It's relax 1.3.4 Actually the command "$ relax --info" is not producing any info.
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edward d'Auvergne Sent: quinta-feira, 7 de Abril de 2011 10:46 To: Tiago Pais Cc: [email protected] 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 <[email protected]> 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: [email protected] [mailto:[email protected]] On > Behalf Of Edward d'Auvergne > Sent: quarta-feira, 6 de Abril de 2011 18:05 > To: Tiago Pais > Cc: [email protected] > 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 <[email protected]> wrote: >> Ok, >> Im sorry to insist but I am probably missing something here. How do I > state >> which bound goes with which parameter? That is, which position in the > array >> bound corresponds to the S2f parameter? >> Regards. >> TP >> >> -----Original Message----- >> From: [email protected] [mailto:[email protected]] On >> Behalf Of Edward d'Auvergne >> Sent: quarta-feira, 6 de Abril de 2011 17:42 >> To: Tiago Pais >> Cc: [email protected] >> 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 <[email protected]> wrote: >>> Hi Ed, >>> Thanks for the quick reply. >>> Let's see if I understand your suggestion. For example, the >> mf_multimodel.py >>> sample 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 possible results, >>> correct? If so, what is the sequence for the parameters in the array? >>> TP >>> >>> >>> >>> -----Original Message----- >>> From: Edward d'Auvergne [mailto:[email protected]] >>> Sent: quarta-feira, 6 de Abril de 2011 17:13 >>> To: Tiago Pais >>> Cc: [email protected] >>> 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 <[email protected]> wrote: >>>> Hi, >>>> >>>> I would like to make an analysis of side-chain relaxation data with the >>> S2f >>>> parameter (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 virus >>> signature >>>> database 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 >>>> [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 >>>> >>>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >>> >>> __________ Information from ESET NOD32 Antivirus, version of virus >> signature >>> database 6019 (20110406) __________ >>> >>> The message was checked by ESET NOD32 Antivirus. >>> >>> http://www.eset.com >>> >>> >>> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> >> >> __________ Information from ESET NOD32 Antivirus, version of virus > signature >> database 6019 (20110406) __________ >> >> The message was checked by ESET NOD32 Antivirus. >> >> http://www.eset.com >> >> >> > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 6019 (20110406) __________ > > The message was checked by ESET NOD32 Antivirus. > > http://www.eset.com > > > > > __________ Information from ESET NOD32 Antivirus, version of virus signature > database 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 _______________________________________________ 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
