James- I think you need to seriously consider using software that's actually designed to compute and refine protein models, such as Modeller. There are forcefield and structural constraints that PyMol is just not designed to do, and your results may not have the scientific validity you require.
Jed Thomas Holder wrote: > Hi James, > > the modeling capabilities of PyMOL are rather limited, there are > probably more powerful tools for such tasks. > > Without guaranty that the result will be reasonable, try this: > > # lock all but the STG tripeptide > protect not pepseq STG > > # activate sculpting > sculpt_activate all > set sculpting > > # switch to edit mode > edit_mode > > Now drag atoms with the mouse or pick bonds and use commands like "torsion". > > Hope that helps. > > Cheers, > Thomas > > James Starlight wrote, On 01/26/12 13:45: >> Dear PyMol users! >> >> I'm looking for the possible way to change some backbone didedral values >> in my peptide and dont perturbe the secondary structure of the rest of >> the peptide. >> >> E.g I have alpha-helix with sequence xxxxx-S-T-G-xxxxx I want to >> make turn motif in the STG tripeptide only by changing dihedral of this >> amino acids. When I've tried make it by means of DYNOPLOT plugin the >> rest of the alpha helix was distorded. >> >> Is there any possible ways to make this conversion ? >> >> James > ------------------------------------------------------------------------------ Keep Your Developer Skills Current with LearnDevNow! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-d2d _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
