On 10/27/06, Sebastien Morin <sebastien.morin.1@xxxxxxxxx> wrote:
Hi all !
I also like the Tensor representation of the diffusion tensor.
If Molmol is a problem for connectivities and heteroatoms, why not change
relax to output script for Pymol instead of Molmol ? This is just a
proposition since I'm a Pymol user... ;)
http://pymol.sourceforge.net/
Pymol is open source, fully scriptable, written in Python and can run on
either Linux, Windows or Mac...
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.
Edward
P.S. Please excuse the following rant! On another note, one thing
with PyMOL that I don't like is that it is dual licenced. Normally
this isn't an issue. However they force PyMOL developers to transfer
the copyright of their own independently created works to DeLano
Scientific LLC. Then DeLano Scientific LLC benfits from your hard
work (while you get nothing) by licencing and selling your work in the
non open source version. It probably also legally means that you can
never use the work you have 'given away' for anything else! And
legally if you have taken that code from another project of yours,
then you may have lost ownership of that as well! You aren't giving a
licence to your work to DeLano Scientific LLC, you're permanently
giving them the ownership of it. This is not how a normal open source
community is supposed to work.
Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.