Holly, 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.
Alternatively, is there any way you could use HETATM records (instead of ATOM) and include explicit CONECT records? Before too long, PyMOL will have pattern-based connectivity determination for normal PDB residues. Cheers, Warren -- mailto:war...@sunesis.com Warren L. DeLano, Ph.D. Informatics Manager Sunesis Pharmaceuticals, Inc. 341 Oyster Point Blvd. S. San Francisco, CA 94080 (650)-266-3606 FAX:(650)-266-3501 > -----Original Message----- > From: Holly Miller [mailto:mil...@pharm.sunysb.edu] > Sent: Friday, March 08, 2002 10:57 AM > To: PyMol Users > Subject: [PyMOL] Loading non-standard PDB file > > > Hi! > > I am a new PyMol user. I want to look at an 'in progress' > structure from > a collaborator. When I load the pdb into PyMol there are bonds between > atoms that shouldn't be bonded. This is mostly (if not only) in the > bound DNA part of the structure. Is it possible to change the > parameters > by which the bonds are automatically calculated (if this is how it > works) or some other way to fix this, other than clicking on > each wrong > bond and deleting it (there are many). > > I apologize for asking such a simple question. > > Thank you, > 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 > ______________________________________________________________ > _____________ > > > > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
