Praedor, The sculpting capability in PyMOL is only intended and/or useful for handling conformational changes when starting from valid 3D geometries.
If you are forming bonds or building molecules from scratch, then you'll need to use an external tool like OpenEye's Szybki or Schrodinger's MacroModel in order to get a valid starting model. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:[email protected] > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of > Praedor Atrebates > Sent: Thursday, May 04, 2006 9:25 AM > To: [email protected] > Subject: [PyMOL] Correcting protiein models > > I have produced several threading models of a protein (the > app threader 3.5 can output pdb format models) I am studying. > The models are OK for the most part but there are often odd > gaps in which the peptide backbone has simply been "broken" > and the ends separated by some distance - but they should be > connected. > > I have been playing around with the sculpting function of > pymol 0.99 for the first time and have managed to get peptide > bonds created between the separated fragments but the problem > is that the bonds are inordinately long. > I have tried, after forming the bond, to move the CA and N > atoms closer together to produce a more realistic bond length > but it seems that pymol wants the initial bond length to > remain what it was when formed. In another case, a very > short peptide fragment that should have connected the end of > one beta strand to the beginning of another was displaced and > separate at an odd location, and inverted. I made peptide > bonds where they should be and have been trying to maneuver > the loop into a reasonable position but pymol is fighting me > on this. Is there a way to get pymol to enforce proper bond > lengths once you form them? > > praedor > -- > The Reichstag fire is to Hitler as 9/11 is to Bush >
