Author: semor
Date: Wed Sep 5 14:48:42 2012
New Revision: 17457
URL: http://svn.gna.org/viewcvs/relax?rev=17457&view=rev
Log:
Corrected the bibliography entries whih were still in plain text and not as a
Latex \cite call...
Also renamed the MorinGagne09 entry to MorinGagne09a as there is now also
MorinGagne09b.
This was proposed by Edward d'Auvergne in a post at:
https://mail.gna.org/public/relax-devel/2012-09/msg00025.html
(Message-id:
<CAED9pY9uKUd_OesCvDLqv2fGPoLDHB4ftrbW1-y6df4oQtbWyg@xxxxxxxxxxxxxx>)
Modified:
trunk/docs/latex/bibliography.bib
trunk/docs/latex/cite.tex
trunk/docs/latex/consistency_tests.tex
trunk/docs/latex/intro.tex
Modified: trunk/docs/latex/bibliography.bib
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/bibliography.bib?rev=17457&r1=17456&r2=17457&view=diff
==============================================================================
--- trunk/docs/latex/bibliography.bib (original)
+++ trunk/docs/latex/bibliography.bib Wed Sep 5 14:48:42 2012
@@ -4227,7 +4227,7 @@
doi = {10.1016/j.pnmrs.2010.12.003}
}
-@Article{MorinGagne09,
+@Article{MorinGagne09a,
author = {Morin, S. and Gagn{\'e}, S.},
affiliation = {Université Laval Département de Biochimie et de
Microbiologie and PROTEO Bureau 3252, 1030 Avenue de la Médecine Québec QC
G1V 0A6 Canada},
title = {Simple tests for the validation of multiple field spin
relaxation data},
@@ -4242,6 +4242,18 @@
doi = {10.1007/s10858-009-9381-4},
abstract = {15N spin relaxation data is widely used to extract detailed
dynamic information regarding bond vectors such as the amide N-H bond of the
protein backbone. Analysis is typically carried using the Lipari-Szabo
model-free approach. Even though the original model-free equation can be
determined from single field R1 , R2 and NOE , over-determination of more
complex motional models is dependent on the recording of multiple field
datasets. This is especially important for the characterization of
conformational exchange which affects R2 in a field dependent manner.
However, severe artifacts can be introduced if inconsistencies arise between
experimental setups with different magnets (or samples). Here, we propose the
use of simple tests as validation tools for the assessment of consistency
between different datasets recorded at multiple magnetic fields. Synthetic
data are used to show the effects of inconsistencies on the proposed tests.
Moreover, an analysis of data currently deposited in the BMRB is performed.
Finally, two cases from our laboratory are presented. These tests are
implemented in the open-source program relax , and we propose their use as a
routine check-up for assessment of multiple field dataset consistency prior
to any analysis such as model-free calculations. We believe this will aid in
the extraction of higher quality dynamics information from 15N spin
relaxation data.},
year = {2009}
+}
+
+@article{Morin2009b,
+ author = {Morin, S. and Gagn{\'e}, S. M.},
+ title = {{NMR dynamics of PSE-4 $\beta$-lactamase: An interplay of ps-ns
order and $\mu$s-ms motions in the active site}},
+ journal = {Biophysical journal},
+ year = {2009},
+ volume = {96},
+ number = {11},
+ pages = {4681-4691},
+ month = jun,
+ doi = {10.1016/j.bpj.2009.02.068}
}
@Article{Orekhov99b,
Modified: trunk/docs/latex/cite.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/cite.tex?rev=17457&r1=17456&r2=17457&view=diff
==============================================================================
--- trunk/docs/latex/cite.tex (original)
+++ trunk/docs/latex/cite.tex Wed Sep 5 14:48:42 2012
@@ -120,7 +120,7 @@
The first is the main citation, whereas the next are the individual tests.
The citation for the consistency testing of NMR relaxation as implemented in
relax is:
\begin{itemize}
-\item \bibentry{MorinGagne09}
+\item \bibentry{MorinGagne09a}
\end{itemize}
Modified: trunk/docs/latex/consistency_tests.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/consistency_tests.tex?rev=17457&r1=17456&r2=17457&view=diff
==============================================================================
--- trunk/docs/latex/consistency_tests.tex (original)
+++ trunk/docs/latex/consistency_tests.tex Wed Sep 5 14:48:42 2012
@@ -29,7 +29,7 @@
For more details on the implementation within relax, see:
\begin{itemize}
-\item \bibentry{MorinGagne09}
+\item \bibentry{MorinGagne09a}
\end{itemize}
Or for the origin of the tests themselves:
@@ -64,7 +64,7 @@
\\
Severe artifacts can be introduced if model-free analysis is performed from
inconsistent multiple magnetic field datasets. The use of simple tests as
validation tools for the consistency assessment can help avoid such problems
in order to extract more reliable information from spin relaxation
experiments. In particular, these tests are useful for detecting
inconsistencies arising from R2 data. Since such inconsistencies can yield
artifactual Rex parameters within model-free analysis, these tests should be
use routinely prior to any analysis such as model-free calculations. \\
\\
-This script will allow one to calculate values for the three consistency tests
$J(0)$, $F\_eta$ and $F\_{R_2}$. Once this is done, qualitative analysis can be
performed by comparing values obtained at different magnetic fields. Correlation
plots and histograms are useful tools for such comparison, such as presented in
Morin \& Gagne (2009a) J. Biomol. NMR, 45: 361-372. \\
+This script will allow one to calculate values for the three consistency
tests $J(0)$, $F\_eta$ and $F\_{R_2}$. Once this is done, qualitative
analysis can be performed by comparing values obtained at different magnetic
fields. Correlation plots and histograms are useful tools for such
comparison, such as presented in \citet{MorinGagne09a}. \\
\\
\\
References \\
@@ -72,22 +72,22 @@
\\
The description of the consistency testing approach: \\
\\
- Morin \& Gagne (2009a) Simple tests for the validation of multiple field
spin relaxation data. J. Biomol. NMR, 45: 361-372.
http://dx.doi.org/10.1007/s10858-009-9381-4 \\
+ \citet{MorinGagne09a} \\
\\
The origins of the equations used in the approach: \\
\\
$J(0)$: \\
- Farrow et al. (1995) Spectral density function mapping using 15N
relaxation data exclusively. J. Biomol. NMR, 6: 153-162.
http://dx.doi.org/10.1007/BF00211779 \\
+ \citet{Farrow95} \\
\\
$F\_eta$: \\
- Fushman et al. (1998) Direct measurement of $^{15}$N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
http://dx.doi.org/10.1021/ja981686m \\
+ \citet{Fushman98} \\
\\
$F\_{R_2}$: \\
- Fushman et al. (1998) Direct measurement of $^{15}$N chemical shift
anisotropy in solution. J. Am. Chem. Soc., 120: 10947-10952.
http://dx.doi.org/10.1021/ja981686m \\
+ \citet{Fushman98} \\
\\
A study where consistency tests were used: \\
\\
- Morin \& Gagne (2009) NMR dynamics of PSE-4 $\beta$-lactamase: An
interplay of ps-ns order and $\mu$s-ms motions in the active site. Biophys. J.,
96: 4681-4691. http://dx.doi.org/10.1016/j.bpj.2009.02.068 \\
+ \citet{MorinGagne09b} \\
""" \\
\\
\# Create the run. \\
Modified: trunk/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/intro.tex?rev=17457&r1=17456&r2=17457&view=diff
==============================================================================
--- trunk/docs/latex/intro.tex (original)
+++ trunk/docs/latex/intro.tex Wed Sep 5 14:48:42 2012
@@ -46,7 +46,7 @@
\begin{itemize}
\item Model-free analysis (\citet{LipariSzabo82a, LipariSzabo82b, Clore90a}
and the specific implementation of
\citet{dAuvergneGooley03,dAuvergneGooley06,dAuvergneGooley07,dAuvergneGooley08a,dAuvergneGooley08b}).
This includes the hybridisation of global diffusion models to study
residual domain dynamics \citep{Horne07}.
\item Reduced spectral density mapping \citep{Farrow95,
Lefevre96}\index{reduced spectral density mapping}.
-\item Consistency testing -- the validation of multiple field NMR relaxation
data \citep{MorinGagne09,Fushman99}.
+\item Consistency testing -- the validation of multiple field NMR relaxation
data \citep{MorinGagne09a,Fushman99}.
\item Exponential curve fitting (to find the $\Rone$ and $\Rtwo$ relaxation
rates)\index{exponential curve fitting}.
\item Steady-state NOE calculation\index{NOE}.
\item Determination of absolute stereochemistry of flexible molecules via
the N-state model using isotropic and anisotropic NMR parameters such as NOE,
ROE, and RDC combined with MD simulation or simulated annealing, and ORD
\citep{Sun11}.
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