Author: bugman
Date: Mon Apr 7 23:15:54 2008
New Revision: 5399
URL: http://svn.gna.org/viewcvs/relax?rev=5399&view=rev
Log:
Merged revisions 5396-5398 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r5396 | bugman | 2008-04-07 22:45:58 +0200 (Mon, 07 Apr 2008) | 6 lines
Fixed a reference in the user manual.
This was reported by Seb at
https://mail.gna.org/public/relax-devel/2008-04/msg00036.html
(Message-id: <20080407163004.gw8s4400w4wsocso@xxxxxxxxxxxxxxx>).
........
r5398 | bugman | 2008-04-07 23:11:58 +0200 (Mon, 07 Apr 2008) | 6 lines
Added all the references for relax.
This was reported by Seb at
https://mail.gna.org/public/relax-devel/2008-04/msg00036.html
(Message-id: <20080407163004.gw8s4400w4wsocso@xxxxxxxxxxxxxxx>).
........
Modified:
1.2/ (props changed)
1.2/docs/latex/bibliography.bib
1.2/docs/latex/model-free.tex
Propchange: 1.2/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Apr 7 23:15:54 2008
@@ -1,1 +1,1 @@
-/1.3:1-2505,2941,2947,2950,2974,2976,2979,2984,2988,3076,3083-3084,3087,3117,3299,3309,3312,3314,3318,3345,3372,4145,4473,4476,4939,5117,5255
+/1.3:1-2505,2941,2947,2950,2974,2976,2979,2984,2988,3076,3083-3084,3087,3117,3299,3309,3312,3314,3318,3345,3372,4145,4473,4476,4939,5117,5255,5396-5398
Modified: 1.2/docs/latex/bibliography.bib
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/bibliography.bib?rev=5399&r1=5398&r2=5399&view=diff
==============================================================================
--- 1.2/docs/latex/bibliography.bib (original)
+++ 1.2/docs/latex/bibliography.bib Mon Apr 7 23:15:54 2008
@@ -1109,12 +1109,13 @@
year = 1998
}
-@Article{PaperII,
- Author = {d'Auvergne, E. J. and Gooley, P. R.},
- Title = {Optimisation of {NMR} dynamic models. ({II}). {S}et
- theory formulation of the model-free problem and
- {K}ay's model-free paradigm.},
- Journal = jbnmr,
+@PhdThesis{dAuvergne06,
+ Author = {d'Auvergne, E. J.},
+ Title = {Protein dynamics: a study of the model-free analysis
+ of {NMR} relaxation data.},
+ School = {Biochemistry and Molecular Biology, University of
+ Melbourne.
http://eprints.infodiv.unimelb.edu.au/archive/00002799/},
+ url = {http://eprints.infodiv.unimelb.edu.au/archive/00002799/},
year = 2006
}
@@ -1192,41 +1193,234 @@
year = 2003
}
-@Article{PaperI,
- Author = {d'Auvergne, Edward J. and Gooley, Paul R.},
- Title = {Optimisation of {NMR} dynamic models. ({I}).
- {M}inimisation algorithms and their performance within
- the model-free space},
+@Article{dAuvergneGooley06,
+ Author = {d'Auvergne, E. J. and Gooley, P. R.},
+ Title = {Model-free model elimination: {A} new step in the
+ model-free dynamic analysis of {NMR} relaxation data.},
Journal = jbnmr,
+ Volume = {35},
+ Number = {2},
+ Pages = {117-135},
+ abstract = {Model-free analysis is a technique commonly used
+ within the field of NMR spectroscopy to extract atomic
+ resolution, interpretable dynamic information on
+ multiple timescales from the R (1), R (2), and steady
+ state NOE. Model-free approaches employ two disparate
+ areas of data analysis, the discipline of mathematical
+ optimisation, specifically the minimisation of a chi(2)
+ function, and the statistical field of model selection.
+ By searching through a large number of model-free
+ minimisations, which were setup using synthetic
+ relaxation data whereby the true underlying dynamics is
+ known, certain model-free models have been identified
+ to, at times, fail. This has been characterised as
+ either the internal correlation times, tau( e ), tau( f
+ ), or tau( s ), or the global correlation time
+ parameter, local tau( m ), heading towards infinity,
+ the result being that the final parameter values are
+ far from the true values. In a number of cases the
+ minimised chi(2) value of the failed model is
+ significantly lower than that of all other models and,
+ hence, will be the model which is chosen by model
+ selection techniques. If these models are not removed
+ prior to model selection the final model-free results
+ could be far from the truth. By implementing a series
+ of empirical rules involving inequalities these models
+ can be specifically isolated and removed. Model-free
+ analysis should therefore consist of three distinct
+ steps: model-free minimisation, model-free model
+ elimination, and finally model-free model selection.
+ Failure has also been identified to affect the
+ individual Monte Carlo simulations used within error
+ analysis. Each simulation involves an independent
+ randomised relaxation data set and model-free
+ minimisation, thus simulations suffer from exactly the
+ same types of failure as model-free models. Therefore,
+ to prevent these outliers from causing a significant
+ overestimation of the errors the failed Monte Carlo
+ simulations need to be culled prior to calculating the
+ parameter standard deviations.},
+ authoraddress = {Department of Biochemistry and Molecular Biology,
+ Bio21 Institute of Biotechnology and Molecular Science,
+ University of Melbourne, Parkville, Victoria, 3010,
+ Australia, edward@xxxxxxxxxxxxxx},
+ language = {eng},
+ medline-aid = {10.1007/s10858-006-9007-z [doi]},
+ medline-da = {20060704},
+ medline-dep = {20060622},
+ medline-edat = {2006/06/23 09:00},
+ medline-fau = {d'Auvergne, Edward J ; Gooley, Paul R},
+ medline-is = {0925-2738 (Print)},
+ medline-jid = {9110829},
+ medline-jt = {Journal of biomolecular NMR.},
+ medline-mhda = {2006/06/23 09:00},
+ medline-own = {NLM},
+ medline-phst = {2005/09/15 [received] ; 2006/03/21 [accepted] ;
+ 2006/06/22 [aheadofprint]},
+ medline-pl = {Netherlands},
+ medline-pmid = {16791734},
+ medline-pst = {ppublish},
+ medline-pt = {Journal Article},
+ medline-pubm = {Print-Electronic},
+ medline-sb = {IM},
+ medline-so = {J Biomol NMR. 2006 Jun;35(2):117-35. Epub 2006 Jun 22.},
+ medline-stat = {In-Data-Review},
+ url =
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=16791734},
year = 2006
}
-@Article{dAuvergneGooley06a,
- Author = {d'Auvergne, Edward J. and Gooley, Paul R.},
- Title = {Model-free model elimination: A new step in the
- model-free dynamic analysis of {NMR} relaxation data},
- Journal = jbnmr,
- Volume = {in press},
- year = 2006
-}
-
-@Article{PaperIV,
- Author = {d'Auvergne, Edward J. and Gooley, Paul R.},
- Title = {Optimisation of {NMR} dynamic models. ({IV}). {T}he
- program relax},
- Journal = jbnmr,
- year = 2006
-}
-
-@Article{PaperIII,
- Author = {d'Auvergne, Edward J. and Gooley, Paul R.},
- Title = {Optimisation of {NMR} dynamic models. ({III}).
- {D}erivation of the brownian diffusion correlation
- functions and a new methodology for the dual
- optimisation of the model-free parameters together with
- the diffusion tensor},
- Journal = jbnmr,
- year = 2006
+@Article{dAuvergneGooley07,
+ Author = {d'Auvergne, E. J. and Gooley, P. R.},
+ Title = {Set theory formulation of the model-free problem and
+ the diffusion seeded model-free paradigm.},
+ Journal = mb,
+ Volume = {3},
+ Number = {7},
+ Pages = {483-494},
+ abstract = {Model-free analysis of NMR relaxation data, which
+ describes the motion of individual atoms, is a problem
+ intricately linked to the Brownian rotational diffusion
+ of the macromolecule. The diffusion tensor parameters
+ strongly influence the optimisation of the various
+ model-free models and the subsequent model selection
+ between them. Finding the optimal model of the dynamics
+ of the system among the numerous diffusion and
+ model-free models is hence quite complex. Using set
+ theory, the entirety of this global problem has been
+ encapsulated by the universal set Ll, and its
+ resolution mathematically formulated as the universal
+ solution Ll. Ever since the original Lipari and Szabo
+ papers the model-free dynamics of a molecule has most
+ often been solved by initially estimating the diffusion
+ tensor. The model-free models which depend on the
+ diffusion parameter values are then optimised and the
+ best model is chosen to represent the dynamics of the
+ residue. Finally, the global model of all diffusion and
+ model-free parameters is optimised. These steps are
+ repeated until convergence. For simplicity this
+ approach to Ll will be labelled the diffusion seeded
+ model-free paradigm. Although this technique suffers
+ from a number of problems many have been solved. All
+ aspects of the diffusion seeded paradigm and its
+ consequences, together with a few alternatives to the
+ paradigm, will be reviewed through the use of set
+ notation.},
+ authoraddress = {Department of Biochemistry and Molecular Biology,
+ Bio21 Institute of Biotechnology and Molecular Science,
+ University of Melbourne, Parkville, Melbourne, Victoria
+ 3010, Australia.},
+ keywords = {Magnetic Resonance Spectroscopy/*methods ; *Models,
+ Theoretical ; Proteins/chemistry ; Thermodynamics},
+ language = {eng},
+ medline-aid = {10.1039/b702202f [doi]},
+ medline-da = {20070620},
+ medline-dcom = {20070823},
+ medline-dep = {20070517},
+ medline-edat = {2007/06/21 09:00},
+ medline-fau = {d'Auvergne, Edward J ; Gooley, Paul R},
+ medline-is = {1742-206X (Print)},
+ medline-jid = {101251620},
+ medline-jt = {Molecular bioSystems},
+ medline-mhda = {2007/08/24 09:00},
+ medline-own = {NLM},
+ medline-phst = {2007/05/17 [aheadofprint] ; 2007/06/20 [epublish]},
+ medline-pl = {England},
+ medline-pmid = {17579774},
+ medline-pst = {ppublish},
+ medline-pt = {Journal Article},
+ medline-pubm = {Print-Electronic},
+ medline-rn = {0 (Proteins)},
+ medline-sb = {IM},
+ medline-so = {Mol Biosyst. 2007 Jul;3(7):483-94. Epub 2007 May 17.},
+ medline-stat = {MEDLINE},
+ url =
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=17579774},
+ year = 2007
+}
+
+@article{dAuvergneGooley2008a,
+ Author = {d'Auvergne, E. J. and Gooley, P. R.},
+title = "{Optimisation of NMR dynamic models I. Minimisation algorithms and
their
+performance within the model-free and Brownian rotational diffusion
+spaces}",
+journal = jbnmr,
+volume = "40",
+number = "2",
+pages = "107-109",
+year = "2008",
+pmid = "18085410",
+abstract = "{
+The key to obtaining the model-free description of the dynamics of a
+macromolecule is the optimisation of the model-free and Brownian
+rotational diffusion parameters using the collected R (1), R (2) and
+steady-state NOE relaxation data. The problem of optimising the
+chi-squared value is often assumed to be trivial, however, the long chain
+of dependencies required for its calculation complicates the model-free
+chi-squared space. Convolutions are induced by the Lorentzian form of the
+spectral density functions, the linear recombinations of certain spectral
+density values to obtain the relaxation rates, the calculation of the NOE
+using the ratio of two of these rates, and finally the quadratic form of
+the chi-squared equation itself. Two major topological features of the
+model-free space complicate optimisation. The first is a long, shallow
+valley which commences at infinite correlation times and gradually
+approaches the minimum. The most severe convolution occurs for motions on
+two timescales in which the minimum is often located at the end of a long,
+deep, curved tunnel or multidimensional valley through the space. A large
+number of optimisation algorithms will be investigated and their
+performance compared to determine which techniques are suitable for use in
+model-free analysis. Local optimisation algorithms will be shown to be
+sufficient for minimisation not only within the model-free space but also
+for the minimisation of the Brownian rotational diffusion tensor. In
+addition the performance of the programs Modelfree and Dasha are
+investigated. A number of model-free optimisation failures were
+identified: the inability to slide along the limits, the singular matrix
+failure of the Levenberg-Marquardt minimisation algorithm, the low
+precision of both programs, and a bug in Modelfree. Significantly, the
+singular matrix failure of the Levenberg-Marquardt algorithm occurs when
+internal correlation times are undefined and is greatly amplified in
+model-free analysis by both the grid search and constraint algorithms. The
+program relax ( http://www.nmr-relax.com ) is also presented as a new
+software package designed for the analysis of macromolecular dynamics
+through the use of NMR relaxation data and which alleviates all of the
+problems inherent within model-free analysis.}",
+}
+
+@article{dAuvergneGooley2008b,
+ Author = {d'Auvergne, E. J. and Gooley, P. R.},
+ Title = {Optimisation of NMR dynamic models II. A new methodology for the
dual
+optimisation of the model-free parameters and the Brownian rotational
+diffusion tensor},
+journal = jbnmr,
+volume = "40",
+number = "2",
+pages = "121-123",
+year = "2008",
+pmid = "18085411",
+abstract = "{
+Finding the dynamics of an entire macromolecule is a complex problem as
+the model-free parameter values are intricately linked to the Brownian
+rotational diffusion of the molecule, mathematically through the
+autocorrelation function of the motion and statistically through model
+selection. The solution to this problem was formulated using set theory as
+an element of the universal set [Formula: see text]-the union of all
+model-free spaces (d'Auvergne EJ and Gooley PR (2007) Mol BioSyst 3(7),
+483-494). The current procedure commonly used to find the universal
+solution is to initially estimate the diffusion tensor parameters, to
+optimise the model-free parameters of numerous models, and then to choose
+the best model via model selection. The global model is then optimised and
+the procedure repeated until convergence. In this paper a new methodology
+is presented which takes a different approach to this diffusion seeded
+model-free paradigm. Rather than starting with the diffusion tensor this
+iterative protocol begins by optimising the model-free parameters in the
+absence of any global model parameters, selecting between all the
+model-free models, and finally optimising the diffusion tensor. The new
+model-free optimisation protocol will be validated using synthetic data
+from Schurr JM et al. (1994) J Magn Reson B 105(3), 211-224 and the
+relaxation data of the bacteriorhodopsin (1-36)BR fragment from Orekhov VY
+(1999) J Biomol NMR 14(4), 345-356. To demonstrate the importance of this
+new procedure the NMR relaxation data of the Olfactory Marker Protein
+(OMP) of Gitti R et al. (2005) Biochem 44(28), 9673-9679 is reanalysed.
+The result is that the dynamics for certain secondary structural elements
+is very different from those originally reported.}",
}
@Article{DellwoWand89,
Modified: 1.2/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/1.2/docs/latex/model-free.tex?rev=5399&r1=5398&r2=5399&view=diff
==============================================================================
--- 1.2/docs/latex/model-free.tex (original)
+++ 1.2/docs/latex/model-free.tex Mon Apr 7 23:15:54 2008
@@ -98,7 +98,7 @@
\subsection{Brownian rotational diffusion}
\index{diffusion!Brownian|textbf}
-In equations~\eqref{eq: J(w) model-free generic} and~\eqref{eq: J(w)
model-free ext generic} the generic Brownian diffusion NMR correlation
function presented in \citet{dAuvergneGooley06b} has been used. This
function is
+In equations~\eqref{eq: J(w) model-free generic} and~\eqref{eq: J(w)
model-free ext generic} the generic Brownian diffusion NMR correlation
function presented in \citet{dAuvergne06} has been used. This function is
\begin{equation} \label{eq: C(tau) generic}
C(\tau) = \frac{1}{5} \sum_{i=-k}^k c_i \cdot e^{-\tau/\tau_i},
\end{equation}
r5399 - in /1.2: ./ docs/latex/bibliography.bib docs/latex/model-free.tex