Hi, I just realised another problem - the changes to the relax manual which complete the model-free chapter have not been released yet. It is located in the main 1.3 line in the relax subversion repository. I will hopefully release relax version 1.3.16 soon so that you can have access to this information.
Regards, Edward On 11 May 2012 09:39, Edward d'Auvergne <[email protected]> wrote: > Hi Fernando, > > Sorry, I forgot to directly answer your question. You can use relax > to analyse single field strength data. relax will not only do > everything that Modelfree4, Dasha, and Tensor2 will do, but a lot > more. Note that these other programs have not been developed since > the turn of the millennium, they are now quite old, and you will still > need to read all of details in my previous mail to understand how to > use these older programs iteratively to implement a full analysis. > > Regards, > > Edward > > > > On 11 May 2012 09:34, Edward d'Auvergne <[email protected]> wrote: >> Hi Fernando, >> >> Welcome to the relax mailing lists! Before I get into the error you >> have encountered, I have noticed that the analysis you have performed >> is far from complete. I will first detail the long list of things you >> will need to do to reimplement a full analysis using single field >> strength data, and all of the reading and learning you will have to do >> to be capable and competent enough to know when things go wrong in the >> analysis, and then you might see that measuring data at a second field >> strength will actually be simpler for you ;) In any case, to have a >> good understanding of the concepts, implementation and pitfalls of a >> model-free analysis, you will be required to do a lot of reading (see >> http://www.nmr-relax.com/refs.html for a few references, with links). >> You will know you are doing the right thing when your full set of >> calculations takes 1-2 weeks to complete! >> >> Firstly, I would recommend you read my previous responses to questions >> relating to single field strength data, and look the other messages in >> those threads. You will find these discussions quite informative and >> highly detailed: >> >> - Shantanu Bhattacharyya: >> http://www.mail-archive.com/[email protected]/msg00940.html >> - Dhanasekaran Muthu: >> http://www.mail-archive.com/[email protected]/msg01005.html >> - Aldino Viegas: >> http://www.mail-archive.com/[email protected]/msg00981.html >> - Pierre-Yves Savard: >> http://www.mail-archive.com/[email protected]/msg00584.html >> - Keith Constantine: >> http://www.mail-archive.com/[email protected]/msg00379.html >> - Clare-Louise Evans: >> http://www.mail-archive.com/[email protected]/msg00196.html >> - Hongyan Li: http://www.mail-archive.com/[email protected]/msg00644.html >> - Vitaly Vostrikov: >> http://www.mail-archive.com/[email protected]/msg01002.html >> >> >> I think that covers it. There might be a little bit of irrelevant >> information in there for you, but most of it will be exactly what you >> need. For information about the implementation that you will need to >> self-assemble for single field strength data, see: >> >> - Maddy Strickland: >> http://www.mail-archive.com/[email protected]/msg00772.html >> >> >> As for using single field strength data, you will need to reimplement >> a full analysis protocol. With the model-free.py sample script, you >> have only optimised the model-free parameters for a single model for >> all spin systems in your system. However this is far from complete. >> You will need to optimise for all model-free models (m0 to m5, >> http://www.nmr-relax.com/manual/model_free_models.html). This is done >> by the mf_multimodel.py sample script. After this you will need to >> perform model elimination, then model selection using AIC, and then >> optimise the global diffusion tensor. This this needs to be done >> iteratively, and this can take up to 15 iterations, see: >> >> d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR >> dynamic models I. Minimisation algorithms and their performance within >> the model-free and Brownian rotational diffusion spaces. J. Biomol. >> NMR, 40(2), 107-119. (http://dx.doi.org/10.1007/s10858-007-9214-2). >> >> >> You will then have to do this separately for all diffusion tensors >> (spherical, prolate spheroid, oblate spheroid, and ellipsoid). Note >> that you will have the problem of the initial diffusion tensor >> estimate, and you will need to know how and when this fails: >> >> d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of the >> model-free problem and the diffusion seeded model-free paradigm. Mol. >> Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f) >> >> d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR >> dynamic models II. A new methodology for the dual optimisation of the >> model-free parameters and the Brownian rotational diffusion tensor. J. >> Biomol. NMR, 40(2), 121-133. >> (http://dx.doi.org/10.1007/s10858-007-9213-3) >> >> >> Another good reference which contains everything you'll ever need is >> my PhD thesis: >> >> d'Auvergne, E. J. (2006). Protein dynamics: a study of the model-free >> analysis of NMR relaxation data. Ph.D. thesis, Biochemistry and >> Molecular Biology, University of Melbourne. (abstract - >> http://eprints.infodiv.unimelb.edu.au/archive/00002799/, PDF - >> http://eprints.infodiv.unimelb.edu.au/archive/00002799/01/thesis.pdf, >> and my book form - >> http://www.amazon.com/Protein-Dynamics-Model-free-Analysis-Relaxation/dp/3639057627) >> >> >> For implementing a single field strength analysis, i.e. reverting back >> to how analyses were performed and published almost 2 decades ago, I >> would recommend a recent copy of the relax user manual >> (http://www.nmr-relax.com/manual/index.html) where I have completed >> the model-free analysis chapter >> (http://www.nmr-relax.com/manual/Model_free_analysis.html). The >> section titled 'The diffusion seeded paradigm' has a figure which >> details the iterative implementation that you will have to write into >> a script. There are full details about this in my PhD thesis if this >> is not enough. >> >> I would also recommend you be very careful with temperature control >> and you look at Sebastien Morin's relaxation data consistency testing >> built into relax. If you do not have temperature control (either via >> single scan interleaving or off-field temperature compensation pulses >> at the start, or both together) as well as per-experiment temperature >> calibration (running a shorted experiment on a MeOH or equivalent >> sample and seeing what the chemical shift and hence temperature is >> during an experiment), then with single field strength data you will >> fall into all of the traps of artificial nanosecond and millisecond >> motions. >> >> So maybe after reading about all of this, collecting data at a second >> field strength would really be easier ;) >> >> Regards, >> >> Edward >> >> >> P. S. The error you encountered is because the calculation you ran >> was not a full analysis - rather only a very tiny shard of a massive >> analysis. The extraction script from Michael Bieri will only operate >> on the final results of a full analysis. But note that it too >> requires an analysis using data at minimally two field strengths. >> >> >> >> On 10 May 2012 01:46, Fernando Amador <[email protected]> wrote: >>> Hi, >>> >>> I wanted to use relax to do some model-free analysis, unfortunately I do not >>> have data from multiple fields. Can I still use relax for model free >>> analysis? In most of the scripts I read it says data from multiple fields >>> is required and the gui version won't even let me run the script without >>> data from multiple fields. I figured I would still give it a shot so I >>> generated R1, R2 and steady state NOE output files using the relax gui and >>> then modified the model-free.py script by commenting out the lines for the >>> second field strength. The script runs without problems from the prompt and >>> it generates a results.bz2 file. I tried to run the >>> final_data_extraction.py script but I get this error >>> >>> relax> pipe.create(pipe_name='Data_extraction', pipe_type='mf') >>> relax> results.read(file='results', dir=None) >>> Opening the file 'results.bz2' for reading. >>> Traceback (most recent call last): >>> File "/sw/bin/relax", line 381, in <module> >>> Relax() >>> File "/sw/bin/relax", line 117, in __init__ >>> self.interpreter.run(self.script_file) >>> File "/sw/lib/relax-py27/prompt/interpreter.py", line 294, in run >>> return run_script(intro=self.__intro_string, local=locals(), >>> script_file=script_file, quit=self.__quit_flag, >>> show_script=self.__show_script, raise_relax_error=self.__raise_relax_error) >>> File "/sw/lib/relax-py27/prompt/interpreter.py", line 597, in run_script >>> return console.interact(intro, local, script_file, quit, >>> show_script=show_script, raise_relax_error=raise_relax_error) >>> File "/sw/lib/relax-py27/prompt/interpreter.py", line 483, in >>> interact_script >>> exec_script(script_file, local) >>> File "/sw/lib/relax-py27/prompt/interpreter.py", line 376, in exec_script >>> runpy.run_module(module, globals) >>> File "/sw/lib/python2.7/runpy.py", line 180, in run_module >>> fname, loader, pkg_name) >>> File "/sw/lib/python2.7/runpy.py", line 72, in _run_code >>> exec code in run_globals >>> File "/Users/Joe/NMR/relax/m4/final_data_extraction.py", line 36, in >>> <module> >>> spin_no = spin_id[spin_id.index(':')+1:spin_id.index('&')] >>> ValueError: substring not found >>> >>> I don't know if my initial model-free.py script worked. If it did, I would >>> like to look at the data. If relax can't analyze single field data, are >>> there any other programs that you would recommend. Any help would be >>> appreciated. >>> >>> >>> Thanks, >>> >>> Fernando >>> >>> >>> _______________________________________________ >>> relax (http://www.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 _______________________________________________ relax (http://www.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
