Model eliminationModel elimination|
Hi, I recently helped someone use relax and got into a small problem related to model elimination, I think. The script used consisted of minimizing one model-free model, doing Monte Carlo simulations, eliminating bad simulations and calculating errors (just as in the sample script on page 30, section 6.2.1, of the manual, v1.2.11). ================================================================== #### Script for model-free analysis: model5 #### Create the run name='m5' run.create(name,'mf') #### Nuclei type nuclei('N') #### Load the sequence sequence.read(name, 'sequence') #### Load relaxation data relax_data.read(name, 'R1', '600', 599.624 * 1e6, 'AMP-600R1s') relax_data.read(name, 'R2', '600', 599.624 * 1e6, 'AMP-600R2s') relax_data.read(name, 'NOE', '600', 599.624 * 1e6, 'AMP-600NOEs') relax_data.read(name, 'R1', '500', 499.897 * 1e6, 'AMP-500R1s') relax_data.read(name, 'R2', '500', 499.897 * 1e6, 'AMP-500R2s') relax_data.read(name, 'NOE', '500', 499.897 * 1e6, 'AMP-500NOEs') #### Setup other values diffusion_tensor.init(name, 6.7 * 1e-9, fixed=1) value.set(name, 1.02 * 1e-10, 'bond_length') value.set(name, -172 * 1e-6, 'csa') #### Select the model-free model model_free.select_model(run=name, model=name) #### Grid search grid_search(name, inc=11) #### Minimise minimise('newton', run=name) #### Monte Carlo simulations monte_carlo.setup(name, number=500) monte_carlo.create_data(name) monte_carlo.initial_values(name) minimise('newton', run=name) eliminate(run=name) monte_carlo.error_analysis(name) #### Finish results.write(run=name, file=name, force=1) ================================================================== R1s, R2s and NOEs were available from 2 magnetic fields for most residues, some of which only had data from 1 magnetic field. For some models (5,6,7,8), model elimination eliminated lots of simulations... When reaching the 'monte_carlo.error_analysis' call, relax crashed with the following error : ================================================================== relax> monte_carlo.error_analysis(run='m5', 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 "/usr/local/packages/relax/prompt/interpreter.py", line 216, in run run_script(intro=self.relax.intro_string, local=self.local, script_file=self.relax.script_file, quit=1) File "/usr/local/packages/relax/prompt/interpreter.py", line 391, in run_script console.interact(intro, local, script_file, quit) File "/usr/local/packages/relax/prompt/interpreter.py", line 343, in interact_script execfile(script_file, local) File "./model5", line 42, in ? monte_carlo.error_analysis(name) File "/usr/local/packages/relax/prompt/monte_carlo.py", line 145, in error_analysis self.__relax__.generic.monte_carlo.error_analysis(run=run, prune=prune) File "/usr/local/packages/relax/generic_fns/monte_carlo.py", line 220, in error_analysis Xav = Xsum / float(n) ZeroDivisionError: float division ================================================================== It seems 'n' was zero for at least one residue... Is this something that should be fixed within relax (adding a test that would skip error analysis when n=0, but allow the script to end without crashing, or adding a more useful error message) ? Thanks ! Séb :) -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 |