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 >>> Processor: x86_64 >>> Processor name: Intel(R) Xeon(R) CPU E5430 @ 2.66GHz >>> Endianness: little >>> Total RAM size: 7983 Mb >>> Total swap size: 8189 Mb >>> >>> Operating system information: >>> System: Linux >>> Release: 2.6.18-164.el5 >>> Version: #1 SMP Thu Sep 3 03:28:30 EDT 2009 >>> Distribution: redhat 5.3 Final >>> Full platform string: >>> Linux-2.6.18-164.el5-x86_64-with-redhat-5.3-Final >>> >>> Python information: >>> Architecture: 64bit ELF >>> Python version: 2.5.1 >>> Python build: r251:54863, Jul 23 2008 17:35:20 >>> Python compiler: GCC Intel(R) C++ gcc 4.1 mode >>> Libc version: glibc 2.3 >>> Python executable: /program/nmr/bin/python >>> Python module path: ['/program/nmr/relax', >>> '/program/nmr/lib/python2.5/site-packages/setuptools-0.6c9-py2.5.egg', >>> '/program/nmr/lib/python25.zip', '/program/nmr/lib/python2.5', >>> '/program/nmr/lib/python2.5/plat-linux2', >>> '/program/nmr/lib/python2.5/lib-tk', >>> '/program/nmr/lib/python2.5/lib-dynload', >>> '/program/nmr/lib/python2.5/site-packages', >>> '/program/nmr/lib/python2.5/site-packages/Scientific/linux2'] >>> >>> Python packages and modules (most are optional): >>> >>> Name Installed Version Path >>> minfx True 1.0.8 >>> /program/nmr/lib/python2.5/site-packages/minfx >>> bmrblib True 1.0.3 >>> /program/nmr/lib/python2.5/site-packages/bmrblib >>> numpy True 1.6.2 >>> /program/nmr/lib/python2.5/site-packages/numpy >>> scipy False >>> wxPython False >>> matplotlib True 0.98.3 >>> /program/nmr/lib/python2.5/site-packages/matplotlib >>> mpi4py True 1.3.1 >>> /program/nmr/lib/python2.5/mpi4py >>> epydoc False >>> optparse True 1.5.3 >>> /program/nmr/lib/python2.5/optparse.pyc >>> readline True >>> /program/nmr/lib/python2.5/lib-dynload/readline.so >>> profile True >>> /program/nmr/lib/python2.5/profile.pyc >>> bz2 True >>> /program/nmr/lib/python2.5/lib-dynload/bz2.so >>> gzip True >>> /program/nmr/lib/python2.5/gzip.pyc >>> io False >>> xml True 0.8.4 (internal) >>> /program/nmr/lib/python2.5/xml/__init__.pyc >>> xml.dom.minidom True >>> /program/nmr/lib/python2.5/xml/dom/minidom.pyc >>> >>> relax information: >>> Version: repository checkout r24533 >>> svn://svn.gna.org/svn/relax/trunk >>> Processor fabric: Uni-processor. >>> >>> relax C modules: >>> >>> Module Compiled File type >>> Path >>> target_functions.relax_fit True ELF 64-bit LSB shared object, AMD >>> x86-64, version 1 (SYSV), not stripped >>> /program/nmr/relax/target_functions/relax_fit.so >>> >>> As for the data itself, I am using data obtained on two fields and use both >>> from the start. >>> >>> Upon closer look at the R20 parameters, I think both of you are right: the >>> R20a and R20b numbers are really funky. I shall follow your suggestions and >>> run the calculations with the CR72 and B14 models instead. >>> >>> Cheers, >>> >>> Chung-ke >>> >>> On Sep 9, 2014, at 4:25 PM, Troels Emtekær Linnet <tlin...@nmr-relax.com> >>> wrote: >>> >>> Hi Chung-ke. >>> >>> Can you put the information about which version of relax you use? >>> >>> You can in terminal do: >>> relax -i >>> >>> and write it here. >>> >>> And then there is the question if you used data from one field or two >>> spectrometer fields. >>> >>> Fitting to one field, can give problems. >>> This is described here: >>> >>> """Faithful estimation of dynamics parameters from CPMG relaxation >>> dispersion measurements.""" >>> Kovrigin, Evgenii L; Kempf, James G; Grey, Michael J; Loria, J Patrick >>> Journal of magnetic resonance, 2006, Vol 180, p 93-104. >>> http://www.ncbi.nlm.nih.gov/pubmed/16458551 >>> DOI: 10.1016/j.jmr.2006.01.010 >>> >>> Figure 9 and 10 shows these "rotten bananas". >>> >>> Clustering data, in some way overcome this problem. >>> Since you now starts to add more data, compared to number of fitting >>> parameters. >>> >>> The problem though, is that if you start from "single fitted" data, >>> and go to "Clustering of data", that >>> an average of the global parameter will be taken for the single fitted data. >>> >>> In previous version of relax (a version or two ago), we changed from >>> taking the average to take the median of the parameters. >>> This was to prevent taking the average of an outliers, if one of the >>> single fitted spins have been fitted "crazy". >>> You don't want to start with a global kex at 10000. >>> >>> I have discussed the CR72 Full model with my supervisor. >>> He have actually never seen it in use in any paper. >>> Always the assumption R20A=R20B is used. >>> >>> If you only have one field, I would not even try this model. >>> If you still would like to try it, please consider using the B14 full >>> model as well, to compare. >>> http://wiki.nmr-relax.com/B14_full >>> >>> Abstract: "Faithful estimation of dynamics parameters from CPMG >>> relaxation dispersion measurements." >>> This work examines the robustness of fitting of parameters describing >>> conformational exchange (k(ex), p(a/b), and Deltaomega) processes from >>> CPMG relaxation dispersion data. We have analyzed the equations >>> describing conformational exchange processes for the intrinsic >>> inter-dependence of their parameters that leads to the existence of >>> multiple equivalent solutions, which equally satisfy the experimental >>> data. We have used Monte-Carlo simulations and fitting to the >>> synthetic data sets as well as the direct 3-D mapping of the parameter >>> space of k(ex), p(a/b), and Deltaomega to quantitatively assess the >>> degree of the parameter inter-dependence. The demonstrated high >>> correlation between parameters can preclude accurate dynamics >>> parameter estimation from NMR spin-relaxation data obtained at a >>> single static magnetic field. The strong parameter inter-dependence >>> can readily be overcome through acquisition of spin-relaxation data at >>> more than one static magnetic field thereby allowing accurate >>> assessment of conformational exchange properties. >>> >>> >>> Troels Emtekær Linnet >>> PhD student >>> Copenhagen University >>> SBiNLab, 3-0-41 >>> >>> 2014-09-09 9:48 GMT+02:00 Edward d'Auvergne <edw...@nmr-relax.com>: >>> >>> Hi Chung-ke, >>> >>> Welcome to the relax mailing lists! Thanks to the hard work of one of >>> the relax developers - Troels Linnet - this long calculation time >>> should now be much, much shorter. Have a look at the following >>> release announcement: >>> >>> http://wiki.nmr-relax.com/Relax_3.3.0 >>> >>> For the 'CR72 full' model (http://wiki.nmr-relax.com/CR72_full), the >>> clustering example here gives a ~22x speed up so your calculation time >>> would then drop from ~20,000 min to ~1000 min. If you would like to >>> receive announcements about new relax versions, please subscribe to >>> the relax-announce mailing list >>> (https://mail.gna.org/listinfo/relax-announce/). This list only >>> receives ~10 emails per year. See >>> http://news.gmane.org/gmane.science.nmr.relax.announce. >>> >>> I have a few questions about how you performed the analysis. Did you >>> use a non-clustered set of results to seed the clustered analysis? In >>> the dispersion auto-analysis protocol exposed via the GUI, the results >>> from the non-clustered analysis will be taken as the starting point >>> for optimisation of the clustered analysis, as described in Morin et >>> al., 2014 (http://dx.doi.org/10.1093/bioinformatics/btu166). If you >>> wish, and are capable with scripting, you can also create your own >>> analysis protocol via a relax script and not use the auto-analysis. >>> The relax software is very flexible and you can create quite complex >>> analysis protocols - the auto-analyses are just large relax scripts. >>> >>> Also, did you look at the results from the non-clustered analysis to >>> see if the kinetics of all 13 residues are similar? Or if the >>> dispersion curves look reasonable? Some data might be of low quality >>> and causing difficulties with the optimisation. You should also note >>> that most dispersion data is not good enough to differentiate R20A >>> from R20B. Do the final results (non-clustered and clustered) look >>> reasonable for these two parameters? It could be that differentiating >>> R20A from R20B in your system is difficult and causing optimisation to >>> take much longer than normal. Do you see the same optimisation times >>> with the clustered CR72 model where R20A=R20B=R20 >>> (http://wiki.nmr-relax.com/CR72)? Also, have a look at the log file >>> from the analysis and see if the total number of minimisation >>> iterations is much longer for the 'CR72 full' model compared to the >>> CR72 model. This will tell you if the optimisation problem is much >>> more complicated for the 'full' model. >>> >>> Regards, >>> >>> Edward >>> >>> >>> On 9 September 2014 09:19, Chung-ke Chang <chun...@ibms.sinica.edu.tw> >>> wrote: >>> >>> Dear all, >>> >>> This is my first post here, and I have a question regarding the time it >>> takes for a relaxation dispersion clustering process to finish. I have one >>> clustering calculation that has been running for ~ 20,000 min on a single >>> Xeon 2.66 GHz core. The cluster consists of 13 residues being fit to the >>> ‘CR72 full’ model. I wonder if the long time it is taking is normal? Would >>> it be possible that relax has been stuck in an infinite loop of some sort, >>> without showing up in the log file? Any input would be greatly appreciated. >>> By the way, using a cluster of only 11 residues out of the 13 did finish in >>> ~13,000 min. >>> >>> Chung-ke Chang >>> Biomacromolecular NMR Lab >>> Institute of Biomedical Science >>> Academia Sinica, Taiwan >>> _______________________________________________ >>> relax (http://www.nmr-relax.com) >>> >>> This is the relax-users mailing list >>> relax-users@gna.org >>> >>> 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 >>> relax-users@gna.org >>> >>> 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 relax-users@gna.org 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
