Hi Ritu, do I understand correctly that resi 3-9 are *not* in helix conformation, and you want to perform a modelling task? Altering the ss property is not sufficient, that's just an annotation and not a modelling constraint. PyMOL is primarily a visualization tool and less a modelling tool, although you have some options here. Have a look at this PyMOLWiki script:
http://pymolwiki.org/index.php/Set_phipsi And this page: http://pymolwiki.org/index.php/Modeling_and_Editing_Structures Hope that helps. Cheers, Thomas Rituparna Sengupta wrote, On 06/13/13 19:30: > Hi All, > > I'm trying to change a stretch of a polypeptide chain (residues 3-9) into a > helix. I use the alter command: > > alter 3-9/, ss='H' > > But when I try to see the updated structure in cartoon, the structure doesn't > appear like a helix. It looks like a distorted helix. How do I correct it? > > Thanks, > Ritu -- Thomas Holder PyMOL Developer Schrödinger Contractor ------------------------------------------------------------------------------ This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev _______________________________________________ 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
