Dear Edward and Troels, Thank you for the additional info. So it seems that although cpmg_fit has the choice to use different R20’s, current literature is still limited to the R20A = R20B assumption. I actually have a copy of Korzhnev’s paper in my computer; will certainly take a closer look. I think my inexperience in the analysis is also a factor, and your information has been a huge help.
We already got 3.3.0 running, but it is still using an older version of numpy in our cluster. I know about canopy (in fact, I have it installed on my personal Mac), but last time I tried to install it on my personal account in the cluster computer, something went wrong and a lot of python-dependent stuff wouldn’t run. Since the system admin already gave his word that he will do his best to update our python system, I’ll just trust him… for now *grin*. Cheers, Chung-ke PS: 3.3.0 does feel zippier than the older version, even using an old numpy (1.6.2?). The speed up is really impressive. Kudos to a job well done! On Sep 11, 2014, at 5:36 PM, Edward d'Auvergne <edw...@nmr-relax.com> wrote: > Hi Chung-ke, > > I actually now remember that I saw the R20A != R20B analysis presented > at a conference somewhere, though again I can't remember by whom. I'm > pretty sure it was real data, very likely at 3 magnetic fields, and > possibly including multiple-quantum data as well, i.e. the MMQ models > in relax (http://wiki.nmr-relax.com/Category:MMQ_CPMG_data). I would > guess it was someone from the Kay, Palmer or Wright groups. You will > probably not find the R20A = R20B assumption written in most papers, > as people just use the software blindly and don't realise that there > is a difference. Most software have the R20A = R20B assumption > hardcoded so you have no choice. The more advanced software from > Dmitry Korzhnev (cpmg_fit) allows you to fit these separately though. > You will however find the text about the assumption in pretty much all > of Dmitry's papers, for example in http://dx.doi.org/10.1021/ja054550e > : > > "The adjustable parameters for the "global" two-state model (F <-> > U) include nc‚nr‚nf intrinsic (transverse relaxation) R2 rates > (assumed to be the same in F and U states), ..." > > This is also well described in Art Palmer's 2001 Methods in Enzymology > review (http://dx.doi.org/10.1016/S0076-6879(01)39315-1). > > Regards, > > Edward > > > P. S. Troels' instructions for setting up your one Python and relax > installation is a great way to quickly have relax available, > especially if you wish to use a new version or the repository version > to obtain a quick bug fix. > > > On 10 September 2014 19:42, Chung-ke Chang <chun...@ibms.sinica.edu.tw> wrote: >> 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 >>>>>> 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
