eliminated many years ago that has somehow returned. I'll definitely
have to fix this. Would you be able to create a bug report for this
automatically with the debug flag in the 1.2 line) to the bug report.
'local_tm/aic/results.bz2' would also be of value for debugging. Or
very useful. With the save state (and the relax version or SVN
revision being used) I will be able to head straight to the problem.
Hi Edward,
I've included the output from the log below, which is produced if the
aforementioned lines are left commented out. If I uncomment them,
the eliminate call does not report an error and the results files
seem to contain the appropriate information. I'm not sure if it has
anything to do with this, but my input rate files include residues
with no rate information:
1 M
2 K
3 S 0.2907 0.0234
...
It seems that relax must unselect residues 1 and 2 in the example
above, so the determine_param_set_type definition in model-free.py
fails unless the aforementioned lines are uncommented ... local_tm
stays equal to 0, causing the problem with the inconsistencies check
on lines 1033-1035.
Doug
#OUTPUT
... starting at the end of the log where the script is read in ...
# The main class.
Main(self.relax)
------------------------------------------------------------------------
----------------------------
relax> run.create(run='local_tm', run_type='mf')
relax> results.read(run='local_tm', file='results', dir='local_tm/
aic', format='columnar')
Opening the file 'local_tm/aic/results.bz2' for reading.
relax> run.create(run='sphere', run_type='mf')
relax> results.read(run='sphere', file='results', dir='sphere/round_5/
opt', format='columnar')
Opening the file 'sphere/round_5/opt/results.bz2' for reading.
Loading all structures from the PDB file.
Structure('../pdb/file.pdb'):
Peptide chain of length 106
relax> run.create(run='prolate', run_type='mf')
relax> results.read(run='prolate', file='results', dir='prolate/
round_5/opt', format='columnar')
Opening the file 'prolate/round_5/opt/results.bz2' for reading.
Using the structures from the run 'sphere'.
Structure('../pdb/file.pdb'):
Peptide chain of length 106
relax> run.create(run='oblate', run_type='mf')
relax> results.read(run='oblate', file='results', dir='oblate/round_8/
opt', format='columnar')
Opening the file 'oblate/round_8/opt/results.bz2' for reading.
Using the structures from the run 'sphere'.
Structure('../pdb/file.pdb'):
Peptide chain of length 106
relax> run.create(run='ellipsoid', run_type='mf')
relax> results.read(run='ellipsoid', file='results', dir='ellipsoid/
round_7/opt', format='columnar')
Opening the file 'ellipsoid/round_7/opt/results.bz2' for reading.
Using the structures from the run 'sphere'.
Structure('../pdb/file.pdb'):
Peptide chain of length 106
relax> run.create(run='final', run_type='mf')
relax> eliminate(run=None, function=None, args=None)
RelaxError: All residues must either have a local tm parameter or not.
Doug
On Oct 25, 2007, at 5:05 PM, Edward d'Auvergne wrote:
Hi,
This is quite a bizarre bug if uncommenting those lines fixed the
problem. Would you have the printout of the 'traceback' error message
of the failure? Or did the script fail without printing a message?
Do you have more information about the point of failure?
These lines were commented out because they cause a fatal bug under
certain rare circumstances. But other code has developed in response
to this removal such that this test of spin system selection is not
necessary. This important function solely determines what type of
model-free analysis is being executed - local tm, diffusion tensor
optimisation, model-free optimisation for a single spin, or
optimisation of all parameters simultaneously. If uncommenting these
lines changes relax's behaviour, then the only reason is that not a
single residue is selected. Can you see this in any of your results
files? Or is there anything else suspicious with one of the results
files?
Regards,
Edward
Hi,
The following comment is present on line 1021 in the specifc_fns/
model-free.py file of the 1.2 svn version of relax:
1021 # This code causes a bug after model elimination if
the model has been eliminated (select = 0).
1022 #if not self.relax.data.res[self.run][i].select:
1023 # continue
The full_analysis.py script works find for the optimization of
local_tm, sphere, etc ... but, I am unable to run the 'final' run in
full_analysis.py unless I uncomment lines 1022-1023 in model-free.py.
I have to manually uncomment these lines to run the final analysis,
then comment out these lines again. Can the code in model-free.py be
modified to something like this:
if not self.relax.data.res[self.run][i].select and self.run ==
'final':
continue
Or should one not need to uncomment lines 1022-1023?
Doug
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bug comment in model-free.py