Author: bugman
Date: Wed Jun 12 16:46:17 2013
New Revision: 20076
URL: http://svn.gna.org/viewcvs/relax?rev=20076&view=rev
Log:
Reverted r20075 as the wrong files were committed!
The command used was:
svn merge -r20075:20074 .
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=20076&r1=20075&r2=20076&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/bibliography.bib (original)
+++ branches/relax_disp/docs/latex/bibliography.bib Wed Jun 12 16:46:17 2013
@@ -922,33 +922,6 @@
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
@@ -1664,70 +1637,6 @@
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,
@@ -2863,60 +2772,6 @@
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,
@@ -3891,32 +3746,6 @@
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}
@@ -4163,7 +3992,7 @@
}
@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=20076&r1=20075&r2=20076&view=diff
==============================================================================
--- branches/relax_disp/docs/latex/relax.tex (original)
+++ branches/relax_disp/docs/latex/relax.tex Wed Jun 12 16:46:17 2013
@@ -13,7 +13,6 @@
\usepackage{booktabs}
\usepackage{longtable}
\usepackage{tabularx}
-\usepackage{rotating}
% Nth.
\usepackage[super]{nth}
@@ -92,21 +91,6 @@
\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}{,}{,}
@@ -272,21 +256,21 @@
% 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.
r20076 - in /branches/relax_disp/docs/latex: bibliography.bib relax.tex