Hi,
Simultaneously with the work with the diffusion tensor PDB
representation (i.e. the code is in the 'tensor_pdb' branch), I have
implemented rudimentary support for PyMOL. The following user
functions
are now available:
pymol.view() # Launches PyMOL opening the loaded PDB file.
pymol.cartoon() # Changes the representation to the cartoon
style and
colours by secondary structure.
pymol.tensor_pdb() # Loads the rotational diffusion tensor PDB
representation created by the 'pdb.create_tensor_pdb()' user function
into PyMOL.
The user functions for creating macros to represent results
superimposed
onto the structure are not functional. Someone will need to generate
sample macros manually and then code them into relax.
Edward
On Mon, 2006-10-30 at 18:17 +1100, Edward d'Auvergne wrote:
In response to the sub-thread started by Sebastien Morin at
https://mail.gna.org/public/relax-devel/2006-10/msg00147.html
(Message-id: <4540F69C.8070403@xxxxxxxxx>), I have started to
implement rudimentary support for interfacing between relax and PyMOL
using the '-p' flag information provided by Douglas Kojetin at
https://mail.gna.org/public/relax-devel/2006-10/msg00164.html
(Message-id: <A6B8CCA7-BCAA-47A2-9A42-8485540CFFC2@xxxxxxxxx>). This
code is in the 'branches/tensor_pdb' directory.
However when running PyMOL through a relax script, the program would
terminate when the script terminates
(https://mail.gna.org/public/relax-devel/2006-10/msg00168.html,
Message-id:
<7f080ed10610290135p7ebce039tda7cd622b7ca30ff@xxxxxxxxxxxxxx>
and https://mail.gna.org/public/relax-devel/2006-10/msg00169.html,
Message-id: <BA58D16C-56EF-4AC3-B415-34A87A0B7FAB@xxxxxxxxx>).
To find out if there was a simple solution, I asked a question about
persistent PyMOL pipes at the "pymol-users at lists.sourceforge.net"
mailing list (http://sourceforge.net/mailarchive/message.php?
msg_id=37186991).
I received an answer from DeLano Scientific, I wonder whom that
could
be, saying that the solution is the '-K' option. The thread of these
posts is located at
http://sourceforge.net/mailarchive/forum.php?
thread_id=30844748&forum_id=60.
I'll add this option and commit the changes to the repository soon.
This should open up a path for the full support of PyMOL.
Edward
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Re: PyMOL is now supported.