Re: [PyMOL] Loading non-standard PDB file
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 [email protected] Stony Brook, NY 11794-8651 Biomail--New references from Medline to your e-mail account http://www.biomail.org ___
RE: [PyMOL] Loading non-standard PDB file
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:[email protected] 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:[email protected]] > 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 [email protected] > Stony Brook, NY 11794-8651 > > ** > ** > > Biomail--New references from Medline to your > e-mail account > > http://www.biomail.org > __ > _ > > > > > ___ > PyMOL-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/pymol-users >
[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 [email protected] Stony Brook, NY 11794-8651 Biomail--New references from Medline to your e-mail account http://www.biomail.org ___
