Re: [PyMOL] Distorted secondary structure using 'alter' command

[Thomas H. <tho...@sc...>]

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