Hello,
It seems to work if I both define the name of the spin to 'N' with the
SEQ_ARGS[6] argument (that is including the spin name, here 'N', in the
sequence file) AND add the argument "spin_id='@N'" in the function
strcutre.vector(), part of the section "Diffusion models MII to MV" (see
last line of the following pasted text):
# Diffusion models MII to MV.
#############################
elif DIFF_MODEL == 'sphere' or DIFF_MODEL == 'prolate' or
DIFF_MODEL == 'oblate' or DIFF_MODEL == 'ellipsoid':
# Loop until convergence if CONV_LOOP is set, otherwise just
loop once.
# This looping could be made much cleaner by removing the
dependence on the determine_rnd() function.
while 1:
# Determine which round of optimisation to do (init,
round_1, round_2, etc).
self.round = self.determine_rnd(model=DIFF_MODEL)
# Inital round of optimisation for diffusion models MII
to MV.
if self.round == 0:
# Base directory to place files into.
self.base_dir = DIFF_MODEL + '/init/'
# Run name.
name = DIFF_MODEL
# Create the data pipe.
pipe.create(name, 'mf')
# Load the local tm diffusion model MI results.
results.read(file='results', dir='local_tm/aic')
# Remove the tm parameter.
model_free.remove_tm()
# Deselect the spins in the EXCLUDE list.
if EXCLUDE:
deselect.read(file=EXCLUDE)
# 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')
However, if the SEQ_ARGS[6] argument is set to None, and, thus, the
following code (you added today) takes care of the spin name:
# Name the spins if necessary.
if SEQ_ARGS[6] == None:
spin.name(HET_NAME)
the following error message is thrown:
Traceback (most recent call last):
File "./full_analysis-prolate.py", line 641, in <module>
Main(self.relax)
File "./full_analysis-prolate.py", line 264, in __init__
self.multi_model()
File "./full_analysis-prolate.py", line 600, in multi_model
spin.name(HET_NAME)
File "/usr/local/packages/relax-1.3/prompt/spin.py", line 269, in name
raise RelaxStrError, ('new spin name', name)
RelaxStrError: RelaxError: The new spin name argument None must be a string.
Do you have any clue of what is happening ?
Thanks
Pierre-Yves
Pierre-Yves Savard wrote:
> 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)
>>>
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>>>
>>>
>>
>>
>
> _______________________________________________
> relax (http://nmr-relax.com)
>
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