On Tue, 2006-10-31 at 21:05 +1100, Edward d'Auvergne wrote:
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
This looks really nice.
A couple of issues...
Stupidly doing pdb.create_tensor_pdb('test') before defining a tensor
gives the fairly criptic:
Traceback (most recent call last):
File "<console>", line 1, in ?
File "/home/chris/relax_devel/pdb_tensor/prompt/pdb.py", line 113, in
create_tensor_pdb
self.__relax__.generic.pdb.create_tensor_pdb(run=run, scale=scale,
file=file, dir=dir, force=force)
File "/home/chris/relax_devel/pdb_tensor/generic_fns/pdb.py", line
257, in create_tensor_pdb
if self.relax.data.diff[self.run].type == 'spheroid':
KeyError: 'test'
A case worth checking for and throwing a more informative error.
doing pymol.tensor_pdb(), everything seems to work, but I get:
relax> PyMOL>reinitialise
Traceback (most recent call last):
File "/home/chris/bin/pymol/modules/pymol/parser.py", line 370, in
parse
exec(com2[nest]+"\n",pymol_names,pymol_names)
File "<string>", line 1, in ?
NameError: name 'reinitialise' is not defined
PyMOL>load ../abp_600MHz_tensorFrame.pdb
CmdLoad: "../abp_600MHz_tensorFrame.pdb" loaded as
"abp_600MHz_tensorFrame".
PyMOL>load tensor.pdb
CmdLoad: "tensor.pdb" loaded as "tensor".
pymol.cartoon() doesn't work for me. The commands go to pymol (they
appear in the tcl gui at least) but have no apparent effect. Just doing:
hide everything
show cartoon
on the pymol cmd line has the expected effect.
And finally, if I do pymol.tensor_pdb(), then close pymol and then do
pymol.view() in the same run, I get the tensor back again (I was just
expecting to get my protein).
Oh, and one last thought. It would be nice to automatically scale the
tensor size for the size of the protein, so we don't have to do
trial-and-error adjustments of the scaling factor. The current fixed
default scaling factor means larger proteins will have smaller tensors
and vice-versa. This is something I could have a go at implimenting if
others think its a godd idea?
Chris
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.