Re: [PyMOL] Set values for dihedral angles

[James S. <jms...@gm...>]

Dear Thomas, Jed!

Firstly, thanks for the advise in further days I'll try Modeller software!

But also I've tried to use above advises in PyMol and in general I was
satisfy with the results.

I have just only several questions


1- What exactly is the Sculpping ? As I've understood its something like
real-time minimisation of the edited structure. Is what cases this might be
better than rigid rotation\edition of the selected bonds/ angles by
mouse-mode editing ? :)

2- I'm looking for the possible way to set the values for psi and phi
dihedral-angles.

As I understood the commands like torsion or set dihedrals need in the
definition of the edited angles. Is there more trivial way to set values
for the pre-defined backbone dihedrals like

set phi value, sele, 120

?
:)

Something like this I can do via DynoPlot plugin where I can move point on
the graph wich correspond to the pair of psi-phy angles but I need in more
accuracy way to define the exactly values of this dihedrals.


Thanks again,


James

2012/1/26 Jed Goldstone <je...@gm...>

> James-
>
> 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.
>
> Jed
>
> 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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