From 8c7241b366e314b97a83418c8df914abb70259f4 Mon Sep 17 00:00:00 2001
From: Tjerk Straatsma <straatsmatp@ornl.gov>
Date: Tue, 17 Jul 2001 22:37:16 +0000
Subject: [PATCH] Add center and rotate documentation

---
 doc/user/analysis.tex | 35 +++++++++++++++++++++++++++++------
 1 file changed, 29 insertions(+), 6 deletions(-)

diff --git a/doc/user/analysis.tex b/doc/user/analysis.tex
index edc8b0ff4b..01e772508d 100644
--- a/doc/user/analysis.tex
+++ b/doc/user/analysis.tex
@@ -116,9 +116,24 @@ back into the box according to the periodic boundary conditions.
 The directive for this operation is
 
 \begin{verbatim}
-center [<integer imol>]
+center <integer imol> [<integer jmol default imol>]
 \end{verbatim}
 
+Coordinates of each frame read from a trajectory file can be 
+rotated using
+
+\begin{verbatim}
+rotate ( off | x | y | z ) <real angle units degrees>
+\end{verbatim}
+
+If \verb+center+ was defined, rotation takes place after
+the system has been centered. The \verb+rotate+ directives
+only apply to frames read from the trajectory files, and not
+to the reference coordinates. Upto 100 \verb+rotate+ directives
+can be specified, which will be carried out in the order in which
+they appear in the input deck. \verb+rotate off+ cancels all
+previously defined \verb+rotate+ directives.
+
 To set hydrogen bond criteria:
 
 \begin{verbatim}
@@ -129,11 +144,12 @@ hbond [distance [[<real rhbmin default 0.0>] <real rhbmin>]] \
 
 \section{Selection}
 
-Analyses can be applied to a selection of solute atoms. The selection
-is determined by
+Analyses can be applied to a selection of solute atoms and solvent molecules. 
+The selection is determined by
 
 \begin{verbatim}
-select [ <integer isgm> [ <integer jsgm> ]] [ { <string atom> } ]
+select ( [ <integer isgm> [ <integer jsgm> ]] [ { <string atom> } ] |
+	solvent <real range> | save <string filename> | read <string filename> )
 \end{verbatim}
 
 where {\rm isgm} is the first segment number, {\rm jsgm} is the last 
@@ -166,6 +182,9 @@ select solvent <real range>
 After solvent selection, the solute atom selection is reset to being all
 selected.
 
+The current selection can be saved to, or read from a file using the 
+\verb+save+ and \verb+read+ keywords, respectively.
+
 \par
 
 Some analysis are performed on groups of atoms. These groups of atoms
@@ -316,16 +335,20 @@ To copy the selected frames from the specified trejctory file(s),
 onto a new file, use
 
 \begin{verbatim}
-copy  [solute] <string filename>
+copy  [solute] [rotate <real tangle>] <string filename>
 \end{verbatim}
 
 To superimpose the selected atoms for each specified frame to the 
 reference coordinates before copying onto a new file, use
 
 \begin{verbatim}
-super [solute] <string filename>
+super [solute] [rotate <real tangle>] <string filename>
 \end{verbatim}
 
+The \verb+rotate+ directive specifies that the structure will make
+a full ratation every tangle ps. This directive only has effect when
+writing povray files.
+
 The format of the new file is determined from the extension, which
 can be one of