Author: bugman
Date: Wed Feb 26 14:24:17 2014
New Revision: 22336
URL: http://svn.gna.org/viewcvs/relax?rev=22336&view=rev
Log:
Fixes for the spacing after e.g. and i.e. in the relax manual.
The character '\' needs to be used after the final dot to indicate that this
is not a sentence stop,
hence the double spacing normally used between sentences should not be used.
Modified:
trunk/docs/latex/consistency_tests.tex
trunk/docs/latex/curvefit.tex
trunk/docs/latex/data_model.tex
trunk/docs/latex/develop.tex
trunk/docs/latex/dispersion.tex
trunk/docs/latex/dispersion_params.tex
trunk/docs/latex/intro.tex
Modified: trunk/docs/latex/consistency_tests.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/consistency_tests.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/consistency_tests.tex (original)
+++ trunk/docs/latex/consistency_tests.tex Wed Feb 26 14:24:17 2014
@@ -13,13 +13,13 @@
In spin relaxation, datasets are often recorded at different magnetic fields.
This is especially important when $\Rtwo$ values are to be used since
$\mu$s-ms motions contribute to $\Rtwo$.
This contribution being scaled quadratically with the strength of the
magnetic field, recording at multiple magnetic fields helps extract it.
-Also, acquiring data at multiple magnetic fields allows over-determination
of the mathematical problems, e.g. in the model-free approach.
+Also, acquiring data at multiple magnetic fields allows over-determination
of the mathematical problems, e.g.\ in the model-free approach.
Recording at multiple magnetic fields is a good practice.
However, it can cause artifacts if those different datasets are inconsistent.
Inconsistencies can originate from, inter alia, the sample or the
acquisition.
Sample variations can be linked to changes in temperature, concentration,
pH, etc.
-Water suppression is the main cause of acquisition variations as it affect
relaxation parameters (especially NOE) of exposed and exchangeable moieties
(e.g. the NH moiety).
+Water suppression is the main cause of acquisition variations as it affect
relaxation parameters (especially NOE) of exposed and exchangeable moieties
(e.g.\ the NH moiety).
It is thus a good idea to assess consistency of datasets acquired at
different magnetic fields.
For this purpose, three tests are implemented in relax.
Modified: trunk/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/curvefit.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/curvefit.tex (original)
+++ trunk/docs/latex/curvefit.tex Wed Feb 26 14:24:17 2014
@@ -81,7 +81,7 @@
\item Phase correction values can be determined easily.
\item If the delay is not a multiple of 1/2 point, the phase of folded
peaks will be distorted.
\item The Hilbert transform (HT) is used, sometimes automatically, to
reconstruct previously deleted imaginary data for interactive rephasing or
inverse processing. But, the HT can only reconstruct imaginary data perfectly
if the phase is a multiple of 1/2 point.
- \item Data with P1 = 360 have the first point t=0 missing (i.e. 1 point
delay). Since the first point of the FID corresponds to the sum of points in
the corresponding spectrum, this missing first point can be ``restored'' by
adding a constant to the phased spectrum. This can be done conveniently by
automated zero-order baseline correction, as shown in table~\ref{table:
NMRPipe -c}.
+ \item Data with P1 = 360 have the first point t=0 missing (i.e.\ 1 point
delay). Since the first point of the FID corresponds to the sum of points in
the corresponding spectrum, this missing first point can be ``restored'' by
adding a constant to the phased spectrum. This can be done conveniently by
automated zero-order baseline correction, as shown in table~\ref{table:
NMRPipe -c}.
\begin{table}
\begin{center}
Modified: trunk/docs/latex/data_model.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/data_model.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/data_model.tex (original)
+++ trunk/docs/latex/data_model.tex Wed Feb 26 14:24:17 2014
@@ -252,7 +252,7 @@
The \uf{spin\ufsep{}isotope} user function is required to define the
magnetic dipole-dipole interaction and is information not present in the PDB
file.
Note that if structural data from the PDB is used to generate the spin
containers, then all subsequent data loaded into relax must follow the exact
naming convention from the PDB file.
-Automatic residue name matching (i.e. `GLY' = `Gly' = `gly' = `G') is
currently not supported.
+Automatic residue name matching (i.e.\ `GLY' = `Gly' = `gly' = `G') is
currently not supported.
Modified: trunk/docs/latex/develop.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/develop.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/develop.tex (original)
+++ trunk/docs/latex/develop.tex Wed Feb 26 14:24:17 2014
@@ -140,7 +140,7 @@
% Variable, function, and class names.
\subsection{Variable, function, and class names}
-In relax a mixture of both camel case (e.g. CamelCase)\index{camel case} and
lower case with underscores is used.
+In relax a mixture of both camel case (e.g.\ CamelCase)\index{camel case}
and lower case with underscores is used.
Despite the variability there are fixed rules which should be adhered to.
These naming conventions should be observed at all times.
@@ -827,7 +827,7 @@
To simplify the process of checking if the message was supposed to be
private, you could copy-and-paste the following message (modifying it as you
see fit):
\begin{exampleenv}
-Sorry in advance, but the following is the standard pre-composed response to
a post not sent to the relax mailing lists and not labelled as private. If
you would like to start a private conversation about relax, please label your
message as such. If you really must start a private exchange, please respond
to this message saying so. If your message was meant to be sent to the relax
mailing list, please send the message again. For this, please copy-and-paste
your message, replying to the original (i.e. no forwarding), and making sure
that the mailing list is in the CC field by clicking on ``reply-to-all''.
+Sorry in advance, but the following is the standard pre-composed response to
a post not sent to the relax mailing lists and not labelled as private. If
you would like to start a private conversation about relax, please label your
message as such. If you really must start a private exchange, please respond
to this message saying so. If your message was meant to be sent to the relax
mailing list, please send the message again. For this, please copy-and-paste
your message, replying to the original (i.e.\ no forwarding), and making sure
that the mailing list is in the CC field by clicking on ``reply-to-all''.
\end{exampleenv}
Modified: trunk/docs/latex/dispersion.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/dispersion.tex (original)
+++ trunk/docs/latex/dispersion.tex Wed Feb 26 14:24:17 2014
@@ -528,7 +528,7 @@
This is the model for 2-site very-slow exchange model for time scales within
range of microsecond to second time scale, where $\pA \gg \pB$, and named
after \citet{Tollinger01}.
It is selected by setting the model to `TSMFK01'.
-A particularly interesting feature of the dispersion curves is the damped
oscillations, which occur at low CPMG field strengths, and is solely a
function of the chemical shift difference between the two sites (i.e.,
independent of the rate of exchange).
+A particularly interesting feature of the dispersion curves is the damped
oscillations, which occur at low CPMG field strengths, and is solely a
function of the chemical shift difference between the two sites (i.e.\
independent of the rate of exchange).
The equation is:
\begin{align}
Modified: trunk/docs/latex/dispersion_params.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/dispersion_params.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/dispersion_params.tex (original)
+++ trunk/docs/latex/dispersion_params.tex Wed Feb 26 14:24:17 2014
@@ -42,9 +42,9 @@
$\omegaHB$ & - & The proton Larmor
frequency of the spin in state B (for MMQ data) & rad.s$^{-1}$ \\
$\omegaHC$ & - & The proton Larmor
frequency of the spin in state C (for MMQ data) & rad.s$^{-1}$ \\
$\aveomega$ & $\pA\omegaA + \pB\omegaB$ & The population
averaged Larmor frequency of the spin & rad.s$^{-1}$
\\
-$\omegaone$ & - & Spin-lock field
strength, i.e. the amplitude of the rf field & rad.s$^{-1}$
\\
+$\omegaone$ & - & Spin-lock field
strength, i.e.\ the amplitude of the rf field & rad.s$^{-1}$
\\
$\omegae$ & $\sqrt{\aveoffset^2 + \omegaone^2}$ & Effective field
in the rotating frame & rad.s$^{-1}$ \\
-$\omegarf$ & - & Spin-lock offset, i.e.
the frequency of the rf field & rad.s$^{-1}$ \\
+$\omegarf$ & - & Spin-lock offset,
i.e.\ the frequency of the rf field & rad.s$^{-1}$ \\
$\theta$ & $\arctan \left( \frac{\omegaone}{\aveoffset} \right)$
& Rotating frame tilt angle & rad \\
$\kAB$ & $\pB\kex$ & The forward exchange
rate from state A to state B (2-site) & rad.s$^{-1}$ \\
$\kBA$ & $\pA\kex$ & The reverse exchange
rate from state B to state A (2-site) & rad.s$^{-1}$ \\
Modified: trunk/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/trunk/docs/latex/intro.tex?rev=22336&r1=22335&r2=22336&view=diff
==============================================================================
--- trunk/docs/latex/intro.tex (original)
+++ trunk/docs/latex/intro.tex Wed Feb 26 14:24:17 2014
@@ -402,7 +402,7 @@
Within relax all user functions operate on data stored within the current
data pipe.
This pipe stores data is input, processed, or output as user functions are
called.
-There are different types of data pipe for different analyses, e.g. a
reduced spectral density mapping pipe, a model-free pipe, an exponential
curve-fitting pipe, etc.
+There are different types of data pipe for different analyses, e.g.\ a
reduced spectral density mapping pipe, a model-free pipe, an exponential
curve-fitting pipe, etc.
Multiple data pipes can be created within relax and various operations
performed in sequence on these pipes.
This is useful for operations such as model selection whereby the function
\uf{model\ufus{}selection} can operate on a number of pipes corresponding to
different models and then assign the results to a newly created pipe.
When running relax you choose which pipe you are currently in by using the
\uf{pipe\ufsep{}switch} user function to jump between pipes.
r22336 - /trunk/docs/latex/