Hi Edward, I need a bit of help figuring out what was going wrong here. I started the fully-automated protocol via the GUI in relax 2.1.0 (multi-processor).
First, relax successfully fitted the local_tm: > relax> results.write(file='results', > dir='/home/tron/relax-martin/b2m/local_tm/aic', compress_type=1, force=True) > Opening the file '/home/tron/relax-martin/b2m/local_tm/aic/results.bz2' for > writing. Then, it started with the spherical diffusion tensor and raised the following error message. > relax> pipe.create(pipe_name='sphere - mf (Thu Sep 13 15:47:14 2012)', > pipe_type='mf', bundle='mf (Thu Sep 13 15:47:14 2012)') > > relax> results.read(file='results', > dir='/home/tron/relax-martin/b2m/local_tm/aic') > Opening the file '/home/tron/relax-martin/b2m/local_tm/aic/results.bz2' for > reading. > > relax> model_free.remove_tm(spin_id=None) > > relax> diffusion_tensor.init(params=1e-08, time_scale=1.0, d_scale=1.0, > angle_units='deg', param_types=0, spheroid_type=None, fixed=False) > > relax> fix(element='all_spins', fixed=True) > > relax> grid_search(lower=None, upper=None, inc=11, constraints=True, > verbosity=1) > > > Over-fit spin deselection. > > Only diffusion tensor parameters will be used. > Parallelised diffusion tensor grid search. > Exception raised in thread. > > Traceback (most recent call last): > File "/opt/relax-2.1.0/gui/analyses/execute.py", line 87, in run > self.run_analysis() > File "/opt/relax-2.1.0/gui/analyses/auto_model_free.py", line 803, in > run_analysis > dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, > pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, > diff_model=self.data.global_models, mf_models=self.data.mf_models, > local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, > diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, > mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, > conv_loop=self.data.conv_loop) > File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 235, in > __init__ > self.execute() > File "/opt/relax-2.1.0/auto_analyses/dauvergne_protocol.py", line 619, in > execute > self.interpreter.grid_search(inc=inc) > File "/opt/relax-2.1.0/prompt/uf_objects.py", line 219, in __call__ > self._backend(*new_args, **uf_kargs) > File "/opt/relax-2.1.0/generic_fns/minimise.py", line 140, in grid_search > grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, > verbosity=verbosity) > File "/opt/relax-2.1.0/specific_fns/model_free/mf_minimise.py", line 1493, > in grid_search > self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, > constraints=constraints, verbosity=verbosity, sim_index=sim_index) > File "/opt/relax-2.1.0/specific_fns/model_free/mf_minimise.py", line 1817, > in minimise > processor.run_queue() > File "/opt/relax-2.1.0/multi/processor.py", line 621, in run_queue > self.run_command_queue(lqueue) > File "/opt/relax-2.1.0/multi/processor.py", line 605, in run_command_queue > result_queue.put(result) > File "/opt/relax-2.1.0/multi/result_queue.py", line 90, in put > super(Threaded_result_queue, self).put(job) > File "/opt/relax-2.1.0/multi/result_queue.py", line 52, in put > self.processor.process_result(job) > File "/opt/relax-2.1.0/multi/multi_processor_base.py", line 123, in > process_result > result.run(self, memo) > File "/opt/relax-2.1.0/multi/result_commands.py", line 141, in run > raise self.exception > Capturing_exception: > > ------------------------------------------------------------------------------------------------------------------------ > > File "/opt/relax-2.1.0/multi/processor.py", line 521, in run > command.run(self, completed) > File > "/opt/relax-2.1.0/specific_fns/model_free/multi_processor_commands.py", line > 129, in run > results = self.optimise() > File > "/opt/relax-2.1.0/specific_fns/model_free/multi_processor_commands.py", line > 175, in optimise > results = grid_point_array(func=self.mf.func, args=(), > points=self.opt_params.subdivision, verbosity=self.opt_params.verbosity) > File "/opt/relax-2.1.0/minfx/grid.py", line 256, in grid_point_array > n = len(points[0]) > > > Nested Exception from sub processor > Rank: 1 Name: hyperion-pid7244 > Exception type: IndexError > Message: index out of bounds > > ------------------------------------------------------------------------------------------------------------------------ I'm not very good in reading these kinds of traceback error messages, and in this case it's hard for me to see why the grid search failed. I noticed that my data are partly faulty: there is a single amino acid with a HetNOE > 1. This is a artifact I have to look into yet, I suppose it is a S/N problem of the original spectra (very weak peak?). Could that be the reason for the exception? I'd be grateful if you could provide a bit of support (again). Cheers Martin _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-users mailing list [email protected] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-users
