Hi Flemming, I forgot to mention, but this was a post to one of the relax mailing lists. So be careful if you reply as the message will be permanently archived on the internet with no way of deleting it.
Cheers, Edward On 2 May 2014 19:59, Edward d'Auvergne <[email protected]> wrote: > Hi Andy, > > Continuing again from > http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5457: > > >>> CATIA also does not handle R1rho data >>> or models. Anyway, relax has a user function called >>> relax_disp.catia_input which can simplify the life of users by >>> creating the required CATIA input files. There is even a >>> relax_disp.catia_execute user function to allow CATIA to be run from >>> within relax. >> >> >> That's actually a great feature I think. Good stuff! How are you dealing >> with e.g. selecting the right cpmg sequence and basis sets in the input >> scripts generated by your code? > > This CATIA interfacing code is still relatively primitive: > > http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.catia-module.html > http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.catia-pysrc.html > > The main problem is that I'm not sure how this is set up in CATIA, or > which different CPMG sequences or basis sets are supported. For the > basis in the CATIA example input files, I can only see Iph_7 and > TrATr_13;estimate_etaZ. But I have no idea what these mean or if > there are others. I unfortunately don't have code in this case to > work out everything that is happening, as there is unfortunately no > CATIA documentation. It would be good to expand the > relax_disp.catia_input user function to select between different basis > sets and also have a human readable description of what these are. In > relax, the experiment types supported are labelled as: > > 'SQ CPMG': The single quantum (SQ) CPMG-type experiments, > 'ZQ CPMG': The zero quantum (ZQ) CPMG-type experiments, > 'DQ CPMG': The double quantum (DQ) CPMG-type experiments, > 'MQ CPMG': The multiple quantum (MQ) CPMG-type experiments, > '1H SQ CPMG': The 1H single quantum (SQ) CPMG-type experiments, > '1H MQ CPMG': The 1H multiple quantum (MQ) CPMG-type experiments, > 'R1rho': The R1rho-type experiments. > > As can be seen at > http://www.nmr-relax.com/api/3.1/specific_analyses.relax_disp.catia-pysrc.html#catia_input, > only the first is handled for the CATIA input. It is set to "seqfil = > CW_CPMG" in CATIA notation as I don't know if there is a pi pulse > equivalent seqfil setting. Setting CW verses pi pulse is therefore > obviously missing from the relax_disp.catia_input user function. > There is no support for the funky half CPMG block that Dmitry's > cpmg_fit software supports, though the back end code for it has been > implemented for the 'NS MMQ 2-site' model in relax: > > http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_mmq_2site-pysrc.html > > As for the TROSY and CEST experiment types, these are also not > supported by relax yet. I should add this to the TODO list > (http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html). > > Another thing on my todo list is to implement a grid search into the > CATIA script, as there is no inbuilt grid search in CATIA. The > current input method requires you to specify exact starting parameter > values. The use of a grid search for finding the initial parameter > values is one of the major reasons why relax appears to be much slower > than CATIA and cpmg_fit, but this is actually a distinct advantage for > relax. > > Anyway, the CATIA support will evolve as relax users provide feedback. > I hope to expand this with time to cover all of CATIA's features. > Just as I hope to have relax expand to support all developments in the > relaxation dispersion field, I also hope to expand relax to support > the input file creation, execution and results reading for all > relaxation dispersion software. I also hope to expand the software > comparison table in the relax manual to properly explain all features > and advantages of all the software available (see table 10.3 in > http://download.gna.org/relax/manual/relax.pdf). > > >>> If a relax_disp.catia_extract user function is added, >>> then CATIA could be used as a replacement optimisation engine in relax >>> and the user will only need to have an executable CATIA binary in >>> their system path. A similar set of user functions exist for Art >>> Palmer's CPMGFit, NESSY and ShereKhan. >>> >>> For relax, the idea is to add the off-resonance support to a few of >>> the numeric models (not all as the Tollinger & Skrynnikov Maple >>> expansion cannot support it). This is in the todo list >>> (http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html). >>> As no other dispersion software supports the scalar coupling and spin >>> flips, as far as I am aware, there are no plans or pressure to add >>> this. >> >> As detailed in my last email, neglecting this stuff will give you wrong >> answers. These things have been standard in Flemming's CATIA since its >> inception. This software was used for the excited state structures you might >> have seen from the Kay lab recent that have encouraged a great many people >> to try CPMG. So if people want to emulate that, probably the responsible >> thing to do is to encourage them to do the analysis rigorously. > > Would you know the best reference for the handling of scalar coupling? > I'm going to guess this is the J coupling talked about in: > > - Hansen, D. F., Vallurupalli, P., Lundstrom, P., Neudecker, P., and > Kay, L. E. (2008). Probing chemical shifts of invisible states of > proteins with relaxation dispersion NMR spectroscopy: how well can we > do? J. Am. Chem. Soc., 130(8), 2667–2675. > (http://dx.doi.org/10.1021/ja078337p). > > And what would be the best reference for the spin flips? Would you > know how these are implemented or set up in CATIA? relax has support > for J couplings, but this is not used in the dispersion analysis. I > should really expand the todo list and the feature table. > > Cheers, > > Edward _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-devel 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-devel
