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From: Thomas H. <tho...@sc...> - 2013-06-14 10:48:18
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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 |