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 <jedgold@gmail.com>
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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