On 13:58 Mon 04 May , Robert Campbell wrote:
> Hi Donnie,
>
> On Mon, 04 May 2009 10:31:33 -0700, Donnie Berkholz
> <[log in to unmask]> wrote:
>
> > I'd like to build a theoretical N-residue peptide manually by setting
> > each torsion angle and building in poly-Ala. Can Coot do this, and if
> > so, how do I do it? If not, any suggestions for other programs?
>
> I have a PyMOL script that will allow you to build a peptide of arbitrary
> sequence with specified phi/psi angles for each amino acid using a file as
> input. See build_seq_phi_psi.py at:
>
> http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/
>
> It also calls another python script of mine for converting sequence formats
> http://pldserver1.biochem.queensu.ca/~rlc/work/scripts/seq_convert.py
> but the simple function in there could have been included directly in the
> first script.
>
> There is another one on the PyMOL Wiki:
> http://pymolwiki.org/index.php/CreateSecondaryStructure
Thanks, Rob!
I've come across a web-based application called PepBuild that I'm using
for the moment because I only need a few right now, so manual creation
is fine. I'll give this a shot later on because I'm thinking about some
more automated testing.
--
Thanks,
Donnie
Donnie Berkholz
P. Andrew Karplus lab
Oregon State University
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