Thank you, Edward (no problem about the delay). I have submitted the bug report (#18807). I am just curious: is there any practical use for the "ave=False" flag then? As far as my data analysis goes, I can separate the NMR ensemble into the individual models and run the calculations on each of them. Does this sound like a reasonable approach?
Vitaly On Tue, Oct 11, 2011 at 14:39, Edward d'Auvergne <[email protected]> wrote: > Hi, > > Sorry for the delay there. I've been quite busy lately. The problem > is that I'm pretty sure that the model-free analysis is not set up to > handle multiple vectors. This lies within the theory itself. The > bond vector should be in the centre of the cone or whatever the vector > distribution is. To be able to use multiple vectors would require > digging into the model-free theory and modifying it. Therefore the > vectors should be averaged or a single structure used. I am surprised > that relax allows the calculation to start without a RelaxError being > thrown. I will modify the code later to give such an error and > prevent the calculation from starting. Thanks for pointing out this > error. If you could submit it as a bug to > https://gna.org/bugs/?func=additem&group=relax, that would be very > useful if some else encounters the same problem. > > Cheers, > > Edward > > > On 11 October 2011 21:29, V.V. <[email protected]> wrote: >> Looks like it is an issue with "ave=False" flag in >> "structure.vectors", rather then "deselect.read". The NMR ensemble I >> have consists of two structured domains, connected with a flexible >> loop, i.e. the overall RMSD is fairly high and the N-H vectors in >> different models are likely to be quite different. Can this be the >> reason for the previously mentioned exception? >> >> Thank you, >> Vitaly >> >> >> On Fri, Oct 7, 2011 at 15:28, V.V. <[email protected]> wrote: >>> Hi Edward, >>> >>> I am running "dauvergne_protocol" script for my protein. The >>> "local_tm" and "sphere" models calculations proceeded fine, but with >>> prolate/oblate/ellipsoid diffusion tensors an exception is thrown (the >>> output is below). I have run the same script successfully before. The >>> difference is that I have excluded several mobile residues and using >>> "ave=False" in "structure.vectors" (the pdb file is an NMR ensemble, >>> 20 models). If necessary, I can send the input files separately. Relax >>> revision is 14809. >>> >>> Thank you, >>> Vitaly >>> >>> Traceback (most recent call last): >>> File "/home/vitalyv/relax/multi/uni_processor.py", line 136, in run >>> self.callback.init_master(self) >>> File "/home/vitalyv/relax/multi/processor.py", line 263, in >>> default_init_master >>> self.master.run() >>> File "/home/vitalyv/relax/relax.py", line 174, in run >>> self.interpreter.run(self.script_file) >>> File "/home/vitalyv/relax/prompt/interpreter.py", line 300, 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 "/home/vitalyv/relax/prompt/interpreter.py", line 610, in run_script >>> return console.interact(intro, local, script_file, quit, >>> show_script=show_script, raise_relax_error=raise_relax_error) >>> File "/home/vitalyv/relax/prompt/interpreter.py", line 495, in >>> interact_script >>> exec_script(script_file, local) >>> File "/home/vitalyv/relax/prompt/interpreter.py", line 383, 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/vitalyv/relax/wtpln/dauvergne_protocol.py", line 218, in >>> <module> >>> dAuvergne_protocol(pipe_name=name, diff_model=DIFF_MODEL, >>> mf_models=MF_MODELS, local_tm_models=LOCAL_TM_MODELS, >>> grid_inc=GRID_INC, min_algor=MIN_ALGOR, mc_sim_num=MC_NUM, >>> conv_loop=CONV_LOOP) >>> File "/home/vitalyv/relax/auto_analyses/dauvergne_protocol.py", line >>> 223, in __init__ >>> self.execute() >>> File "/home/vitalyv/relax/auto_analyses/dauvergne_protocol.py", line >>> 596, in execute >>> self.interpreter.grid_search(inc=inc) >>> File "/home/vitalyv/relax/prompt/minimisation.py", line 106, in grid_search >>> minimise.grid_search(lower=lower, upper=upper, inc=inc, >>> constraints=constraints, verbosity=verbosity) >>> File "/home/vitalyv/relax/generic_fns/minimise.py", line 146, in >>> grid_search >>> processor_box.processor.run_queue() >>> File "/home/vitalyv/relax/multi/uni_processor.py", line 149, in run_queue >>> command.run(self, completed) >>> File >>> "/home/vitalyv/relax/specific_fns/model_free/multi_processor_commands.py", >>> line 144, in run >>> raise Capturing_exception(rank=processor.rank(), >>> name=processor.get_name()) >>> Capturing_exception: >>> >>> ------------------------------------------------------------------------------------------------------------------------ >>> >>> File >>> "/home/vitalyv/relax/specific_fns/model_free/multi_processor_commands.py", >>> line 132, in run >>> results = self.optimise() >>> File >>> "/home/vitalyv/relax/specific_fns/model_free/multi_processor_commands.py", >>> line 185, in optimise >>> results = grid_point_array(func=self.mf.func, args=(), >>> points=self.opt_params.subdivision, >>> verbosity=self.opt_params.verbosity) >>> File "/usr/lib/python2.7/site-packages/minfx/grid.py", line 282, in >>> grid_point_array >>> f = func(*(points[k],)+args) >>> File "/home/vitalyv/relax/maths_fns/mf.py", line 517, in func_diff >>> self.diff_data.calc_ci(data, self.diff_data) >>> File "/home/vitalyv/relax/maths_fns/weights.py", line 80, in >>> calc_spheroid_ci >>> data.ci[0] = 0.25 * data.three_dz2_one**2 >>> >>> >>> Nested Exception from sub processor >>> Exception type: ValueError >>> Message: setting an array element with a sequence. >>> >> > _______________________________________________ relax (http://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
