000
> radius of atom 6948 goes from 1.760000 to 1.860000
> radius of atom 6987 goes from 1.460000 to 1.560000
> radius of atom 6988 goes from 1.760000 to 1.860000
> Partial mode
> Segmentation fault
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