On 1/8/07, Hongyan Li <[EMAIL PROTECTED]> wrote:
Dear Relax-users, I am trying to use RELAX to fit my dynamic data and now I have tried the simplest model (isotropic) to simulate the data and get a proper model for each residue and I would like to do Mone Carlo Simulations like that: monte_carlo.setup('aic', number=100) monte_carlo.create_data('aic') monte_carlo.initial_values('aic') minimise('newton', run='aic') eliminate(run='aic') monte_carlo.error_analysis('aic') # Write the results. state.save('save', force=1) results.write(run='aic', file='results', force=1) The simulations appear finished, but error was found (as follow) and no output results. relax> eliminate(run='aic', function=None, args=None)relax> monte_carlo.error_analysis(run='aic', prune=0.0) Traceback (most recent call last): File "/usr/local/bin/relax", line 454, in ? Relax() File "/usr/local/bin/relax", line 166, in __init__ self.interpreter.run() File "/data2/usr-local/relax-1.2.9/prompt/interpreter.py", line 213, in run run_script(intro=self.relax.intro_string, local=self.local, script_file=self.relax.script_file, quit=1) File "/data2/usr-local/relax-1.2.9/prompt/interpreter.py", line 388, in run_script console.interact(intro, local, script_file, quit) File "/data2/usr-local/relax-1.2.9/prompt/interpreter.py", line 340, in interact_script execfile(script_file, local) File "modelfree-final.py", line 37, in ? monte_carlo.error_analysis('aic') File "/data2/usr-local/relax-1.2.9/prompt/monte_carlo.py", line 145, in error_analysis self.__relax__.generic.monte_carlo.error_analysis(run=run, prune=prune) File "/data2/usr-local/relax-1.2.9/generic_fns/monte_carlo.py", line 236, in error_analysis sd = sqrt(sd / (float(n) - 1.0)) ZeroDivisionError: float division
Would you be able to create a bug report for this problem? It would be appreciated. The relax bug tracker is located at https://gna.org/bugs/?group=relax and bugs can be submitted at https://gna.org/bugs/?func=additem&group=relax. More information about bug submission is given in the relax manual under 'Reporting bugs' section (Section 3.3 in the relax version 1.2.9 manual). Thanks. The problem here is that 'n' is equal to 1 hence the zero division issue. 'n' is the number of Monte Carlo simulations that remain after elimination (removal of failed simulations). If you save the model-free results prior to the 'monte_carlo.error_analysis()' user function (using the 'results.write()' user function), examination of the file may tell you what the issue is. Oh, do you have the diffusion tensor fixed during the Monte Carlo simulations? If you are optimisation the global problem (diffusion tensor parameters simultaneously with all model-free parameters of all spin systems), then if the model-free model of a single residue fails, then the entire simulation is thrown out. This is because the model-free model and diffusion model all part of the same single global model. I would recommend that if you eliminate failed Monte Carlo simulations that you hold the diffusion tensor fixed so that each model-free model is independent. This will also significantly decrease the time required for the simulations. I've discussed all these issues in extensive detail at the end of the paper "d'Auvergne, E. J. and Gooley, P. R. (2006). Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data. J. Biomol. NMR, 35(2), 117–135". Edward _______________________________________________ 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
