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 > > > _______________________________________________ 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
