Hi Edward,
Thank you for your quick answer.
I tried with the new script, defining the name of the spin to N with the
SEQ_ARGS[6] argument, but I still encounter the following error messages
(which I also get when SEQ_ARGS[6]=None):
relax> structure.vectors(attached='H', spin_id=None, model=None,
verbosity=1, ave=True, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
Traceback (most recent call last):
File "/usr/local/packages/relax-1.3/relax", line 418, in <module>
Relax()
File "/usr/local/packages/relax-1.3/relax", line 127, in __init__
self.interpreter.run(self.script_file)
File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 273,
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/packages/relax-1.3/prompt/interpreter.py", line 534,
in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/packages/relax-1.3/prompt/interpreter.py", line 430,
in interact_script
execfile(script_file, local)
File "full_analysis-sphere.py", line 641, in <module>
Main(self.relax)
File "full_analysis-sphere.py", line 230, in __init__
structure.vectors(attached='H')
File "/usr/local/packages/relax-1.3/prompt/structure.py", line 586, in
vectors
generic_fns.structure.main.vectors(attached=attached,
spin_id=spin_id, model=model, verbosity=verbosity, ave=ave, unit=unit)
File "/usr/local/packages/relax-1.3/generic_fns/structure/main.py",
line 353, in vectors
warn(RelaxWarning("Either the spin number or name must be set for
the spin " + `id` + " to identify the corresponding atom in the molecule."))
RelaxWarning: Either the spin number or name must be set for the spin
':15' to identify the corresponding atom in the molecule.
I checked the pdb and names are fine:
...
ATOM 31 N ASN 6 -21.732 2.728 -13.120 1.00 25.52
ATOM 32 H ASN 6 -11.923 7.967 -12.183 1.00 0.00
...
Thank you,
Pierre-Yves
Edward d'Auvergne wrote:
> Hi,
>
> The addition of spin_id='@N' should not be necessary if the sequence
> data you have loaded using this script has the atom/spin name set to
> 'N'. If not, I have modified the full_analysis.py script in the
> repository 1.3 line to name your spins in that way. The problem is
> that the spins are unnamed so they cannot be matched to anything in
> the PDB file. Hence the NH bond vectors are not extracted for any
> spins. Then when it comes to optimisation, all the spins without bond
> vector information are deselected. But as this is all spins, then
> there are essentially no model-free models to optimise and there is
> only the diffusion tensor. But this is fixed by the fix() function,
> the one you can't fix and can't be fixed. So as the only parameters
> remaining are those of the diffusion tensor, and these are fixed,
> relax cannot do anything. There should be warning messages describing
> this problem much further up in the script. I would guess thought
> that they have been suppressed by your addition in point one, as there
> are no spins with a spin id of '@N' and hence no NH bond vectors will
> be loaded.
>
> Regards,
>
> Edward
>
>
> On Tue, Feb 10, 2009 at 5:00 PM, Pierre-Yves Savard
> <[email protected]> wrote:
>
>> Hi,
>>
>> I am starting a new relax analysis with the full_analysis.py script,
>> together with relax 1.3 revision 8769. I performed the first step,
>> 'local_tm', with success.
>>
>> However, for what concerns diffusion models 'sphere', 'prolate', 'oblate
>> and 'ellipsoid', I encountered the following errors:
>>
>> 1. I had to add: "spin_id='@N'" in the function structure.vector()
>> in order to read the pdb and extract vectors properly:
>>
>>
>> # Load the PDB file and calculate the unit vectors parallel to
>> the XH bond.
>> if not local_tm and PDB_FILE:
>> structure.read_pdb(PDB_FILE)
>> structure.vectors(attached='H', spin_id='@N')
>>
>> ...
>>
>> # Load the PDB file and calculate the unit vectors parallel to
>> the XH bond.
>> if PDB_FILE:
>> structure.read_pdb(PDB_FILE)
>> structure.vectors(attached='H', spin_id='@N')
>>
>>
>> 2. Then, I encountered the following error message (using the debug
>> option -d) when trying to optimise models 'prolate', 'oblate' and
>> 'ellipsoid':
>>
>> Traceback (most recent call last):
>> File "full_analysis_prolate.py", line 640, in <module>
>> Main(self.relax)
>> File "full_analysis_prolate.py", line 267, in __init__
>> self.multi_model()
>> File "full_analysis_prolate.py", line 631, in multi_model
>> grid_search(inc=GRID_INC)
>> File "/usr/local/packages/relax-1.3/prompt/minimisation.py", line 156,
>> in grid_search
>> minimise.grid_search(lower=lower, upper=upper, inc=inc,
>> constraints=constraints, verbosity=verbosity)
>> File "/usr/local/packages/relax-1.3/generic_fns/minimise.py", line
>> 185, in grid_search
>> grid_search(lower=lower, upper=upper, inc=inc,
>> constraints=constraints, verbosity=verbosity)
>> File
>> "/usr/local/packages/relax-1.3/specific_fns/model_free/mf_minimise.py",
>> line 479, in grid_search
>> self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc,
>> constraints=constraints, verbosity=verbosity, sim_index=sim_index)
>> File
>> "/usr/local/packages/relax-1.3/specific_fns/model_free/mf_minimise.py",
>> line 788, in minimise
>> model_type = self.determine_model_type()
>> File "/usr/local/packages/relax-1.3/specific_fns/model_free/main.py",
>> line 1026, in determine_model_type
>> raise RelaxError, "All parameters are fixed."
>> RelaxError: RelaxError: All parameters are fixed.
>>
>>
>> There seems to be a problem with the fix() function, although I was not
>> able to fix (!) it...
>>
>> Thank you very much for your help,
>>
>>
>> Pierre-Yves
>>
>> _______________________________________________
>> relax (http://nmr-relax.com)
>>
>> This is the relax-users mailing list
>> [email protected]
>>
>> To unsubscribe from this list, get a password
>> reminder, or change your subscription options,
>> visit the list information page at
>> https://mail.gna.org/listinfo/relax-users
>>
>>
>
>
_______________________________________________
relax (http://nmr-relax.com)
This is the relax-users mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
