Author: bugman
Date: Wed Jun 12 16:36:30 2013
New Revision: 20075
URL: http://svn.gna.org/viewcvs/relax?rev=20075&view=rev
Log:
Added all of the contents of the relax_disp.select_model user function
docstring to the manual.
Modified:
branches/relax_disp/docs/latex/bibliography.bib
branches/relax_disp/docs/latex/relax.tex
Modified: branches/relax_disp/docs/latex/bibliography.bib
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/bibliography.bib?rev=20075&r1=20074&r2=20075&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/bibliography.bib (original)
+++ branches/relax_disp/docs/latex/bibliography.bib Wed Jun 12 16:36:30 2013
@@ -922,6 +922,33 @@
year = 2004
}
+@Article{CarverRichards72,
+ Author = {Carver, J.P. and Richards, R.E.},
+ Title = {General 2-site solution for chemical exchange
+ produced dependence of {T2} upon {C}arr-{P}urcell pulse
+ separation},
+ Journal = jmr,
+ Volume = {6},
+ Number = {1},
+ Pages = {89-105},
+ address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495},
+ doc-delivery-number = {L5576},
+ doi = {10.1016/0022-2364(72)90090-X},
+ issn = {1090-7807},
+ journal-iso = {J. Magn. Reson.},
+ language = {English},
+ number-of-cited-references = {13},
+ publisher = {ACADEMIC PRESS INC},
+ research-areas = {Biochemistry \& Molecular Biology; Physics;
+ Spectroscopy},
+ times-cited = {224},
+ type = {Article},
+ unique-id = {ISI:A1972L557600008},
+ web-of-science-categories = {Biochemical Research Methods; Physics, Atomic,
+ Molecular \& Chemical; Spectroscopy},
+ year = 1972
+}
+
@Article{Chen04,
Author = {Chen, J. and Brooks, 3rd, C. L. and Wright, P. E.},
Title = {Model-free analysis of protein dynamics: assessment of
@@ -1637,6 +1664,70 @@
medline-stat = {MEDLINE},
url =
{http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?cmd=prlinks&dbfrom=pubmed&retmode=ref&id=18085411},
year = 2008
+}
+
+@Article{Davis94,
+ Author = {Davis, D.G. and Perlman, M.E. and London, R.E.},
+ Title = {Direct measurements of the dissociation-rate constant
+ for inhibitor-enzyme complexes via the {T}1rho and {T}2
+ ({CPMG}) methods},
+ Journal = jmr,
+ Volume = {104},
+ Number = {3},
+ Pages = {266-275},
+ abstract = {The unimolecular dissociation rate constant, k(-1),
+ for the inhibitor-enzyme complex tubercidin-Escherichia
+ coli purine nucleoside phosphorylase (PNPase) has been
+ determined directly via two related H-1 NMR methods for
+ studying exchange-mediated transverse relaxation. One
+ method involves measurements of the decay rate, 1/T-1
+ rho, of spin-locked magnetization in the rotating frame
+ as a function of the strength of the spin-locking
+ field, omega(SL) The second method involves
+ measurements of the Carr-Purcell-Meiboom-Gill (CPMG)
+ spin-echo decay rate, 1/T-2(CPMG) as a function of the
+ repetition rate, 1/t(cp), of the refocusing pulses.
+ Expressions describing the dependence of T-2(CPMG) as a
+ function of 1/t(cp) and k(-1) have been previously
+ derived with sufficient generality to include the
+ two-site inhibitor-enzyme exchange case. Existing
+ expressions for T-1 rho as a function of k(ex) and
+ omega(SL), however, had to be reformulated to take into
+ account differences between T-2(b) and T-1(b) for the
+ bound form of the inhibitor as well as offset
+ corrections important at low values of omega(SL) A new
+ expression for exchange-mediated T-1 rho has been
+ derived to take these factors into account and is shown
+ to provide a more accurate description of observed T-1
+ rho data than previous models. Numerical analysis of
+ relaxation rates, measured independently by either the
+ rotating-frame or the spin-echo method for the H-1 and
+ H-2 protons of tubercidin at different inhibitor:enzyme
+ ratios, yields comparable values for k(-1) of 2400
+ (+/-350) and 900 (+/-80) s(-1) at 20 and 10 degrees C,
+ respectively. The merits of both methods are compared
+ and suggestions for optimizing the experiments are
+ discussed. (C) 1994 Academic Press, Inc.},
+ address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495},
+ affiliation = {DAVIS, DG (Reprint Author), NIEHS,MOLEC BIOPHYS
+ LAB,POB 12233,RES TRIANGLE PK,NC 27709, USA.},
+ doc-delivery-number = {NX809},
+ doi = {10.1006/jmrb.1994.1084},
+ issn = {1064-1866},
+ journal-iso = {J. Magn. Reson. Ser. B},
+ keywords-plus = {RELAXATION-MATRIX ANALYSIS; SPIN-LATTICE RELAXATION;
+ CHEMICAL EXCHANGE; ROTATING FRAME; NUCLEAR;
+ CONFORMATIONS; PROTEINS; T2},
+ language = {English},
+ month = {JUL},
+ number-of-cited-references = {34},
+ publisher = {ACADEMIC PRESS INC JNL-COMP SUBSCRIPTIONS},
+ research-areas = {Physics},
+ times-cited = {182},
+ type = {Article},
+ unique-id = {ISI:A1994NX80900008},
+ web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
+ year = 1994
}
@Article{DellwoWand89,
@@ -2772,6 +2863,60 @@
sourceid = {ISI:A1989AE13400012},
doi = {10.1093/biomet/76.2.297},
year = 1989
+}
+
+@Article{IshimaTorchia99,
+ Author = {Ishima, R. and Torchia, D.A.},
+ Title = {Estimating the time scale of chemical exchange of
+ proteins from measurements of transverse relaxation
+ rates in solution},
+ Journal = jbnmr,
+ Volume = {14},
+ Number = {4},
+ Pages = {369-372},
+ abstract = {Chemical (conformational) exchange on the ms-mu s
+ time scale is reliably identified by the observation of
+ transverse relaxation rates, R-ex, that depend upon the
+ strength of the effective field (omega(1eff) = gamma
+ B-1eff) used in spin lock or CPMG experiments. In order
+ to determine if the exchange correlation time, tau(ex),
+ is the fast or slow limit, measurements of (i) signal
+ line shape and (ii) temperature dependence of R-ex have
+ been commonly used in studies of stable, small
+ molecules. However, these approaches are often not
+ applicable to proteins, because sample stability and
+ solubility, respectively, limit the temperature range
+ and signal sensitivity of experiments. Herein we use a
+ complex, but general, two-site exchange equation to
+ show when the simple fast exchange equations for R-ex
+ are good approximations, in the case of proteins. We
+ then present a simple empirical equation that
+ approximately predicts R-ex in all exchange regimes,
+ and explains these results in a clear, straightforward
+ manner. Finally we show how one can reliably determine
+ whether tau(ex) is in the fast or slow exchange limit.},
+ address = {SPUIBOULEVARD 50, PO BOX 17, 3300 AA DORDRECHT,
+ NETHERLANDS},
+ affiliation = {Torchia, DA (Reprint Author), Natl Inst Dent \&
+ Craniofacial Res, Struct Mol Biol Unit, NIH, Bethesda,
+ MD 20892 USA. Natl Inst Dent \& Craniofacial Res,
+ Struct Mol Biol Unit, NIH, Bethesda, MD 20892 USA.},
+ doc-delivery-number = {234VK},
+ doi = {10.1023/A:1008324025406},
+ issn = {0925-2738},
+ journal-iso = {J. Biomol. NMR},
+ keywords = {chemical exchange; protein; relaxation},
+ keywords-plus = {N-15},
+ language = {English},
+ month = {AUG},
+ number-of-cited-references = {15},
+ publisher = {KLUWER ACADEMIC PUBL},
+ research-areas = {Biochemistry \& Molecular Biology; Spectroscopy},
+ times-cited = {58},
+ type = {Article},
+ unique-id = {ISI:000082504900007},
+ web-of-science-categories = {Biochemistry \& Molecular Biology;
Spectroscopy},
+ year = 1999
}
@Article{Jin98,
@@ -3746,6 +3891,32 @@
year = 1997
}
+@Article{LuzMeiboom63,
+ Author = {Luz, Z. and Meiboom, S.},
+ Title = {Nuclear magnetic resonance study of protolysis of
+ trimethylammonium ion in aqueous solution - order of
+ reaction with respect to solvent},
+ Journal = jcp,
+ Volume = {39},
+ Number = {2},
+ Pages = {366-370},
+ address = {CIRCULATION FULFILLMENT DIV, 500 SUNNYSIDE BLVD,
+ WOODBURY, NY 11797-2999},
+ doc-delivery-number = {4164B},
+ doi = {10.1063/1.1734254},
+ issn = {0021-9606},
+ journal-iso = {J. Chem. Phys.},
+ language = {English},
+ number-of-cited-references = {13},
+ publisher = {AMER INST PHYSICS},
+ research-areas = {Physics},
+ times-cited = {375},
+ type = {Article},
+ unique-id = {ISI:A19634164B00022},
+ web-of-science-categories = {Physics, Atomic, Molecular \& Chemical},
+ year = 1963
+}
+
@Article{Mackay96,
Author = {MacKay, J. P. and Shaw, G. L. and King, G. F.},
Title = {Backbone dynamics of the c-{J}un leucine zipper: 15{N}
@@ -3992,7 +4163,7 @@
}
@Article{Meiboom61,
- Author = {Meiboom, S},
+ Author = {Meiboom, S.},
Title = {Nuclear magnetic resonance study of proton transfer
in water},
Journal = jcp,
Modified: branches/relax_disp/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/docs/latex/relax.tex?rev=20075&r1=20074&r2=20075&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax.tex (original)
+++ branches/relax_disp/docs/latex/relax.tex Wed Jun 12 16:36:30 2013
@@ -13,6 +13,7 @@
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{tabularx}
+\usepackage{rotating}
% Nth.
\usepackage[super]{nth}
@@ -91,6 +92,21 @@
\newcommand{\Mfset}{\mathfrak{F}}
\newcommand{\Localset}{\mathfrak{T}}
\newcommand{\KL}{\Delta_{\scriptscriptstyle \text{K-L}}}
+
+\newcommand{\dw}{\Delta\omega}
+\newcommand{\kex}{\textrm{k}_\textrm{ex}}
+\newcommand{\nucpmg}{\nu_\textrm{CPMG}}
+\newcommand{\omegae}{\omega_\textrm{e}}
+\newcommand{\omegaone}{\omega_1}
+\newcommand{\pA}{p_\textrm{A}}
+\newcommand{\pB}{p_\textrm{B}}
+\newcommand{\Phiex}{\Phi_\textrm{ex}}
+\newcommand{\Rex}{\mathrm{R}_\textrm{ex}}
+\newcommand{\Ronerhoprime}{\mathrm{R}_{1\rho}'}
+\newcommand{\Rtwoeff}{\mathrm{R}_{2\textrm{eff}}}
+\newcommand{\Rtwozero}{\mathrm{R}_2^0}
+\newcommand{\tex}{\tau_\textrm{ex}}
+\newcommand{\taucpmg}{\tau_\textrm{CPMG}}
% Natbib Citation format.
\bibpunct{(}{)}{;}{a}{,}{,}
@@ -256,21 +272,21 @@
% The chapters.
%%%%%%%%%%%%%%%
-\include{intro}
-\include{citations}
-\include{install}
-\include{infrastruct}
-\include{data_model}
-\include{curvefit}
-\include{noe}
-\include{model-free}
-\include{jw_mapping}
-\include{consistency_tests}
+%\include{intro}
+%\include{citations}
+%\include{install}
+%\include{infrastruct}
+%\include{data_model}
+%\include{curvefit}
+%\include{noe}
+%\include{model-free}
+%\include{jw_mapping}
+%\include{consistency_tests}
\include{relax_disp}
-\include{maths}
-\include{develop}
-\include{functions}
-\include{licence}
+%\include{maths}
+%\include{develop}
+%\include{functions}
+%\include{licence}
% End of the main chapters.
r20075 - in /branches/relax_disp/docs/latex: bibliography.bib relax.tex