Re: [PyMOL] Fwd: Torsion angles

[Thomas H. <sp...@us...>]

Hi James,

> 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 ?

circle is for all other amino acids that are not Gly or Pro.

> Could I make some changges that the circle and
> squire were for any residues in the alpha- helix and betta sheet
> respectually ?

sure, it requires little modifications in the script.

> 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 ?

almost the same modification as for previous question. See attachment 
for modified script. It colors by atom color and has symbols for 
secondary structure (sheet=square, helix=triangle).

> 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?

I don't know of any easy solution to that, sorry. Maybe someone else?

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology