Author: bugman
Date: Tue Aug 19 16:07:37 2014
New Revision: 25077
URL: http://svn.gna.org/viewcvs/relax?rev=25077&view=rev
Log:
Added a table for dispersion model nesting in the auto-analysis to the manual.
This adds the ideas discussed in the thread
http://thread.gmane.org/gmane.science.nmr.relax.devel/6684.
Modified:
trunk/docs/latex/dispersion.tex
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=25077&r1=25076&r2=25077&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Tue Aug 19 16:07:37 2014
@@ -1689,8 +1689,9 @@
For the cluster specific parameters, i.e.\ the populations of the
states and the exchange parameters, an average value will be used as the
starting point.
For all other parameters, the $\Rtwozero$ values for each spin and
magnetic field, as well as the parameters related to the chemical shift
difference $\dw$, the optimised values of the previous run will be directly
copied.
\item[Model nesting:] If two models are nested, then the parameters of
the simpler will be used as the starting point for optimisation of the more
complex.
- The currently supported nested model pairs are `LM63' and `LM63
3-site', `CR72' and `CR72 full', `CR72' and `MMQ CR72', `NS CPMG 2-site 3D'
and `NS CPMG 2-site 3D full', and `NS CPMG 2-site star' and `NS CPMG 2-site
star full'.
- In these cases, the $\RtwozeroA$ and $\RtwozeroB$ parameter values are
set to the simpler model $\Rtwozero$ value and the grid search is bypassed.
+ The currently supported nested model sets are presented in
Table~\ref{table: dispersion model nesting} on page~\pageref{table:
dispersion model nesting}.
+ The models are optimised in the order presented in that table.
+ In some cases, the $\RtwozeroA$ and $\RtwozeroB$ parameter values are
set to the simpler model $\Rtwozero$ value and the grid search is bypassed.
\item[Model equivalence:] When two models are equivalent, the optimised
parameters of one model can be used as the starting point of the other rather
than performing a grid search.
This is used in the auto-analysis for avoiding the grid search in the
numeric models.
The optimised `CR72' model is used for the `NS CPMG 2-site expanded',
`NS CPMG 2-site 3D', and `NS CPMG 2-site star' models.
@@ -1722,6 +1723,103 @@
If you are a power user, you are free to use all of the relax user
functions, the relax library, and the relax data store to implement your own
protocol.
If you wish, the protocol can be converted into a new auto-analysis and
distributed as part of relax.
The relax test suite will ensure the protocol remains functional for the
lifetime of relax.
+
+\begin{landscape}
+\begin{center}
+\begin{small}
+
+% The longtable environment.
+\begin{longtable}{ll}
+
+% Caption.
+\caption{Model nesting for the relaxation dispersion auto-analysis.}
+
+% Header.
+\\
+\toprule
+Model & Nested models\footnotemark[1] \\
+\midrule
+\endhead
+
+% Footer.
+\bottomrule
+\endfoot
+
+% Label.
+\label{table: dispersion model nesting}
+
+
+% Experiment independent models.
+\\[-5pt]
+Base models \\
+\cline{1-1}
+$\Rtwoeff/\Ronerhoprime$ & - \\
+No Rex & - \\
+
+% CPMG-type models.
+\\[-5pt]
+Single quantum (SQ) CPMG-type \\
+\cline{1-1}
+LM63 & - \\
+LM63 3-site & LM63 \\
+CR72 & NS CPMG 2-site 3D, NS CPMG 2-site star,
NS CPMG 2-site expanded, B14 \\
+CR72 full & NS CPMG 2-site 3D full, NS CPMG 2-site
star full, B14 full, NS CPMG 2-site 3D, \\
+ & NS CPMG 2-site star, NS CPMG 2-site
expanded, B14, CR72 \\
+IT99 & - \\
+TSMFK01 & - \\
+B14 & NS CPMG 2-site 3D, NS CPMG 2-site star,
NS CPMG 2-site expanded, CR72 \\
+B14 full & NS CPMG 2-site 3D full, NS CPMG 2-site
star full, CR72 full, NS CPMG 2-site 3D, \\
+ & NS CPMG 2-site star, NS CPMG 2-site
expanded, B14, CR72 \\
+NS CPMG 2-site expanded & NS CPMG 2-site 3D, NS CPMG 2-site star,
B14, CR72 \\
+NS CPMG 2-site 3D & NS CPMG 2-site star, NS CPMG 2-site
expanded, B14, CR72 \\
+NS CPMG 2-site 3D full & NS CPMG 2-site star full, B14 full, CR72
full, NS CPMG 2-site 3D, NS CPMG 2-site star, \\
+ & NS CPMG 2-site expanded, B14, CR72 \\
+NS CPMG 2-site star & NS CPMG 2-site 3D, NS CPMG 2-site
expanded, B14, CR722 \\
+NS CPMG 2-site star full & NS CPMG 2-site 3D full, B14 full, CR72
full, NS CPMG 2-site 3D, NS CPMG 2-site star, \\
+ & NS CPMG 2-site expanded, B14, CR72 \\
+
+% SQ, ZQ, DQ and MQ CPMG-type models.
+\\[-5pt]
+MMQ (SQ, ZQ, DQ, \& MQ) CPMG-type \\
+\cline{1-1}
+MMQ CR72 & NS MMQ 2-site \\
+NS MMQ 2-site & MMQ CR72 \\
+NS MMQ 3-site linear & NS MMQ 2-site, MMQ CR72 \\
+NS MMQ 3-site & NS MMQ 3-site linear, NS MMQ 2-site, MMQ
CR72 \\
+
+% R1rho-type models.
+\clearpage
+\\[-5pt]
+$\Ronerho$-type \\
+\cline{1-1}
+M61 & - \\
+M61 skew & - \\
+DPL94 & - \\
+DPL94 $\Rone$ fit & DPL94 \\
+TP02 & MP05, TAP03 \\
+TP02 $\Rone$ fit & MP05 $\Rone$ fit, TAP03 $\Rone$ fit \\
+TAP03 & MP05, TP02 \\
+TAP03 $\Rone$ fit & MP05 $\Rone$ fit, TP02 $\Rone$ fit \\
+MP05 & TAP03, TP02 \\
+MP05 $\Rone$ fit & TAP03 $\Rone$ fit, TP02 $\Rone$ fit \\
+NS $\Ronerho$ 2-site & MP05, TAP03, TP02 \\
+NS $\Ronerho$ 2-site $\Rone$ fit & MP05 $\Rone$ fit, TAP03 $\Rone$ fit, TP02
$\Rone$ fit \\
+NS $\Ronerho$ 3-site linear & NS $\Ronerho$ 2-site, MP05, TAP03, TP02 \\
+NS $\Ronerho$ 3-site & NS $\Ronerho$ 3-site linear, NS
$\Ronerho$ 2-site, MP05, TAP03, TP02 \\
+
+\footnotetext[1]{The nested models are ordered by preference.
+The earliest model in the list which has been optimised in the auto-analysis
will be used as the nested model.
+For example for the 'B14 full' model, the 'CR72 full' model is the first
preference, followed by 'B14', then the final fall back is 'CR72' is neither
'CR72 full' or 'B14' have been optimised.
+If none of the nested models have been optimised, the grid search will be
performed.
+In this example, 'CR72 full' is preferred as it has perfect parameter
nesting -- all parameters of 'B14 full' are found in 'CR72 full'.
+The B14 and CR72 are fallbacks, and for these R20A and R20B are copied from
R20 so they start optimisation as R20A == R20B.
+Hence 'CR72 full' whereby R20A != R20B is a much better starting point as
R20A and R20B have been optimised to different values.
+But because of the large model instability in the 'CR72 full' model, you may
wish to instead start with 'B14'.}
+
+\end{longtable}
+\end{small}
+\end{center}
+\end{landscape}
% Dispersion curve insignificance.
r25077 - /trunk/docs/latex/dispersion.tex