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
Re: [sr #3155] An R1rho expression for a spin in chemical exchange between two sites with unequal transverse relaxation rates