Sorry,
My mistake!
Seems to be working now but the line has to be changed to:
Spin.name(name='N')
In the script file it is missing the 'name' expression so the program
interprets it as the spin_id argument.
Cheers
TiagoP
-----Original Message-----
From: Tiago Pais [mailto:tpais@xxxxxxxxxxx]
Sent: segunda-feira, 14 de Dezembro de 2009 12:28
To: 'Edward d'Auvergne'
Cc: 'relax-devel@xxxxxxx'
Subject: RE: [bug #14886] mf_multimodel does not plot out any s2 values
Hi Edward,
Not at all offended by the "invalid" marking. ;)
Meanwhile been trying the new script, still with relax version 1.3.4
I had to change the vector lines because I was getting some error messages
about spin.name (it would tell me that name would have to be a string and
then that 'N' was an invalid string) so now it looks like this:
# Set the spin name and then load the NH vectors.
spin.name('@N', name='N')
structure.vectors(spin_id='@N', attached='H', ave=False)
However, I have now an error message that I don't understand saying that "No
vectors could be extracted. This is what I get:
"relax> structure.read_pdb(file='snPHSinDiffFrame2.pdb', dir=None,
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
parser='internal')
Internal relax PDB parser.
Opening the file 'snPHSinDiffFrame2.pdb' for reading.
Adding molecule 'snPHSinDiffFrame2_mol1' to model None (from the original
molecule number 1 of model None)
relax> spin.name(spin_id='@N', name='N', force=False)
relax> structure.vectors(attached='H', spin_id='@N', model=None,
verbosity=1, ave=False, unit=True)
Extracting vectors from the single model.
Calculating the unit vectors.
The attached atom is a proton.
RelaxError: No vectors could be extracted."
Perhaps it is a problem with this version or with my PDB file?
-----Original Message-----
From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On
Behalf Of Edward d'Auvergne
Sent: segunda-feira, 14 de Dezembro de 2009 12:18
Cc: Tiago Pais; relax-devel@xxxxxxx
Subject: Re: [bug #14886] mf_multimodel does not plot out any s2 values
Hi Tiago,
Please don't be offended by the 'invalid' marking, this is just the
only technical category this fits into. The fix for bug #14885
(https://gna.org/bugs/index.php?14885) should help as that solution
will remove the need for you to run mf_multimodel.py without
model-free optimisation. Note that the results are meaningless as no
NH bond vectors have been loaded into the program.
Regards,
Edward
2009/12/14 Edward d Auvergne <NO-REPLY.INVALID-ADDRESS@xxxxxxx>:
Update of bug #14886 (project relax):
Status: None => Invalid
Assigned to: None => bugman
Open/Closed: Open => Closed
_______________________________________________________
Follow-up Comment #1:
This bug has been marked as invalid because the behaviour is what should
happen. No model-free parameters have been optimised or set, so the file
of
S2 values just looks like:
# mol_name res_num res_name spin_num spin_name value
error
None 1 A None None
None
None
None 2 T None None
None
None
None 3 S None None
None
None
None 4 T None None
None
None
...
The final save state contains the optimised diffusion tensor but no
model-free results. This again is the expected program behaviour.
_______________________________________________________
Reply to this item at:
<http://gna.org/bugs/?14886>
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RE: [bug #14886] mf_multimodel does not plot out any s2 values