Dear all :)

By the way, I havent tested Dangle software yet but could you tell me any other software wich I could use for torsion angles measurements?

As I've mentioned previously I want to calculate different torsions for enssemble of pdb structures and then plot this values on rammachandran plots ( something like I've done via PyMol)
Also I'd like to calculate energy difference of the particular structure in accordance to the changing in torsions.
What I could use for this purposes besides pymol?

Thanks again,
James

2011/11/18 Thomas Holder <speleo3@users.sourceforge.net>
Hi James,

in principle every python module can be used together with PyMOL!

With matplotlib I had trouble opening plots on screen because both PyMOL and matplotlib use Tk. But writing plots to files (png, eps, ...) with matplotlib should be no problem I guess.

I again updated http://pymolwiki.org/index.php/DynoPlot to enable postscript export (was quite easy).

Cheers,
 Thomas


On 11/18/2011 10:31 AM, James Starlight wrote:
Thomas, hello!

In the past I've wrote some scripts in Python biological software but in
that case I've used matlibplot python module for ploting my graphs.
Does this module supported by PyMol?


James


2011/11/18 Thomas Holder <speleo3@users.sourceforge.net
<mailto:speleo3@users.sourceforge.net>>


   Hi James,


       by the way how I could save that plots in desired format
       Finally is it possible to make legend on that plot? E.g I want
       indicate
       what marker correspond to what SS and provide my plot with the
       colour
       description ( what colour correspond to what pdb structure ).
       How I could make those things?


   I guess the easyest way is to take screenshots and add the legend
   with some real drawing tool (like Illustrator, Inkscape, ...).

   If you know how to script in python, you may modify the script to
   export the canvas as postscript:

   self.canvas.postscript(file='/__tmp/canvas.ps <http://canvas.ps>')



   Cheers,
     Thomas

   --
   Thomas Holder
   MPI for Developmental Biology




--
Thomas Holder
MPI for Developmental Biology