[Bug-AUCTeX] 11.83; Wrong intendation and vertical shifting in math mode display

[Frank Küster]

Remember to cover the basics, that is, what you expected to happen and
what in fact did happen.


In the following equation code, some things go wrong:

- the closing brace for the exponent that is started by `e^{' in the
  ninth-last line is wrongly indented, and the `-\frac' in the line
  following `e^{' should be indented by two more places, too.

- The index zero two lines later looks weird - the underscore is in the
  middle of the `0' instead near its bottom where it should be

- in the two occurences of `^2' below, the digit is shifted below the
  baseline instead above.

Here is a screenshot:

and here is the file:

\documentclass{scrartcl}
\usepackage[latin1]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{ngerman}
\usepackage{lmodern}
\usepackage{amsmath}
\usepackage{nicefrac}

\begin{document}
\title{End-to-end Distance Distribution in a Rigid Rod with flexible
  linkers}
\author{Frank Küster}
\maketitle{}

\section{A simpler model:  Gaussian chain at one end}
\label{sec:simpl-model:-gauss}

We assume that the linker can be modelled by a gaussian chain.  For
the sake of simplicity, in a first step we consider a rod with one
flexible linker, while the other dye fixed is the other end of the
rod\footnote{but of course completely free to rotate}.

\subsection{Two dimensions}
\label{sec:two-dimensions}

To dissect the problem, we first look at a two-dimensional system:

\vspace{5cm}

We have
\begin{equation}
  \label{eq:1}
  r = r_0 + r_g \cos \theta \text{ and } r_g = \frac{r - r_0}{\cos \theta}
\end{equation}
The angles are equally distributed with $-\pi < \theta < \pi$,
$P(\theta)=\text{const.}$.  The normalization condition is
\begin{equation}
  \notag
  1 = \int_{-\pi}^{\pi} P(\theta) d\theta = \text{const.} (\pi -
  (-\pi)) = 2 \pi \text{const.}
\end{equation}
hence
\begin{equation}
  \label{eq:3}
  P(\theta) = \frac{1}{2 \pi}
\end{equation}

For any given $\theta$, the probability of the distance being $r$ is
the product of the probability of that angle, and the distance being
$r$ at that angle:
\begin{equation}
  \label{eq:4}
  P_{\theta}(r) = P(\theta) P_g(r_g=\frac{r-r_0}{cos \theta}
\end{equation}
To get the overall probability $P(r)$, we have to integrate over all
angles:

\begin{equation}
  \label{eq:5}
  P(r) = 2 \int_0^{\pi} P(\theta) P_g(\frac{r-r_0}{\cos \theta}) d\theta
\end{equation}

\subsection{Three dimensions}
\label{sec:three-dimensions}

This gives an additional angle $\phi$, which is also equally
distributed between $-\pi$ and $\pi$, but here $r$ is independent of
$\phi$.  Therefore

\begin{equation}
  \label{eq:6}
  P(r) = 2 \int_{0}^{\pi} P(\phi)\; 2 \int_{0}^{\pi} P(\theta)
  P_g(\frac{r-r_0}{\cos \theta}) \;d\theta\, d\phi
\end{equation}

Since the inner integral is independent of $\theta$, we can separate
the integrations:
\begin{equation}
  \label{eq:7}
  P(r) = 2 \int_{0}^{\pi} P(\phi) \;d\phi \cdot 
         2 \int_0^{\pi} P(\theta) P_g(\frac{r-r_0}{\cos \theta}) \;d\theta
\end{equation}
Substituting the expressions for the individual distribution
functions, we get
\begin{equation}
  \label{eq:8}
  P(r) = 2 \int_0^{\pi} \frac{1}{2\pi} d\phi \cdot 
         2 \int_0^{\pi} \frac{1}{2\pi} 
                        \frac{
                          4 \pi \left( 
                            \frac{
                              r - r_0
                            }{
                              \cos\theta
                            }\right)^2
                        }{
                          \left(
                            \nicefrac{2}{3}\pi \langle r^2\rangle
                          \right)^{\nicefrac{3}{2}}
                        }
                        e^{
                          -\frac{
                            3\left(
                              \frac{r-r_0}{\cos\theta}
                            \right)^2
                          }{
                            2\langle r^2\rangle
                          }
                      }
\end{equation}



\end{document}

%%% Local Variables: 
%%% mode: latex
%%% TeX-master: t
%%% End: 

Of course, any hints how to make AUCTeX's display the equation better by
changing line breads etc. are also appreciated.  As well as corrections
for the physics ;-)

Regards, Frank


Emacs  : GNU Emacs 22.0.50.1 (i386-pc-linux-gnu, X toolkit, Xaw3d scroll bars)
 of 2006-06-26 on pacem, modified by Debian
Package: 11.83

current state:
==============
(setq
 AUCTeX-date "2006-06-07"
 window-system 'x
 LaTeX-version "2e"
 TeX-style-path '("style" "auto" "/home/frank/texmf/tex/latex/style" 
"/home/frank/texmf/tex/latex/auto"
                  "/usr/share/emacs/22.0.50/site-lisp/auctex/style" 
"/var/lib/auctex/emacs-snapshot"
                  "/home/frank/.auctex-styles/" "/home/frank/.auctex-styles/" 
"/home/frank/.auctex-styles/")
 TeX-auto-save t
 TeX-parse-self t
 TeX-master t
 TeX-command-list '(("TeX" "%(PDF)%(tex) %S%(PDFout) \"%(mode)\\input %t\"" 
TeX-run-TeX nil
                     (plain-tex-mode texinfo-mode ams-tex-mode) :help "Run 
plain TeX")
                    ("LaTeX" "%l \"%(mode)\\input{%t}\"" TeX-run-TeX nil 
(latex-mode doctex-mode) :help "Run LaTeX")
                    ("MakePDF" "make %s.pdf" TeX-run-TeX nil t) ("MakeTeil1" 
"make teil1" TeX-run-command nil t)
                    ("MakeTeil2" "make teil2" TeX-run-command nil t)
                    ("Makeinfo" "makeinfo %t" TeX-run-compile nil 
(texinfo-mode) :help "Run Makeinfo with Info output")
                    ("Makeinfo HTML" "makeinfo --html %t" TeX-run-compile nil 
(texinfo-mode) :help
                     "Run Makeinfo with HTML output")
                    ("AmSTeX" "%(PDF)amstex %S%(PDFout) \"%(mode)\\input %t\"" 
TeX-run-TeX nil (ams-tex-mode) :help
                     "Run AMSTeX")
                    ("ConTeXt" "texexec --once --texutil %(execopts)%t" 
TeX-run-TeX nil (context-mode) :help
                     "Run ConTeXt once")
                    ("ConTeXt Full" "texexec %(execopts)%t" TeX-run-TeX nil 
(context-mode) :help
                     "Run ConTeXt until completion")
                    ("ConTeXt Clean" "texutil --purgeall" TeX-run-interactive 
nil (context-mode) :help
                     "Clean temporary ConTeXt files")
                    ("BibTeX" "bibtex %s" TeX-run-BibTeX nil t :help "Run 
BibTeX")
                    ("View" "%V" TeX-run-discard t t :help "Run Viewer")
                    ("Print" "%p" TeX-run-command t t :help "Print the file")
                    ("Queue" "%q" TeX-run-background nil t :help "View the 
printer queue" :visible TeX-queue-command)
                    ("File" "%(o?)dvips %d -o %f " TeX-run-command t t :help 
"Generate PostScript file")
                    ("Index" "makeindex %s" TeX-run-command nil t :help "Create 
index file")
                    ("Check" "lacheck %s" TeX-run-compile nil (latex-mode) 
:help "Check LaTeX file for correctness")
                    ("Spell" "<ignored>" TeX-run-ispell-on-document nil t :help 
"Spell-check the document")
                    ("Other" "" TeX-run-command t t :help "Run an arbitrary 
command"))
 )
-- 
Frank Küster
Single Molecule Spectroscopy, Protein Folding @ Inst. f. Biochemie, Univ. Zürich
Debian Developer (teTeX/TeXLive)