Hi,
I am using the script "palmer.py" to extract dynamic information using
AIC model selection, but ModelFree4 as an optimization tool.
I tried the script several times before with a good success, however, I
now get an error message when trying to extract parameters for model
"m5" during stage 2.
=========================
relax> palmer.extract(run='m5', dir=None)
Traceback (most recent call last):
File "/home/semor/packages/relax-1.2/relax", line 454, in ?
Relax()
File "/home/semor/packages/relax-1.2/relax", line 166, in __init__
self.interpreter.run()
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 216,
in run
run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 391,
in run_script
console.interact(intro, local, script_file, quit)
File "/home/semor/packages/relax-1.2/prompt/interpreter.py", line 343,
in interact_script
execfile(script_file, local)
File "./palmer__stage_2.py", line 142, in ?
exec_stage_2(runs)
File "./palmer__stage_2.py", line 76, in exec_stage_2
palmer.extract(run=name)
File "/home/semor/packages/relax-1.2/prompt/palmer.py", line 263, in
extract
self.__relax__.generic.palmer.extract(run=run, dir=dir)
File "/home/semor/packages/relax-1.2/generic_fns/palmer.py", line 562,
in extract
data.ts = data.ts / 1e12
TypeError: unsupported operand type(s) for /: 'NoneType' and 'float'
=========================
I had a look at the "te" parameter (sometimes called "ts" in relax, but
always "te" in ModelFree4) and the values and errors are sometimes
extremely high... For example :
=========================
...
41 0.000 1279767296.000 1 0.000
0.000 0.000 0.000
...
59 10000.000 215564320.000 1 0.000
0.000 0.000 0.000
60 10000.000 3750023168.000 1 0.000
0.000 0.000 0.000
61 10000.000 11655.404 1 0.000
0.000 0.000 0.000
...
=========================
Also, on line is badly formatted with an absent separating field :
=========================
246 10000.00019682363392.000 1 0.000
0.000 0.000 0.000
=========================
I modified the "mfout" file so this line is now :
=========================
246 10000.00 19682363392.000 1 0.000
0.000 0.000 0.000
=========================
and the script now passes without any problem...
This issue is probably caused by the ModelFree4 parser... However, do
you think it could be catched by relax and re-formatted so that relax
doesn't crash ?
Thanks !
Cheers,
Séb :)
Error message with the script "palmer.py"