[PyMOL] Fwd: Torsion angles

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

Hi, Thomas!

Thank you for your responce

I've tested DynoPlot and have some questions

1- What are the meaning of the symbols in the ramachandran plot ?
As I understood the tringle always for the Gly and the square for the Pro.
What is the circle ? Could I make some changges that the circle and squire
were for any residues in the alpha- helix and betta sheet respectually ?

2- I'm intresting in working with the enssembles of the pdbs' So I 'd like
to compare  torsions of different residues for different structures in one
plot. But when Ive done such comparison I noticed that residues from
differen structures were marked on Ramachandran map with the one default
colour. How I can specify that residued from different strctures were
represented with different colour ?

3- Finally I'd like to compare Chi-1 angle ( rotation on first bond
beetween backbone and side chain groups) for my enssemble. How I could mark
Chi-1 angle for all my structures and plot in on Rama map?



Thanks again,


James


2011/11/17 Thomas Holder <sp...@us...>

> Hi James,
>
> ramachandran plot for the *current* state can be created with the DynoPlot
> plugin:
> http://pymolwiki.org/index.**php/DynoPlot<http://pymolwiki.org/index.php/DynoPlot>
>
> It uses the API function "get_phipsi", which can calculate phi/psi angles
> for given states:
> cmd.get_phipsi(selection='(**name ca)', state=-1)
>
> Torsion angles other than phi/psi can be calculated with the
> "get_dihedral" fuction:
> http://pymolwiki.org/index.**php/Get_Dihedral<http://pymolwiki.org/index.php/Get_Dihedral>
>
> You can also modify torsion angles with "torsion" and "set_dihedral":
> http://pymolwiki.org/index.**php/Set_Dihedral<http://pymolwiki.org/index.php/Set_Dihedral>
> http://pymolwiki.org/index.**php/Torsion<http://pymolwiki.org/index.php/Torsion>
>
> And you can modify torsion angles interactively using the mouse while in
> editing mode (pick one atom, then CTRL-Drag).
>
> Hope that helps.
>
> Cheers,
>  Thomas
>
>
> On 11/16/2011 06:50 PM, James Starlight wrote:
>
>> Dear PyMol Users!
>>
>> I wounder to know about posible ways to plot for my structures different
>> torsion angles (phy, psi, chi ) on the ramachandran map via pymol.
>>
>> In particular I would like to obtain the next information
>>
>> 1- I d like to visualise and measure different torsions for my structure
>> and plot this values on the ramachandran plot
>>
>> 2- I'd like to make such measurements for the enssemble of the pdb
>> structures and plot on the ramachandran map values  for each structure (
>> by points or other markers)
>>
>> Finaly could you show me some tutorials wich could help me working with
>> torsions in pymol?
>>
>> Thanks for your help,
>>
>> James
>>
>
> --
> Thomas Holder
> MPI for Developmental Biology
>