Re: r17457 - in /trunk/docs/latex: bibliography.bib cite.tex consistency_tests.tex intro.tex -- September 05, 2012 - 17:27

Hi Seb,

I just picked up another LaTeX compilation error.  The 'Morin2009b'
label in the bibtex file should be changed to 'MorinGagne09b'.  This
matches the rest of the bibtex labelling and the consistency testing
figure uses "\citep{MorinGagne09b}".

Cheers,

Edward




On 5 September 2012 14:48,  <sebastien.morin@xxxxxxxxx> wrote:
> 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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