Re: R1rho RD analysis
Hi Peixiang, Please see below: Congratulations about the new version of 3.2.2, I tried, it works well :) Cheers. If you notice any other problems or strange behaviour, please don't hesitate to submit a bug report (https://gna.org/bugs/?func=additemgroup=relax). Then that problem will likely be fixed for the next relax version. Still one question of using the different relaxation time periods. My R1rho RD experiment has different relaxation time periods, I could input all the peaks by the loop. Then I fit with 'NS 2-site R1 model', they could also do the fitting and give the results and also a nice fitting of the dispersion curve. Still I did not figure out, which Trelax is it using in the NS model in the case of different relaxation time periods. Only the last relaxation time period? Then fit as fixed time experiment? As this code was directly contributed by Paul Schanda and Dominique Marion, and I'm guessing that their offices are not too far from yours at the IBS, maybe you could ask them directly ;) Well, it was Paul who organised that the code be contributed to relax. In reality the original authors were Nikolai Skrynnikov and Martin Tollinger. The API documentation is also a useful resource for answering such questions (http://www.nmr-relax.com/api/3.2/). For this, see the relax library documentation for that model: http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-module.html This documentation describes the origin and history of the code. You could even look at the source code for the direct implementation: http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-pysrc.html Trelax is the 'relax_time' argument here. You can find all implementation details in this API documentation. Which relaxation time would you suggest as being correct? I'm actually no longer sure which is being used. And I'm not sure if the original code or even the numeric model itself was designed to handle variable time data. Maybe I am the minority to use such time consuming experiments, so I always have such strange questions ... relax should still handle the situation. Do you know if there is a special treatment for the numerical models for such data? Do you know of a good citation? Maybe the 'NS R1rho 2-site' model (http://wiki.nmr-relax.com/NS_R1rho_2-site) is not suitable for variable time data, and a different - and importantly published - solution is required. The analytic models do not use the relaxation time value, so those are safe. Hence, as a check, you should see very similar results from the 'DPL94' model (http://wiki.nmr-relax.com/DPL94) and the 'NS R1rho 2-site' model. If not, something is wrong. If the 'NS R1rho 2-site' model is really only for fixed-time data, then we should modify relax to raise a RelaxError when this model is chosen for optimisation and the data is variable time. As not many people optimise numeric models to variable-time data, your input into this question would be very valuable. Cheers! Maybe another annoying question for the fix time people: Another question, does it necessary to check how mono-exponential about their relaxation curve under certain rf-field? If not, how did they make sure they can use the mono-exponential assumption to get R2eff by two points? From what I've seen and heard, some people do check, but the majority just assume that the curves will be mono-exponential and publish the fixed-time data and results. Such a check is probably much more important for those collecting R1rho-type data rather than CPMG-type data. Anyway, maybe you should ask people in front of their posters at conferences to get a better overview of what the field does. Regards, Edward Best, Peixiang On 05/19/2014 05:49 PM, Edward d'Auvergne wrote: Hi Peixiang, Welcome to the relax mailing lists! The relaxation dispersion analysis implemented in relax is quite flexible, and the data you have is supported. This is well documented in the relax manual which you should have with your copy of relax (the docs/relax.pdf file). Have a look at section 'The R2eff model' in the dispersion chapter of the manual (http://www.nmr-relax.com/manual/R2eff_model.html), specifically the 'Variable relaxation period experiments' subsection. Unfortunately the sample scripts are all for the fixed time dispersion experiments. However you could have a look at one of the scripts used for the test suite in relax: test_suite/system_tests/scripts/relax_disp/exp_fit.py This script is run in the test suite to ensue that the data you have will always be supported. There are many more scripts in that directory which you might find interesting. The 'r1rho_on_res_m61.py' script also involve an exponential fit with many different relaxation time periods. ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this
Re: R1rho RD analysis
Hi Peixiang, Actually, for comparison purposes for applying the 'NS R1rho 2-site' model (http://wiki.nmr-relax.com/NS_R1rho_2-site) to variable-time R1rho-type data, Art Palmer's MP05 model would be much better (http://wiki.nmr-relax.com/MP05) than the DPL94 model (http://wiki.nmr-relax.com/DPL94) as it is of much higher quality. Andy Baldwin apparently has derived an even better analytic model, especially when R20A and R20B are significantly different, see: http://gna.org/support/?3155#comment0 and the discussions in the thread: http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5447 and: http://thread.gmane.org/gmane.science.nmr.relax.devel/5410/focus=5433 This last thread is about the B14 model (Baldwin 2014, http://wiki.nmr-relax.com/B14) implemented in relax by Troels Linnet, but there are mentions of Andy's R1rho model. However the R1rho model from Andy is not implemented in relax yet. Do you have much experience with variable-time R1rho numeric models? Looking at the code for where the relax_time variable comes from, it is not very clear which relaxation time is being used: http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.data-module.html#loop_time From the code itself: http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.data-pysrc.html#loop_time it looks like this loop_time() function assumes fixed-time data and hence only the first encountered time value for the given experiment, magnetic field strength, offset, and dispersion point is used. So your expertise will be very useful for resolving this variable-time R1rho numeric model problem! Note that there are a few improvements to the R1rho models that are yet to be implemented in relax: http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5808 http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html Cheers, Edward On 11 June 2014 10:07, Edward d'Auvergne edw...@nmr-relax.com wrote: Hi Peixiang, Please see below: Congratulations about the new version of 3.2.2, I tried, it works well :) Cheers. If you notice any other problems or strange behaviour, please don't hesitate to submit a bug report (https://gna.org/bugs/?func=additemgroup=relax). Then that problem will likely be fixed for the next relax version. Still one question of using the different relaxation time periods. My R1rho RD experiment has different relaxation time periods, I could input all the peaks by the loop. Then I fit with 'NS 2-site R1 model', they could also do the fitting and give the results and also a nice fitting of the dispersion curve. Still I did not figure out, which Trelax is it using in the NS model in the case of different relaxation time periods. Only the last relaxation time period? Then fit as fixed time experiment? As this code was directly contributed by Paul Schanda and Dominique Marion, and I'm guessing that their offices are not too far from yours at the IBS, maybe you could ask them directly ;) Well, it was Paul who organised that the code be contributed to relax. In reality the original authors were Nikolai Skrynnikov and Martin Tollinger. The API documentation is also a useful resource for answering such questions (http://www.nmr-relax.com/api/3.2/). For this, see the relax library documentation for that model: http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-module.html This documentation describes the origin and history of the code. You could even look at the source code for the direct implementation: http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-pysrc.html Trelax is the 'relax_time' argument here. You can find all implementation details in this API documentation. Which relaxation time would you suggest as being correct? I'm actually no longer sure which is being used. And I'm not sure if the original code or even the numeric model itself was designed to handle variable time data. Maybe I am the minority to use such time consuming experiments, so I always have such strange questions ... relax should still handle the situation. Do you know if there is a special treatment for the numerical models for such data? Do you know of a good citation? Maybe the 'NS R1rho 2-site' model (http://wiki.nmr-relax.com/NS_R1rho_2-site) is not suitable for variable time data, and a different - and importantly published - solution is required. The analytic models do not use the relaxation time value, so those are safe. Hence, as a check, you should see very similar results from the 'DPL94' model (http://wiki.nmr-relax.com/DPL94) and the 'NS R1rho 2-site' model. If not, something is wrong. If the 'NS R1rho 2-site' model is really only for fixed-time data, then we should modify relax to raise a RelaxError when this model is chosen for optimisation and the data is variable time. As not many people optimise numeric models to variable-time data, your input into this
Re: dimer
Hi Stefano,
For what has happened here, you need to open up your log file. Did
you use relax with the --log or --tee command line options to capture
the messages? If you go to the start of the messages, you will very
likely find RelaxWarnings which say something like deselecting the
spin due to missing {relaxation data; bond vector information; etc.}
or due to something else in the set up. In relax, everything that
happens is sent to the log so you can always go back and see exactly
what happened. I hope this solves your problem.
Regards,
Edward
On 10 June 2014 23:53, Stefano Luciano Ciurli stefano.ciu...@unibo.it wrote:
Hi Edward, an additional question: in the output file I noticed that the last
four residues at the C-terminus, for which I provided relaxation data, are
not included. Any reason for it? (for the previous 9 residues we did not have
the assignment because they are not observed due to intermediate exchange
phenomena that broaden them too much to be visible, while the last four
residues are clearly visible and they appear to be very mobile, and yet, no
output from relax.
Stefano
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