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@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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users