[Chimera-users] chimera segmentation fault

[Eric Pettersen]

Yes, in fact if you get the current daily build then surfacing for  
1EP4 will work.  Chimera first tries disjoint surfacing (which fails)  
and then falls back to single-component surfacing (which works).  The  
first URL that Elaine supplied discusses how to force the production  
version of Chimera to use single-component surfacing for a structure.

--Eric

On Apr 1, 2008, at 3:22 PM, Elaine Meng wrote:

> 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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>
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