Re: Relaxation dispersion clustering calculation time
Hi Chung-ke, The aim of relax is to support absolutely every NMR dynamics theory in existence! For the relaxation dispersion analysis section of relax, this means supporting all published models for the dispersion data, and all parametric restrictions of these models. Many of the dispersion models have been derived with the assumption that R20A and R20B are different, the Carver and Richards model is a good example of this (http://wiki.nmr-relax.com/CR72_full). These are the '* full' models in relax. However in the literature the parametric restriction R20A = R20B (= R20) is almost always used. For the analytic models this can significantly simplify the equations, whereas for the numeric models the equations do not change. In both cases, two dimensions of the the optimisation space collapse into one and the optimisation problem massively simplifies. That is why in relax we also provide the collapsed models (those with the ' full' part of the label removed). It is true most literature data is not suitable for the '* full' models. That is why they are not turned on by default in the GUI or listed in the sample scripts. From memory though, there are cases whereby the measured data is of high enough quality and collected on enough magnets that the R20A != R20B assumption can be made. I cannot remember the reference(s), but it shouldn't be too hard to find. Anyway, the full R20A != R20B models are provided in relax for a number of reasons: - The rare cases whereby the data is good enough. - Academic studies. - Future developments could significantly improve the quality of measured dispersion data so that the R20A != R20B assumption can be regularly made. - Chemists have a different perspective on life compared to biologists. Small organic molecules make the R20A vs. R20B distinction much, much easier. I hope it is now clearer why there are these models in relax. Regards, Edward On 10 September 2014 15:27, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote: Dear Edward and Troels, Thank you all for the help! We are currently testing the new version of relax (yes, we are using the “normal” release), and making sure it plays along nicely with other software - we have a plethora of different python versions, which the system manager is doing his best to avoid interfering with each other. I am curious about one thing though: If the ‘CR72 full’ model has not been used in any published studies, then is there any reason to include it when trying to fit “real-world” data? It seems that Troels is implying that “real-world” data is too noisy to obtain meaningful fitting parameters from the model. Or am I misunderstanding something? Cheers, Chung-ke On Sep 9, 2014, at 8:56 PM, Edward d'Auvergne edw...@nmr-relax.com wrote: Hi Chung-ke, The only way to find out about new relax releases is the relax-announce mailing list (http://news.gmane.org/gmane.science.nmr.relax.announce). Some relax users were signed up for the freecode announcements (http://freecode.com/projects/nmr-relax), but freecode has unfortunately shut down (http://freecode.com/about). For the version you are currently using, note that this is the repository version of relax installed by the superuser. You should make sure you use the normal releases, as the repository version can sometimes be in a broken or buggy state as development occurs. You can also have a copy in your home directory by typing: $ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk $ cd relax-trunk $ scons If you already have a repository version on your system, these commands should just work. But you should only use the repository version if you would like a bug fix and cannot wait until the next relax release. Regards, Edward On 9 September 2014 10:37, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote: Dear Troels and Edward, Thank you for the pointers. I was not aware that a new version was out last week, so I’ve asked the IT people to install it on our cluster. Below is the output from ‘relax -i’: [chungke@nmrc10 onc_dAUGA_MES_310K]$ relax -i relax repository checkout r24533 svn://svn.gna.org/svn/relax/trunk Molecular dynamics by NMR data analysis Copyright (C) 2001-2006 Edward d'Auvergne Copyright (C) 2006-2014 the relax development team This is free software which you are welcome to modify and redistribute under the conditions of the GNU General Public License (GPL). This program, including all modules, is licensed under the GPL and comes with absolutely no warranty. For details type 'GPL' within the relax prompt. Assistance in using the relax prompt and scripting interface can be accessed by typing 'help' within the prompt. Processor fabric: Uni-processor. Hardware information: Machine: x86_64
Re: Relaxation dispersion clustering calculation time
Dear Edward, Thank you for the thorough explanation. Yes, I now see why having the “full” models would be useful. I will try to track down the references you mentioned - I hope they are indexed in PubMed, I really have little idea on how to search for “pure” chemistry papers - and take a look at the scenarios where using the full models would be appropriate. I guess that I also need to re-read some of the literature on how to apply relaxation dispersion analysis to biological systems. The R20A = R20B assumption must be buried somewhere in the materials and methods section…. Cheers, Chung-ke On Sep 10, 2014, at 10:08 PM, Edward d'Auvergne edw...@nmr-relax.com wrote: Hi Chung-ke, The aim of relax is to support absolutely every NMR dynamics theory in existence! For the relaxation dispersion analysis section of relax, this means supporting all published models for the dispersion data, and all parametric restrictions of these models. Many of the dispersion models have been derived with the assumption that R20A and R20B are different, the Carver and Richards model is a good example of this (http://wiki.nmr-relax.com/CR72_full). These are the '* full' models in relax. However in the literature the parametric restriction R20A = R20B (= R20) is almost always used. For the analytic models this can significantly simplify the equations, whereas for the numeric models the equations do not change. In both cases, two dimensions of the the optimisation space collapse into one and the optimisation problem massively simplifies. That is why in relax we also provide the collapsed models (those with the ' full' part of the label removed). It is true most literature data is not suitable for the '* full' models. That is why they are not turned on by default in the GUI or listed in the sample scripts. From memory though, there are cases whereby the measured data is of high enough quality and collected on enough magnets that the R20A != R20B assumption can be made. I cannot remember the reference(s), but it shouldn't be too hard to find. Anyway, the full R20A != R20B models are provided in relax for a number of reasons: - The rare cases whereby the data is good enough. - Academic studies. - Future developments could significantly improve the quality of measured dispersion data so that the R20A != R20B assumption can be regularly made. - Chemists have a different perspective on life compared to biologists. Small organic molecules make the R20A vs. R20B distinction much, much easier. I hope it is now clearer why there are these models in relax. Regards, Edward On 10 September 2014 15:27, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote: Dear Edward and Troels, Thank you all for the help! We are currently testing the new version of relax (yes, we are using the “normal” release), and making sure it plays along nicely with other software - we have a plethora of different python versions, which the system manager is doing his best to avoid interfering with each other. I am curious about one thing though: If the ‘CR72 full’ model has not been used in any published studies, then is there any reason to include it when trying to fit “real-world” data? It seems that Troels is implying that “real-world” data is too noisy to obtain meaningful fitting parameters from the model. Or am I misunderstanding something? Cheers, Chung-ke On Sep 9, 2014, at 8:56 PM, Edward d'Auvergne edw...@nmr-relax.com wrote: Hi Chung-ke, The only way to find out about new relax releases is the relax-announce mailing list (http://news.gmane.org/gmane.science.nmr.relax.announce). Some relax users were signed up for the freecode announcements (http://freecode.com/projects/nmr-relax), but freecode has unfortunately shut down (http://freecode.com/about). For the version you are currently using, note that this is the repository version of relax installed by the superuser. You should make sure you use the normal releases, as the repository version can sometimes be in a broken or buggy state as development occurs. You can also have a copy in your home directory by typing: $ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk $ cd relax-trunk $ scons If you already have a repository version on your system, these commands should just work. But you should only use the repository version if you would like a bug fix and cannot wait until the next relax release. Regards, Edward On 9 September 2014 10:37, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote: Dear Troels and Edward, Thank you for the pointers. I was not aware that a new version was out last week, so I’ve asked the IT people to install it on our cluster. Below is the output from ‘relax -i’: [chungke@nmrc10 onc_dAUGA_MES_310K]$ relax -i relax repository checkout r24533
