Hi,
I'm unsure if this is a bug in full_analysis.py, in the internal
relax code, or user error. The optimization of the 'sphere' model
will not converge, now after 160+ rounds. The chi-squared test has
converged (long, long ago):
"" from output
Chi-squared test:
chi2 (k-1): 100.77647517006251
chi2 (k): 100.77647517006251
The chi-squared value has converged.
""
However, the identical model-free models test does has not converged:
"" from output
Identical model-free models test:
The model-free models have not converged.
Identical parameter test:
The model-free models haven't converged hence the
parameters haven't converged.
""
Something that confuses me is that the output files in the round_??/
aic directory suggest that, for example, the round_160 and round_161
AIC model selections are equivalent. Here are the models for the
first few residues:
""
1 None None
2 None None
3 None None
4 m2 m2
5 m2 m2
6 m2 m2
7 m2 m2
8 m2 m2
9 m4 m4
10 m1 m1
11 None None
12 m2 m2
13 m2 m2
14 m1 m1
15 m2 m2
16 m3 m3
17 m3 m3
18 None None
""
However, I modified the full_analysis.py protocol to print the
differences in the model selection, within the 'Identical model-free
model test' section of the 'convergence' definition. Here is the
beginning of the output (which only contains differences between the
previous and current rounds):
""
residue 1: prev=None curr=m2
residue 2: prev=None curr=m2
residue 3: prev=None curr=m2
residue 6: prev=m2 curr=m4
residue 7: prev=m2 curr=m1
residue 9: prev=m4 curr=m2
residue 11: prev=None curr=m2
residue 12: prev=m2 curr=m3
residue 13: prev=m2 curr=m3
residue 15: prev=m2 curr=m1
residue 16: prev=m3 curr=m2
residue 17: prev=m3 curr=m1
residue 18: prev=None curr=m3
""
There should be no data for residues 1-3, 11 and 18 (None), however
the 'Identical model-free model test' seems as if it ignores residues
for which 'None' was selected in the curr_model call in the following
code:
""
# Create a string representation of the model-free models of
the previous run.
prev_models = ''
for i in xrange(len(self.relax.data.res['previous'])):
if hasattr(self.relax.data.res['previous'][i], 'model'):
#prev_models = prev_models + self.relax.data.res
['previous'][i].model
prev_models = prev_models + ' ' + self.relax.data.res
['previous'][i].model
# Create a string representation of the model-free models of
the current run.
curr_models = ''
for i in xrange(len(self.relax.data.res[run])):
if hasattr(self.relax.data.res[run][i], 'model'):
#curr_models = curr_models + self.relax.data.res[run]
[i].model
curr_models = curr_models + ' ' + self.relax.data.res
[run][i].model
""
For what it's worth, I have residues 1,2,3,11 and 18 in the file
'unresolved' which is read by the full_analysis.py protocol. I
created a separate sequence file (variable = SEQUENCE) that contains
all residues (those with data and those without), instead of using a
data file (noe data, in the default full_analysis.py file). However,
these residues are not specified in the data (r1, r2 and noe) files,
as I did not have data for them. Should I add them but place 'None'
in the data and error columns? Could that be causing the problems?
Or should I create a bug report for this?
Doug
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