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://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
