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:
> <[EMAIL PROTECTED]>).
>
> * 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:
> <[EMAIL PROTECTED]>).
>
> * 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:
> <[EMAIL PROTECTED]>).
>
> * 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:
> <[EMAIL PROTECTED]>).
>
> * 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:
> <[EMAIL PROTECTED]>).
>
>
> 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
> <[EMAIL PROTECTED]> 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
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
>> This is the relax-users mailing list
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>>
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>>
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