hi all, typically when i import a paired back active site of a protein, chimera wants to connect atoms that should not be connected. is there a way to select bonds that violate a certain bond length so i can remove them? or a possible work around? thanks for your help. victor Victor A. Kenyon kenyon@chemistry.ucsc.edu 831.252.7667.
Hi Victor, Missing segments in structures are indicated with dotted lines (pseudobonds) that can be hidden with the command: ~longbond (show the command line by choosing Favorites... Command Line from the menu) http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/longbond.html That should take care of it. Another possible cause is when PDB files have ATOM lines that should be HETATM, but it sounds like missing segments are the reason here. 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 Feb 21, 2008, at 4:46 PM, Victor Kenyon wrote:
hi all, typically when i import a paired back active site of a protein, chimera wants to connect atoms that should not be connected. is there a way to select bonds that violate a certain bond length so i can remove them? or a possible work around? thanks for your help. victor
Victor A. Kenyon kenyon@chemistry.ucsc.edu 831.252.7667.
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Victor Kenyon