Hi Edward,
As an example, can you tell me how the following portion of
diff_tensor_pdb.py would need to be edited to work with the unstable
1.3 branch? The code below fails on the results.read(...) call. I
have a feeling it has something to do with the pipe.create(...)
function and the what you wrote on how the pipe name is not passed
into each user function.
### start error_output
% relax1.3 diff_tensor_pdb.py
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
relax repository checkout
Protein dynamics by NMR relaxation data
analysis
Copyright (C) 2001-2006 Edward d'Auvergne
Copyright (C) 2006-2008 the relax
development team
This is free software which you are welcome to modify and
redistribute under the conditions of the
GNU General Public License (GPL). This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'.
Assistance in using this program
can be accessed by typing 'help'.
script = 'diff_tensor_pdb.py'
------------------------------------------------------------------------
----------------------------
# Script for creating a PDB representation of the Brownian rotational
diffusion tensor.
# Create the run.
name = 'sims'
pipe.create(name, 'mf')
# Read the results.
results.read(name, dir='final')
# Display the diffusion tensor.
diffusion_tensor.display(name)
# Create the tensor PDB file.
tensor_file = 'tensor.pdb'
structure.create_diff_tensor_pdb(name, file=tensor_file, force=1)
# PyMOL.
#pymol.view(name)
#pymol.cartoon(name)
#pymol.tensor_pdb(name, file=tensor_file)
------------------------------------------------------------------------
----------------------------
relax> pipe.create(pipe_name='sims', pipe_type='mf')
relax> results.read(run='sims', file='results', dir='final',
format='columnar')
Traceback (most recent call last):
File "/usr/local/bin/relax1.3", line 421, in ?
Relax()
File "/usr/local/bin/relax1.3", line 142, in __init__
self.interpreter.run(self.script_file)
File "/usr/local/relax/1.3/prompt/interpreter.py", line 241, in run
return run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/usr/local/relax/1.3/prompt/interpreter.py", line 502, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/relax/1.3/prompt/interpreter.py", line 398, in
interact_script
execfile(script_file, local)
File "diff_tensor_pdb.py", line 8, in ?
results.read(name, dir='final')
File "/usr/local/relax/1.3/prompt/results.py", line 125, in read
self.__relax__.generic.results.read(run=run, file=file,
directory=dir, format=format)
AttributeError: 'module' object has no attribute 'results'
### end error_output
Thanks,
Doug
On Jan 24, 2008, at 10:18 AM, Edward d'Auvergne wrote:
Hi,
The problem is simply differences between the stable 1.2 versions and
the unstable 1.3 line. In the development of relax 1.3, many of the
user functions have been renamed. There has also been a significant
redesign of relax. For full details, have a look at the following
links and the threads that they start:
* The parent message 'Redesign of the relax data model: A HOWTO for
breaking relax.' located at
https://mail.gna.org/public/relax-devel/2006-10/msg00053.html
(Message-id:
<1160550133.9523.54.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 1 'Redesign of the relax data model: 1. Why change?'
located at https://mail.gna.org/public/relax-devel/2006-10/
msg00054.html
(Message-id:
<1160551172.9523.60.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 2 'Subject: Redesign of the relax data model: 2. A new run
concept' located at
https://mail.gna.org/public/relax-devel/2006-10/msg00056.html
(Message-id:
<1160555137.9523.70.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 3 'Redesign of the relax data model: 3. Molecules,
residues, and spins' located at
https://mail.gna.org/public/relax-devel/2006-10/msg00057.html
(Message-id:
<1160557041.9523.74.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
* Section 4 'Redesign of the relax data model: 4. Conclusion'
located at https://mail.gna.org/public/relax-devel/2006-10/
msg00058.html
(Message-id:
<1160557876.9523.79.camel@xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx>).
Note also that the 1.3 line code is not fully functional yet as this
redesign has been slow and is still in progress. But if you do want
to play with the current code, note that the name 'run' has been
replaced by the name 'pipe' and that the concept of a data pipe has
been introduced so that the pipe name is not passed into each user
function. That user functions apply automatically to the 'current'
data pipe in which you are currently sitting. And that you can switch
between data pipes, merge them, branch them, etc.
Regards,
Edward
On Jan 24, 2008 3:14 PM, Douglas Kojetin
<douglas.kojetin@xxxxxxxxx> wrote:
Hi All,
When trying to use relax 1.3 (current svn version), I see the
following error when trying to use run.create():
% /usr/local/relax/1.3/relax
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
relax repository checkout
Protein dynamics by NMR relaxation data
analysis
Copyright (C) 2001-2006 Edward
d'Auvergne
Copyright (C) 2006-2008 the relax
development team
This is free software which you are welcome to modify and
redistribute under the conditions of the
GNU General Public License (GPL). This program, including all
modules, is licensed under the GPL
and comes with absolutely no warranty. For details type 'GPL'.
Assistance in using this program
can be accessed by typing 'help'.
relax> run.create('test','mf')
Traceback (most recent call last):
File "<console>", line 1, in ?
NameError: name 'run' is not defined
relax>
Any ideas about this problem?
Thanks,
Doug
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Re: relax 1.3: run.create error