Hi, This really looks like a bug I fixed a long time ago, although unfortunately I cannot find it at the moment. Are you able to try out the latest version of relax, version 1.3.10 from http://www.nmr-relax.com/download.html? The grid search code of minfx (https://gna.org/projects/minfx/), which is now bundled with relax, is now radically different to that of 1.3.4 and is much more powerful. Regards, Edward On 7 April 2011 12:04, Tiago Pais <tpais@xxxxxxxxxxx> wrote:
It's relax 1.3.4 Actually the command "$ relax --info" is not producing any info. -----Original Message----- From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On Behalf Of Edward d'Auvergne Sent: quinta-feira, 7 de Abril de 2011 10:46 To: Tiago Pais Cc: relax-users@xxxxxxx Subject: Re: How to set S2f to 0.111? Hi, I've looked up that line in the specific_fns/model_free/mf_minimise.py file, and it looks like you are using an older version of relax. Could you copy the output of: $ relax --info This looks like an ancient bug that was eliminated a long, long time ago. Cheers, Edward On 6 April 2011 19:51, Tiago Pais <tpais@xxxxxxxxxxx> wrote:I used the expression like this: grid_search(lower=[0.111, 0, 0], upper=[0.111, 2, 1E12], inc=[1, 11, 11]) But I get the following error: Unconstrained grid search size: 121 (constraints may decrease this size). Traceback (most recent call last): File "/usr/local/bin/relax", line 418, in <module> Relax() File "/usr/local/bin/relax", line 127, in __init__ self.interpreter.run(self.script_file) File "/usr/local/relax/prompt/interpreter.py", line 276, in run return run_script(intro=self.__intro_string, local=self.local, script_file=script_file, quit=self.__quit_flag, show_script=self.__show_script,raise_relax_error=self.__raise_relax_error)File "/usr/local/relax/prompt/interpreter.py", line 537, in run_script return console.interact(intro, local, script_file, quit, show_script=show_script, raise_relax_error=raise_relax_error) File "/usr/local/relax/prompt/interpreter.py", line 433, in interact_script execfile(script_file, local) File "mf_multimodel_m5S2f0111.py", line 82, in <module> grid_search(lower=[0.111, 0, 0], upper=[0.111, 1, 11], inc=[1, 11, 11]) File "/usr/local/relax/prompt/minimisation.py", line 156, in grid_search minimise.grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity) File "/usr/local/relax/generic_fns/minimise.py", line 191, in grid_search grid_search(lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 479, in grid_search self.minimise(min_algor='grid', lower=lower, upper=upper, inc=inc, constraints=constraints, verbosity=verbosity, sim_index=sim_index) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 922, in minimise min_options = self.grid_search_config(num_params, spin=spin, lower=lower, upper=upper, inc=inc, scaling_matrix=scaling_matrix) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 554, in grid_search_config self.grid_search_config_fin(min_options, lower, upper, scaling_matrix) File "/usr/local/relax/specific_fns/model_free/mf_minimise.py", line 631, in grid_search_config_fin for i in xrange(n): NameError: global name 'n' is not defined Any ideas? Cheers Tiago -----Original Message----- From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 6 de Abril de 2011 18:05 To: Tiago Pais Cc: relax-users@xxxxxxx Subject: Re: How to set S2f to 0.111? Hi, These match the parameters as listed in the help for the model_free.select_model() user function. The grid search arrays match the parameter arrays. Regards, Edward On 6 April 2011 18:54, Tiago Pais <tpais@xxxxxxxxxxx> wrote:Ok, Im sorry to insist but I am probably missing something here. How do Istatewhich bound goes with which parameter? That is, which position in thearraybound corresponds to the S2f parameter? Regards. TP -----Original Message----- From: edward.dauvergne@xxxxxxxxx [mailto:edward.dauvergne@xxxxxxxxx] On Behalf Of Edward d'Auvergne Sent: quarta-feira, 6 de Abril de 2011 17:42 To: Tiago Pais Cc: relax-users@xxxxxxx Subject: Re: How to set S2f to 0.111? Hi, That is roughly correct. Just set the lower and upper bound to 0.111 and set the number of increments for that parameter to 1. Then it is like a grid search without S2f being present, or being fixed to 0.111. Regards, Edward On 6 April 2011 18:38, Tiago Pais <tpais@xxxxxxxxxxx> wrote:Hi Ed, Thanks for the quick reply. Let's see if I understand your suggestion. For example, themf_multimodel.pysample script performs a grid search minimization using the grid_search function. So if I insert an array of upper and lower bounds for the parameters in the model I can constrain the interval of possibleresults,correct? If so, what is the sequence for the parameters in the array? TP -----Original Message----- From: Edward d'Auvergne [mailto:edward.dauvergne@xxxxxxxxx] Sent: quarta-feira, 6 de Abril de 2011 17:13 To: Tiago Pais Cc: relax-users@xxxxxxx Subject: Re: How to set S2f to 0.111? Hi, Unfortunately, there is no ability to fix one of the model-free parameters during optimisation in relax yet. This is something that has been requested one or two times over the years. This is complicated as the gradients and Hessians (first and second partial derivates) need to be modified with this in mind, as the curvature of the space changes. The fixed parameter is not part of the gradient or Hessian, and has to be removed. This really complicates the target function, gradient, and Hessian and, due to the low demand, has not been implemented. Are you able to optimise this parameter and see if you get 0.111? And are you able to extract the timescale of this process (the methyl group rotamer jumps)? From memory, someone has optimsed these models using a grid search. This coarse optimisation can be performed in relax as you are able to specify the fine details of the grid search. It is slower, but will do the job. You could even implement a zooming grid search if your scripting skills are up to it to be able to relatively quickly find the parameters to high precision. Anyway, I hope this info helps. Regards, Edward On 6 April 2011 17:39, Tiago Pais <tpais@xxxxxxxxxxx> wrote:Hi, I would like to make an analysis of side-chain relaxation data with theS2fparameter (in model 5) set to 0.111. Is it possible to do this with RELAX? How? Thanks in advance. Cheers Tiago P ************************************** Tiago Pais, PhD. student Cell Physiology & NMR Instituto de Tecnologia Química e Biológica-Oeiras __________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@xxxxxxx 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__________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com__________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com__________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __________ Information from ESET NOD32 Antivirus, version of virussignaturedatabase 6019 (20110406) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com__________ Information from ESET NOD32 Antivirus, version of virus signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com __________ Information from ESET NOD32 Antivirus, version of virus signature database 6021 (20110407) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com