Hi Chung-ke. You will be fine with numpy 1.6.2, as long as you stay in the analytical models + "NS 2-site expanded"
If you would like to do the numerical models, "NS 2-site 3D plus NS 2-site Star", you should try to get numpy 1.8. This is because, that numpy 1.8 can handle linear algebra in 5 dimensional data array, and will be 5x faster. When users only have 1.6, I had to make a hack by striding through the data dimensions, and do the linear algebra matrix operations per dimension. That is 5x slower. Best Troels 2014-09-11 11:59 GMT+02:00 Chung-ke Chang <chun...@ibms.sinica.edu.tw>: > 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
