Hello,
I was trying to get the palmer.py working and got stuck at the stage 2 of
the process. Here is the output :
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relax> state.load(state='stage1.save', dir=None, force=False)
Opening the file 'stage1.save' for reading.
Loading all the Modelfree 4 data.
relax> pipe.switch(pipe_name='m1')
relax> palmer.extract(dir='m1')
relax> pipe.switch(pipe_name='m2')
relax> palmer.extract(dir='m2')
relax> pipe.switch(pipe_name='m3')
relax> palmer.extract(dir='m3')
relax> pipe.switch(pipe_name='m4')
relax> palmer.extract(dir='m4')
relax> pipe.switch(pipe_name='m5')
relax> palmer.extract(dir='m5')
Model selection.
relax> model_selection(method='AIC', modsel_pipe='aic', bundle=None,
pipes=None)
AIC model selection.
Global model - all diffusion tensor parameters and spin specific
model-free parameters.
Data pipe Num_params_(k) Num_data_sets_(n) Chi2
Criterion
m1 49 144 1877.92080
1975.92080
m2 97 144 1804.10160
1998.10160
m3 97 144 336.55080
530.55080
m4 145 144 310.36180
600.36180
m5 145 144 628.19930
918.19930
The model from the data pipe 'm3' has been selected.
Traceback (most recent call last):
File "/usr/local/relax/multi/processor.py", line 479, in run
self.callback.init_master(self)
File "/usr/local/relax/multi/__init__.py", line 318, in default_init_master
self.master.run()
File "/usr/local/relax/relax.py", line 184, in run
self.interpreter.run(self.script_file)
File "/usr/local/relax/prompt/interpreter.py", line 278, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 585, in run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
File "/usr/local/relax/prompt/interpreter.py", line 468, in interact_script
exec_script(script_file, local)
File "/usr/local/relax/prompt/interpreter.py", line 341, in exec_script
runpy.run_module(module, globals)
File "/usr/lib/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
File "/usr/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/home/rulelab/Documents/dynamics/palmer.py", line 158, in <module>
exec_stage_2(pipes)
File "/home/rulelab/Documents/dynamics/palmer.py", line 114, in
exec_stage_2
model_selection(method='AIC', modsel_pipe='aic')
File "/usr/local/relax/prompt/uf_objects.py", line 219, in __call__
self._backend(*new_args, **uf_kargs)
File "/usr/local/relax/generic_fns/model_selection.py", line 298, in select
duplicate_data[best_model](best_model, modsel_pipe, model_info,
global_stats=global_flag, verbose=False)
File "/usr/local/relax/specific_fns/model_free/main.py", line 1489, in
duplicate_data
interatomic.copy(pipe_from=pipe_from, pipe_to=pipe_to, verbose=verbose)
File "/usr/local/relax/generic_fns/interatomic.py", line 71, in copy
for interatom in interatomic_loop(pipe=pipe_from):
File "/usr/local/relax/generic_fns/interatomic.py", line 234, in
interatomic_loop
mol_index1, res_index1, spin_index1 =
cdp.mol._spin_id_lookup[interatom.spin_id1]
KeyError: ':1@N'
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I must tell you that I am not using any PDB structure yet.
Thanks a lot for any guidance or help.
On a slightly unrelated note, I have got the mf_multimodel.py followed by
modsel.py working for me. But I don't know how to optimise the diffusion
tensor now while passing on the selected model information to the script.
Is there something I need to change in the diff_min.py script ?
Again any help will be very appreciated.
Thanks,
Shantanu S. Bhattacharyya
--
Shantanu S. Bhattacharyya
Grad Student, Biological Sciences
Carnegie Mellon University
url : http://esesbee.com
Stage 2 of palmer.py