Comparison of dispersion analysis software

Diverse software exists for analysing relaxation dispersion data. The following is a list of the officially released software which you can use instead of relax:

CPMGFit

Art Palmer's original dispersion analysis software at http://www.palmer.hs.columbia.edu/software/cpmgfit.html.

cpmg_fit

Dmitry Korzhnev's dispersion software available upon request.

CATIA

Flemming Hansen's dispersion software at http://www.biochem.ucl.ac.uk/hansen/catia/. The reference is Hansen et al. (2008).

NESSY

Michael Bieri's dispersion software at https://sourceforge.net/projects/nmr-nessy/. The reference is Bieri and Gooley (2011).

GUARDD

Ian Kleckner's dispersion software at http://code.google.com/p/guardd/. The reference is Kleckner and Foster (2012).

ShereKhan

See the web server at http://sherekhan.bionmr.org/. The reference is Mazur et al. (2013).

GLOVE

Peter Wright's dispersion software at http://www.scripps.edu/wright/. The reference is Sugase et al. (2013).

chemex

Guillaume Bouvignies' dispersion software which can be found at http://code.google.com/p/chemex/.

There is currently support in relax for generating the input files for CPMGFit, CATIA, NESSY, and ShereKhan and for running CPMGFit and CATIA from within relax.

The features of the different software are compared in Table 11.4 on page . Note that this table is likely to be incomplete so please see the websites of the respective software for an up to date list of features. The aim of this table is to provide a fair comparison between all of the available dispersion software. Therefore if you do find deficiencies or errors in this table please report these either to the relax users mailing list at “nmr-relax-users at lists.sourceforge.net” or submit a bug report (see section 3.4 on page ) so that the details can be corrected.

Table 11.4: Comparison of the features for the different dispersion software.

		CPMGFit	cpmg_fit	CATIA	NESSY	GUARDD	ShereKhan	GLOVE	chemex	relax
Dispersion models
Base models
R2eff/R1ρ'		-	-	-	✓	✓	✓	✓	-	✓
No Rex		-	✓	-	✓	✓	-	✓	-	✓
Single quantum (SQ) CPMG-type
LM63		✓	-	-	✓	-	✓	✓	-	✓
LM63 3-site		✓	-	-	✓	-	-	-	-	✓
CR72		✓	-	-	✓	-	✓	✓	-	✓
IT99		✓	-	-	-	-	-	✓	-	✓
TSMFK01		-	-	-	-	-	-	-	-	✓
B14		-	-	-	-	-	-	-	-	✓
NS 2-site		-	✓	✓	-	-	✓	?	-	✓
MMQ (SQ, ZQ, DQ, & MQ) CPMG-type
MMQ CR72		-	✓	-	-	✓	-	?	-	✓
NS MMQ 2-site		-	✓	-	-	-	-	?	-	✓
NS MMQ 3-site linear		-	✓	-	-	-	-	?	-	✓
NS MMQ 3-site		-	✓	-	-	-	-	?	-	✓
R1ρ-type
M61		-	-	-	-	-	-	-	-	✓
DPL94		-	-	-	-	-	-	-	-	✓
TP02		-	✓	-	-	-	-	-	-	✓
TAP03		-	-	-	-	-	-	-	-	✓
TP04		-	-	-	-	-	-	-	-	-
MP05		-	-	-	-	-	-	-	-	✓
BK13		-	-	-	-	-	-	-	-	-
NS R1ρ 2-site		-	✓	-	-	-	-	?	-	✓
NS R1ρ 3-site linear		-	✓	-	-	-	-	-	-	✓
NS R1ρ 3-site		-	✓	-	-	-	-	-	-	✓
General features
Parallelisation via MPI for running on clusters		-	-	-	-	-	-	-	-	✓
Off-resonance effects (CPMG-type data)		-	-	✓	-	-	-	-	-	-
Off-resonance effects ( R1ρ-type data)		-	✓	-	-	-	-	-	-	✓
Support for TROSY-type data		-	-	✓	-	-	-	-	-	-
Support for CEST-type data		-	-	-	-	-	-	-	✓	-
Support for scalar coupling effects		-	-	✓	-	-	-	-	-	-
Arrhenius / Van't Hoff analysis		-	✓	-	✓	✓	-	-	-	-
Dispersion data back calculation (BC)		-	✓	-	✓	✓	-	-	-	✓
User interface
Graphical user interface (GUI)		-	-	-	✓	✓	-	-	-	✓
Web user interface (Web UI)		-	-	-	-	-	✓	-	-	-
Scripting user interface (Script UI)		-	✓	✓	-	-	✓	✓	-	✓
Shell interface		✓	-	-	-	-	-	-	✓	-
Temperature and field-dependent simulator
UI for experimental planning (data BC)		-	-	-	-	✓	-	-	-	-
Optimisation
Grid search algorithm		✓	-	-	✓	✓	✓	✓	-	✓
Grid search (via scripting)		-	-	✓	-	-	-	-	-	-
Nelder-Mead simplex algorithm		-	-	-	-	-	-	-	-	✓
Levenberg-Maquardt algorithm		✓	✓	✓	✓	-	✓	✓	✓	-
Numeric gradient approximation		✓	✓	✓	✓	-	✓	✓	✓	-
Logarithmic-barrier constraint algorithm		-	-	-	-	-	-	✓	-	✓
MATLAB interior-point black magic		-	-	-	-	✓	-	-	-	-
Visualisation of the chi-squared space		-	-	-	-	✓	-	-	-	✓
Error propagation
Covariance matrix (lowest quality)		✓	✓	✓	-	✓	✓	✓	-	-
Jackknife simulations (for missing errors)		✓	-	-	-	-	-	✓	-	-
Bootstrapping simulations (false errors)		-	-	-	-	-	-	-	-	-
Monte Carlo simulations (gold standard)		✓	-	-	✓	✓	-	✓	✓	✓
Inbuilt statistical comparisons
Akaike's Information Criterion (AIC)		-	-	-	✓	-	-	-	-	✓
Small sample size AIC (AICc)		-	-	-	✓	-	-	-	-	✓
Bayesian Information Criterion (BIC)		-	-	-	-	-	-	-	-	✓
F-testing (ANOVA statistics)		-	-	-	✓	✓	-	-	-	-
Data and model testing
Insignificant dispersion curve tests		-	-	-	✓	-	-	-	-	✓
Model elimination tests		-	-	-	-	-	-	-	-	✓
Programming languages
Python		-	-	-	✓	-	✓	-	✓	✓
C		-	✓	✓	-	-	-	✓	-	✓
Perl		-	-	-	-	-	-	✓	-	-
MATLAB		-	-	-	-	✓	-	-	-	-
FORTRAN		✓	-	-	-	-	-	-	-	-
Ruby on Rails		-	-	-	-	-	✓	-	-	-
Free software licencing
GNU General Public Licence (version 2+)		✓	-	-	-	-	-	-	-	-
GNU General Public Licence (version 3+)		-	-	-	✓	✓	-	-	✓	✓
Free software infrastructure		-	-	-	✓	✓	-	-	✓	✓
Proprietary		-	✓	✓	-	-	✓	✓	-	-