Hi Edward, I have updated relax to revision 16237. The "ave=False" flag is working fine in the "structure.read()", but when it comes to the diffusion tensor optimization the error is returned:
File "/home/vvostri/relax/math_fns/mf.py", line 80 in calc_spheroid_ci data.ci[0] = 0.25 * data.three_dz2_one**2 ValueError: setting an array element with a sequence Vitaly On Wed, May 9, 2012 at 2:50 AM, Edward d'Auvergne <[email protected]> wrote: > Hi Vitaly, > > I have just made a change to the relax repository version to improve > remove this error message and replace it with an informative > RelaxError (http://www.mail-archive.com/[email protected]/msg13833.html). > I have added a check to the model-free analysis which will hopefully > catch the condition of multiple vectors loaded per spin. Do you still > have copy of the repository? If so, could you update it with 'svn up' > and check if this error message is improved? If the message is clear, > I will then close the bug (https://gna.org/bugs/?18807). > > Cheers, > > Edward > > > On 11 October 2011 22:16, Edward d'Auvergne <[email protected]> wrote: >> Hi, >> >> Thanks for that. Setting the 'ave' flag to False is used in the other >> parts of relax, specifically the N-state model analyses using RDCs, >> PCSs, NOEs, etc. Then each state or structure N has a separate bond >> vector. But for a model-free analysis, this has no use. >> >> For your data, I would use the best of the NMR structures. You could >> compare this to an average, or to one of the other structures. But >> note that the calculation can take between 1 to 2 weeks to complete! >> So doing this for 20 structures would be expensive. >> >> Regards, >> >> Edward >> >> >> On 11 October 2011 21:52, V.V. <[email protected]> wrote: >>> 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://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
