Re: [PyMOL] trying to build cyclic peptides with PyMOL

[<gol...@fh...>]

I need to build a cyclic peptide as the initial conformation for  
further simulations, not only for displaying purposes.
I will try what you say and I will see.

Thank you.
-- Moshe Goldstein

Quoting Tsjerk Wassenaar <ts...@gm...>:

> Hi Moshe,
>
> No it isn't. PyMOL is a molecular viewer/graphics engine, not a
> modeling package. However, it's not too hard to do using your
> favourite MD package. With the definition of a bond and some energy
> minimization you'd get close. If it's for displaying purposes only,
> that might even be enough.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Feb 15, 2008 at 1:17 AM,  <gol...@fh...> wrote:
>>
>>  Hello.
>>
>>  I am new to PyMOL.
>>  Very easily I succeeded to build a linear peptide, given its sequence.
>>  I want to build a cyclic peptide for the same sequence, connecting the
>>  C-terminus with the N-terminus. I know that the bond that is created
>>  that way is too long - it should be, also, some
>>  (automatic/algorithmic) way to rearrange the cyclic structure in order
>>  to have an acceptable bond length.
>>  Is this possible to do with PyMOL?
>>
>>  Thanks for your help.
>>  -- Moshe Goldstein
>>
>>
>>
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
>



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