Re: Representing the Brownian rotational diffusion tensor in Molmol, etc. -- October 27, 2006 - 17:19

Hi Edward-

I am able to feed commands into PyMOL from Tcl/Tk scripts through the  
use of UNIX pipes.  From within the Tcl/Tk script, a pipe is opened  
to PyMOL, and the script sends commands to PyMOL.  I can tell PyMOL  
to open a PDB file, display it in a certain way (cartoon, ribbon),  
highlight certain atoms or residues (by sticks, spheres, etc.), color  
them, etc.  I've never tried writing images, but I don't think it  
would be too difficult.  Is this the type of functionality you are  
looking to incorporate into relax?

Doug


On Oct 27, 2006, at 3:51 AM, Edward d'Auvergne wrote:

> I use PyMOL as well, the graphics are much better.  However I have
> tried getting relax to interface with PyMOL but this has been
> problematic.  Essentially to access the internals of PyMOL, relax
> would have to run within PyMOL's python prompt as a PyMOL plugin.  The
> same situation occurs with VMD.  Molmol on the other hand can be
> controlled from within relax.
>
> To use these molecular viewers relax must be able to control them -
> not the other way around where the viewers control relax (which, in
> the case of PyMOL and VMD, is probably not too difficult).  If someone
> knows how to control PyMOL or VMD, or any other molecular viewing
> program, to generate images using the data in relax, and would like to
> add the feature into relax, that would very much be welcome.  Much of
> the code used to generate the Molmol images can be used to generate
> images in other programs.  The ultimate solution would be to have
> PyMOL expose it's API to the command prompt or to expose it's python
> interface to the prompt to allow relax to feed commands into it.  Btw,
> I'm not a fan of turning relax into multiple plugins for different
> programs just to make this work.