Also I've tried to test set_dihedral command but failed
:)
E.g I want to change PHI value ( the angle beetween H-N and C-alpha-C-beta
in the residue)
I've type
set_dihedral resi 40 and name H, resi 40 and name N, resi 40 and name
CA, resi 40 and name CB, -30
and obtain error
Selection 1 doesn't contain a single atom/vertex.
I suppose this error might be due to incorect definition of H atom in the
first selection. By the way how I could define PHI in case if my structure
lack for hydrogens at all ?
James
2012/1/27 James Starlight <jmsstarli...@gmail.com>
> 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 <jedg...@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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