Warren, Thanks for the quick reply!
> > Right now PyMOL has pretty limited connectivity detection > capabilities for "in-process" structures, which do not exhibit normal > bond lengths and atom separations. A workaround would be to passage > the structure through energy minimization (using an external tool) > before loading it into PyMOL (which will establish correct connectivity > for the object) and to then load the original in-process coordinates as > state 2 of the object. I don't think that the structure has abnormal atom distances. Is it just that the pdb file does not have HETATM or CONECT or other 'extras' ???? > > Alternatively, is there any way you could use HETATM records (instead > of ATOM) and include explicit CONECT records? I think this would solve the problem. I tried to search for a program/script that would do this and didn't find one. Seems like there should be many of these. Again, I am sorry for taking up your time on this simple problem but I want to use PyMol and I have been struggling with this for a week now. Cheers, Holly -- ____________________________________________________________________________ Holly Miller, Ph.D. voice: 631 444-8018 Res. Asst. Prof. FAX: 631 444-7641 Dept. Pharm. Sci. http://www.pharm.sunysb.edu/faculty/miller/ SUNY Stony Brook mil...@pharm.sunysb.edu Stony Brook, NY 11794-8651 **************************************************************************** Biomail--New references from Medline to your e-mail account http://www.biomail.org ___________________________________________________________________________
