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: <[EMAIL PROTECTED]>), 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: <[EMAIL PROTECTED]>). 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: <[EMAIL PROTECTED]>
> > and https://mail.gna.org/public/relax-devel/2006-10/msg00169.html,
> > Message-id: <[EMAIL PROTECTED]>).
> >
> > 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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