Author: bugman
Date: Thu May 1 14:11:53 2008
New Revision: 6023
URL: http://svn.gna.org/viewcvs/relax?rev=6023&view=rev
Log:
Improvements and expansion of the introduction chapter.
These changes are in response to the email by Johnny Croy at
https://mail.gna.org/public/relax-users/2008-04/msg00028.html (Message-id:
<4E4F6DB4-5F27-4447-9EC9-6D2E9973A539@xxxxxxxxx>). The thread continues at
https://mail.gna.org/public/relax-users/2008-05/msg00000.html (Message-id:
<50dac1510bcb.510bcb50dac1@xxxxxxxxx>).
Most of this text comes from the relax website (http://nmr-relax.com).
Modified:
1.3/docs/latex/bibliography.bib
1.3/docs/latex/intro.tex
Modified: 1.3/docs/latex/bibliography.bib
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/bibliography.bib?rev=6023&r1=6022&r2=6023&view=diff
==============================================================================
--- 1.3/docs/latex/bibliography.bib (original)
+++ 1.3/docs/latex/bibliography.bib Thu May 1 14:11:53 2008
@@ -1337,7 +1337,7 @@
year = 2007
}
-@article{dAuvergneGooley2008a,
+@article{dAuvergneGooley08a,
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
@@ -1384,7 +1384,7 @@
problems inherent within model-free analysis.}",
}
-@article{dAuvergneGooley2008b,
+@article{dAuvergneGooley08b,
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
@@ -1699,6 +1699,52 @@
medline-stat = {MEDLINE},
url =
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks\&dbfrom=pubmed\&retmode=ref\&id=7514039},
year = 1994
+}
+
+@Article{Farrow95,
+ Author = {Farrow, N. A. and Zhang, O. W. and Szabo, A. and
+ Torchia, D. A. and Kay, L. E.},
+ Title = {Spectral density-function mapping using
+ {N}-15 relaxation data exclusively},
+ Journal = jbnmr,
+ Volume = {6},
+ Number = {2},
+ Pages = {153-162},
+ abstract = {A method is presented for the determination of values
+ of the spectral density function, J(omega), describing
+ the dynamics of amide bond vectors from N-15 relaxation
+ parameters alone. Assuming that the spectral density is
+ given by the sum of Lorentzian functions, the approach
+ allows values of J(omega) to be obtained at omega=0,
+ omega(N), and 0.870 omega(H), where omega(N) and
+ omega(H) are Larmor frequencies of nitrogen and proton
+ nuclei, respectively, from measurements of N-15 T-1,
+ T-2 and H-1-N-15 steady-state NOE values at a single
+ spectrometer frequency. Alternatively, when
+ measurements are performed at two different
+ spectrometer frequencies of i and j MHz, J(omega) can
+ be mapped at omega=0, omega(N)(i), omega(N)(j), 0.870
+ omega(H)(i) and 0.870 omega Hj, where omega Ni, for
+ example, is the N-15 Larmor frequency for a
+ spectrometer operating at i MHz. Additionally,
+ measurements made at two different spectrometer
+ frequencies enable contributions to transverse
+ relaxation from motions on millisecond-microsecond time
+ scales to be evaluated and permit assessment of whether
+ a description of the internal dynamics is consistent
+ with a correlation function describing the dynamics of
+ the N-15-NH bond vector are necessary, provided that
+ dJ(omega)/d omega is relatively constant between
+ omega=omega(H) + omega(N) to omega=omega(H)-omega(N).
+ Simulations demonstrate that the method is accurate for
+ a wide range of protein motions and correlation times,
+ and experimental data establish the validity of the
+ methodology. Results are presented for a folded and an
+ unfolded form of the N-terminal SH3 domain of the
+ protein drk.},
+ month = {Sep},
+ sourceid = {ISI:A1995RY39200006},
+ year = 1995
}
@Article{Favro60,
@@ -2205,6 +2251,91 @@
size = {28 p.},
sourceid = {ISI:A1952UN38500008},
year = 1952
+}
+
+@Article{Horne07,
+ Author = {Horne, J. and d'Auvergne, E.J. and Coles, M. and
+ Velkov, T. and Chin, Y. and Charman, W.N. and Prankerd,
+ R. and Gooley, P.R. and Scanlon, M.J.},
+ Title = {Probing the flexibility of the {D}sb{A} oxidoreductase
+ from {V}ibrio cholerae--a 15{N} - 1{H} heteronuclear
+ {NMR} relaxation analysis of oxidized and reduced forms
+ of {D}sb{A}.},
+ Journal = jmb,
+ Volume = {371},
+ Number = {3},
+ Pages = {703-716},
+ abstract = {We have determined the structure of the reduced form
+ of the DsbA oxidoreductase from Vibrio cholerae. The
+ reduced structure shows a high level of similarity to
+ the crystal structure of the oxidized form and is
+ typical of this class of enzyme containing a
+ thioredoxin domain with an inserted alpha-helical
+ domain. Proteolytic and thermal stability measurements
+ show that the reduced form of DsbA is considerably more
+ stable than the oxidized form. NMR relaxation data have
+ been collected and analyzed using a model-free approach
+ to probe the dynamics of the reduced and oxidized
+ states of DsbA. Akaike's information criteria have been
+ applied both in the selection of the model-free models
+ and the diffusion tensors that describe the global
+ motions of each redox form. Analysis of the dynamics
+ reveals that the oxidized protein shows increased
+ disorder on the pico- to nanosecond and micro- to
+ millisecond timescale. Many significant changes in
+ dynamics are located either close to the active site or
+ at the insertion points between the domains. In
+ addition, analysis of the diffusion data shows there is
+ a clear difference in the degree of interdomain
+ movement between oxidized and reduced DsbA with the
+ oxidized form being the more rigid. Principal
+ components analysis has been employed to indicate
+ possible concerted movements in the DsbA structure,
+ which suggests that the modeled interdomain motions
+ affect the catalytic cleft of the enzyme. Taken
+ together, these data provide compelling evidence of a
+ role for dynamics in the catalytic cycle of DsbA.},
+ authoraddress = {Department of Medicinal Chemistry, Victorian College
+ of Pharmacy, Monash University, 381 Royal Parade,
+ Parkville, VIC 3052, Australia.},
+ keywords = {Amino Acid Sequence ; Catalytic Domain ;
+ Crystallography, X-Ray ; Diffusion ; Enzyme Stability ;
+ Hydrogen ; Models, Molecular ; Molecular Sequence Data
+ ; Nitrogen Isotopes ; *Nuclear Magnetic Resonance,
+ Biomolecular ; Oxidation-Reduction ; *Pliability ;
+ Protein Disulfide-Isomerase/*chemistry ; Protein
+ Structure, Secondary ; Vibrio cholerae/*enzymology},
+ language = {eng},
+ medline-aid = {S0022-2836(07)00707-3 [pii] ;
+ 10.1016/j.jmb.2007.05.067 [doi]},
+ medline-da = {20070730},
+ medline-dcom = {20070927},
+ medline-dep = {20070531},
+ medline-edat = {2007/06/26 09:00},
+ medline-fau = {Horne, James ; d'Auvergne, Edward J ; Coles, Murray ;
+ Velkov, Tony ; Chin, Yanni ; Charman, William N ;
+ Prankerd, Richard ; Gooley, Paul R ; Scanlon, Martin J},
+ medline-is = {0022-2836 (Print)},
+ medline-jid = {2985088R},
+ medline-jt = {Journal of molecular biology},
+ medline-mhda = {2007/09/28 09:00},
+ medline-own = {NLM},
+ medline-phst = {2006/12/11 [received] ; 2007/04/18 [revised] ;
+ 2007/05/21 [accepted] ; 2007/05/31 [aheadofprint]},
+ medline-pl = {England},
+ medline-pmid = {17585933},
+ medline-pst = {ppublish},
+ medline-pt = {Journal Article ; Research Support, Non-U.S. Gov't},
+ medline-pubm = {Print-Electronic},
+ medline-rn = {0 (Nitrogen Isotopes) ; 1333-74-0 (Hydrogen) ; EC
+ 5.3.4.1 (Protein Disulfide-Isomerase)},
+ medline-sb = {IM},
+ medline-si = {PDB/2IJY},
+ medline-so = {J Mol Biol. 2007 Aug 17;371(3):703-16. Epub 2007 May
+ 31.},
+ medline-stat = {MEDLINE},
+ url =
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=17585933},
+ year = 2007
}
@Article{Hubbard69,
Modified: 1.3/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/1.3/docs/latex/intro.tex?rev=6023&r1=6022&r2=6023&view=diff
==============================================================================
--- 1.3/docs/latex/intro.tex (original)
+++ 1.3/docs/latex/intro.tex Thu May 1 14:11:53 2008
@@ -2,6 +2,124 @@
%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Introduction}
+
+The program relax is designed for the study of the dynamics of proteins or
other macromolecules though the analysis of NMR relaxation data. It is a
community driven project created by NMR spectroscopists for NMR
spectroscopists. It supports exponential curve fitting for the calculation
of the $\Rone$ and $\Rtwo$ relaxation rates, calculation of the NOE, reduced
spectral density mapping, and the Lipari and Szabo model-free analysis.
+
+
+The aim of relax is to provide a seamless and extremely flexible environment
able to accept input in any format produced by other NMR software, able to
faultlessly create input files, control, and read output from various
programs including Modelfree and Dasha, output results in many formats, and
visualise the data by controlling programs such as
Grace\index{software!Grace|textbf}, OpenDX\index{software!OpenDX|textbf},
MOLMOL\index{software!MOLMOL|textbf}, and PyMOL\index{software!PyMOL|textbf}.
All data analysis tools from optimisation to model selection to Monte Carlo
simulations are inbuilt into relax. Therefore the use of additional programs
is optional.
+
+The flexibility of relax arises from the choice of either relax's scripting
capabilities or its Python\index{Python|textbf} prompt interface. Extremely
complex scripts can be created from simple building blocks to fully automate
data analysis. A number of sample scripts have been provided to help
understand script construction. In addition, any of Python's powerful
features or functions can be incorporated as the script is executed as an
arbitrary Python source file within relax's environment. The modules of
relax can also used as a vast library of dynamics related functions by your
own software.
+
+relax is free software (free as in freedom) which is licenced under the GNU
General Public Licence (GPL)\index{GPL|textbf}. You are free to copy, modify,
or redistribute relax under the terms of the GPL.
+
+
+% Program features.
+%%%%%%%%%%%%%%%%%%%
+
+\section{Program features}
+
+
+% Literature.
+%~~~~~~~~~~~~
+
+\subsection{Literature}
+
+The primary references for the program relax are \citet{dAuvergneGooley08a}
and \citet{dAuvergneGooley08b}.
+
+Other literature related to the improved model-free analysis used within
relax, which can nevertheless be applied to other techniques such as
SRLS\index{SRLS}, include model-free model selection
\citep{dAuvergneGooley03, Chen04}\index{model selection}, model-free model
elimination \citep{dAuvergneGooley06}\index{model elimination}, the theory
\citep{dAuvergneGooley07} behind the new model-free optimisation protocol
\citep{dAuvergneGooley08b}, and the hybridisation of different models
\citep{Horne07, dAuvergneGooley08b}. Most of these details can be found in
the PhD thesis of \citet{dAuvergne06}.
+
+
+% Supported NMR theories.
+%~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Supported NMR theories}
+
+The following relaxation data analysis techniques are currently supported by
relax:
+
+\begin{itemize}
+\item Model-free analysis \citep{LipariSzabo82a, LipariSzabo82b, Clore90a}.
+\item Reduced spectral density mapping \citep{Farrow95,
Lefevre96}\index{reduced spectral density mapping}.
+\item Exponential curve fitting (to find the $\Rone$ and $\Rtwo$ relaxation
rates)\index{exponential curve fitting}.
+\item Steady-state NOE calculation\index{NOE}.
+\end{itemize}
+
+
+% The future.
+\subsubsection{The future}
+
+At some time in the future the following techniques are planned to be
implemented within relax:
+
+\begin{itemize}
+\item Relaxation dispersion\index{relaxation dispersion}.
+\item SRLS -- Slowly relaxing local structure
\citep{Tugarinov01}\index{SRLS}.
+\end{itemize}
+
+Because relax is free software, if you would like to contribute addition
features, functions, or modules which you have written for your own
publications for the benefit of the field, almost anything relating to
molecular dynamics may be accepted. Please see the Open Source chapter for
more details.
+
+
+
+% Data analysis tools.
+%~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Data analysis tools}
+
+The following tools are implemented as modular components to be used by any
data analysis technique:
+
+\begin{itemize}
+\item Numerous high-precision optimisation algorithms\index{minisation}.
+\item Model selection \citep{dAuvergneGooley03, Chen04}\index{model
selection}:
+ \begin{itemize}
+ \item Akaike's Information Criteria (AIC)\index{model selection!AIC}.
+ \item Small sample size corrected AIC (AICc)\index{model selection!AICc}.
+ \item Bayesian or Schwarz Information Criteria (BIC)\index{model
selection!BIC}.
+ \item Bootstrap model selection\index{model selection!bootstrap}.
+ \item Single-item-out cross-validation (CV)\index{model
selection!cross-validation}.
+ \item Hypothesis testing ANOVA model selection (only the model-free
specific technique of \citet{Mandel95} is supported)\index{model
selection!hypothesis testing}\index{model selection!ANOVA}.
+ \end{itemize}
+\item Monte Carlo simulations (error analysis for all data analysis
techniques)\index{Monte Carlo simulation}.
+\item Model elimination -- the removal of failed models prior to model
selection \citep{dAuvergneGooley06}\index{model elimination}.
+\end{itemize}
+
+
+% Data visualisation.
+%~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Data visualisation}
+
+The results of an analysis, or any data input into relax, can be visualised
using a number of programs:
+
+\begin{description}
+\item[MOLMOL] 1D data can be mapped onto a structure either by the creation
of MOLMOL macros or by direct control of the program\index{software!MOLMOL}.
+\item[PyMOL] 3D objects such as the diffusion tensor representation can be
displayed with the structure\index{software!PyMOL}.
+\item[Grace] any 2D data can be plotted\index{software!Grace}.
+\item[OpenDX] The chi-squared space of models with three parameters can be
mapped and 3D images of the space produced\index{software!OpenDX}.
+\end{description}
+
+
+% Interfacing with other programs.
+%~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{Interfacing with other programs}
+
+relax can create the input files, execute in-line, and then read the output
of the following programs. These programs can be used as optimisation engines
replacing the minimisation algorithms built into relax:
+
+\begin{itemize}
+\item Dasha (model-free analysis)\index{software!Dasha}.
+\item Modelfree (model-free analysis)\index{software!Modelfree}.
+\end{itemize}
+
+
+% The user interfaces (UI).
+%~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+\subsection{The user interfaces (UI)}
+
+relax can be used through the following UIs:
+
+\begin{description}
+\item[The prompt] this is the primary interface of relax. Rather than
reinventing a new command language, relax's interface is the powerful Python
prompt. This gives the power user full access to a proven programming
language.
+\item[Scripting] this provides a more powerful and flexible framework for
controlling the program. The script will be executed as Python code enabling
advanced programming for automating data analysis. All the features available
within the prompt environment are accessible to the script.
+\end{description}
r6023 - in /1.3/docs/latex: bibliography.bib intro.tex