Hi Edward, I have been trying several combinations but the grid search does not appear to be doing its job. I have used the following command in the script: "grid_search(lower=[0.111, 0, -0.0], upper=[0.111, 1.00, 200], inc=[16, 16, 16], verbosity=7)"
But I keep seeing this during the calculations: "Min f: 3474.82 k: 3860 xk: [ 0.111, 0.066667, -0] fk: nan Increment: array([ 5, 16, 16]) Params: array([ 0.111, 1. , Inf]) Min params: array([ 0.111 , 0.06666667, -0. ]) f: nan Min f: 3474.82 k: 3861 xk: [ 0.111, 0.066667, -0] fk: nan Increment: array([ 6, 16, 16]) Params: array([ 0.111, 1. , Inf]) Min params: array([ 0.111 , 0.06666667, -0. ]) f: nan " And at the end the tauS is zero for all spins and the S2s is always close to 1. It appears that the space is not being adequately created... Any suggestion? Thanks Tiago P -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Edward d'Auvergne Sent: quinta-feira, 7 de Abril de 2011 12:15 To: Tiago Pais Cc: [email protected] Subject: Re: How to set S2f to 0.111? - SOLVED with 1.3.8 Ah, right. I did fix that bug! I thought so :) Ok, if you have any problems, don't hesitate to ask. Bye, Edward On 7 April 2011 13:09, Tiago Pais <[email protected]> wrote: > I have now also running the 1.3.8 version and the problem seems to have > disappeared. Took me some time to use this version because the column > numbering has changed, now columns start at number one! Important! ;-) > > I hope now this goes well. > > Thanks once more for your valuable help. > Cheers > Tiago > > -----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 > > > __________ 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 6031 (20110410) __________ 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
