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.


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

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