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 <speleo3@users.sourceforge.net>
Hi James,

ramachandran plot for the *current* state can be created with the DynoPlot plugin:
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

You can also modify torsion angles with "torsion" and "set_dihedral":
http://pymolwiki.org/index.php/Set_Dihedral
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