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 > > > _______________________________________________ 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
