Difference between revisions of "NS CPMG 2-site expanded"
Jump to navigation
Jump to search
(→Intro) |
m (Switch to the {{gna task link}} template to remove dead Gna! links.) |
||
| (10 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | |||
The relaxation dispersion model for the numeric solution (NS) to the Bloch-McConnell equations for [[SQ CPMG-type data]]. This uses the Maple expanded and fast equations from Nikolai Skrynnikov. The model is labelled as '''NS CPMG 2-site expanded''' in [[Relaxation dispersion citation for relax|relax]]. | The relaxation dispersion model for the numeric solution (NS) to the Bloch-McConnell equations for [[SQ CPMG-type data]]. This uses the Maple expanded and fast equations from Nikolai Skrynnikov. The model is labelled as '''NS CPMG 2-site expanded''' in [[Relaxation dispersion citation for relax|relax]]. | ||
This type of model can be called '''silico''' derived, as it is a computer-assisted derivation for the equivalent computations, of the much more expensive numerical matrix-form. | This type of model can be called '''silico''' derived, as it is a computer-assisted derivation for the equivalent computations, of the much more expensive numerical matrix-form. | ||
| + | |||
| + | This function is exact, just as the explicit Bloch-McConnell numerical treatments. It comes from a Maple derivation based on the Bloch-McConnell equations. It is much faster than the numerical Bloch-McConnell solution. It was derived by Nikolai Skrynnikov and is provided with his permission. | ||
== Parameters == | == Parameters == | ||
| − | The NS CPMG 2-site expanded model has the parameters { | + | The NS CPMG 2-site expanded model has the parameters {{{:R2zero}}, ..., {{:pA}}, {{:Deltaomega}}, {{:kex}}}. |
== Code == | == Code == | ||
| − | The library code | + | The library code: {{relax url|path=lib/dispersion/ns_cpmg_2site_expanded.py}} |
| − | |||
== Reference == | == Reference == | ||
| Line 17: | Line 17: | ||
The reference for the NS CPMG 2-site expanded model is: | The reference for the NS CPMG 2-site expanded model is: | ||
| − | * | + | * {{#lst:Citations|Tollinger01}} |
| − | |||
| − | |||
| − | |||
== Code origin == | == Code origin == | ||
| − | The code originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see | + | The code originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see the [http://thread.gmane.org/gmane.science.nmr.relax.devel/4138 mailing list discussion], the {{gna task link|7712|comment=2|text=relax task with attached code}} and the [https://gna.org/support/download.php?file_id=18262 file]). |
Links to the copyright licensing agreements from all authors are: | Links to the copyright licensing agreements from all authors are: | ||
| − | + | * [http://article.gmane.org/gmane.science.nmr.relax.devel/4279 Nikolai Skrynnikov], | |
| − | + | * [http://article.gmane.org/gmane.science.nmr.relax.devel/4276 Martin Tollinger], | |
| − | + | * [http://article.gmane.org/gmane.science.nmr.relax.devel/4271 Paul Schanda], | |
| − | + | * [http://article.gmane.org/gmane.science.nmr.relax.devel/4138 Mathilde Lescanne], | |
| − | + | * [http://article.gmane.org/gmane.science.nmr.relax.devel/4157 Dominique Marion]. | |
== Links == | == Links == | ||
The [[Relaxation dispersion citation for relax|implementation of the NS CPMG 2-site expanded model in relax]] can be seen in the: | The [[Relaxation dispersion citation for relax|implementation of the NS CPMG 2-site expanded model in relax]] can be seen in the: | ||
| − | * [http://www.nmr-relax.com/manual/ | + | * [http://www.nmr-relax.com/manual/The_NS_2_site_expanded_CPMG_model.html relax manual], |
* [http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html API documentation], | * [http://www.nmr-relax.com/api/3.1/lib.dispersion.ns_cpmg_2site_expanded-module.html API documentation], | ||
* [http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_expanded relaxation dispersion page of the relax website]. | * [http://www.nmr-relax.com/analyses/relaxation_dispersion.html#NS_CPMG_2-site_expanded relaxation dispersion page of the relax website]. | ||
== See also == | == See also == | ||
| − | [[Category: | + | [[Category:Models]] |
| + | [[Category:Dispersion models]] | ||
| + | [[Category:Relaxation dispersion analysis]] | ||
Latest revision as of 12:34, 16 October 2020
The relaxation dispersion model for the numeric solution (NS) to the Bloch-McConnell equations for SQ CPMG-type data. This uses the Maple expanded and fast equations from Nikolai Skrynnikov. The model is labelled as NS CPMG 2-site expanded in relax.
This type of model can be called silico derived, as it is a computer-assisted derivation for the equivalent computations, of the much more expensive numerical matrix-form.
This function is exact, just as the explicit Bloch-McConnell numerical treatments. It comes from a Maple derivation based on the Bloch-McConnell equations. It is much faster than the numerical Bloch-McConnell solution. It was derived by Nikolai Skrynnikov and is provided with his permission.
Parameters
The NS CPMG 2-site expanded model has the parameters {R20, ..., pA, Δω, kex}.
Code
The library code: https://sourceforge.net/p/nmr-relax/code/ci/master/tree/lib/dispersion/ns_cpmg_2site_expanded.py
Reference
The reference for the NS CPMG 2-site expanded model is:
- Tollinger, M., Skrynnikov, N. R., Mulder, F. A. A., Forman-Kay, J. D., and Kay, L. E. (2001). Slow dynamics in folded and unfolded states of an sh3 domain. J. Am. Chem. Soc., 123(46), 11341-11352. (DOI: 10.1021/ja011300z)
Code origin
The code originates as optimization function number 5 from the fitting_main_kex.py script from Mathilde Lescanne, Paul Schanda, and Dominique Marion (see the mailing list discussion, the relax task with attached code and the file).
Links to the copyright licensing agreements from all authors are:
Links
The implementation of the NS CPMG 2-site expanded model in relax can be seen in the:
