--- a/README	Mon Sep 22 21:53:16 2008 -0700
+++ b/README	Mon Sep 22 21:53:25 2008 -0700
@@ -1,30 +1,46 @@
-Dependencies
-  CGAL-3.3 -    for alpha-shapes and kinetic data structures
-  DSR-PDB -     for reading in PDB files (if use_dsrpdb is turned on in cmake)
-  CMake -       for controlling the build process
-  boost -       great set of C++ libraries
-  Doxygen -     for building documentation
-  rlog -        for logging only (is not needed by default)
-  SYNAPS -      for solving polynomials (for kinetic kernel), which in turn requires GMP
+% Dionysus README
+% Dmitriy Morozov
+
+## Dependencies
 
-Configuration
-  The path to CGAL's Makefile is expected to be set in $CGAL_MAKEFILE, the rest
+  * [CGAL]-3.3 ---  for alpha-shapes and kinetic data structures
+  * [DSR-PDB] ---   for reading in PDB files (if use_dsrpdb is turned on in cmake)
+  * [CMake] ---     for controlling the build process
+  * [boost] ---     great set of C++ libraries
+  * [Doxygen] ---   for building documentation
+  * [rlog] ---      for logging only (is not needed by default)
+  * [SYNAPS] ---    for solving polynomials (for kinetic kernel), which in turn requires GMP
+
+[CGAL]:         http://www.cgal.org
+[DSR-PDB]:      http://www.salilab.org/~drussel/pdb/
+[CMake]:        http://www.cmake.org
+[boost]:        http://www.boost.org
+[Doxygen]:      http://www.stack.nl/~dimitri/doxygen/
+[rlog]:         http://www.arg0.net/rlog
+[SYNAPS]:       http://www-sop.inria.fr/galaad/synaps/
+
+## Configuration
+  The path to CGAL's Makefile is expected to be set in `$CGAL_MAKEFILE`, the rest
   is just the usual CMake configuration
 
-Building
+## Building
   To build examples, create a directory build (to keep everything in one place),
   go to that directory and run cmake and make:
-  mkdir build
-  cd build
-  cmake ..   (or "ccmake .." if you want a curses interface)
-  make
+
+    mkdir build
+    cd build
+    cmake ..   (or "ccmake .." if you want a curses interface)
+    make
   
-  In the cmake line you can provide -Ddebug:bool=on to turn on debugging,
-  -Dcounters:bool=on to turn on counters, -Doptimize:bool=on to turn on
-  optimization, -Duse_dsrpdb:bool=on to turn on reading PDB files.  Depending on
-  the combination of debugging and optimization, a particular CMAKE_CXX_FLAGS*
+  In the cmake line you can provide `-Ddebug:bool=on` to turn on debugging,
+  `-Dcounters:bool=on` to turn on counters, `-Doptimize:bool=on` to turn on
+  optimization, `-Duse_dsrpdb:bool=on` to turn on reading PDB files.  Depending on
+  the combination of debugging and optimization, a particular `CMAKE_CXX_FLAGS*`
   is chosen.  All of this can be set using a text user interface by running
-  ccmake instead of cmake.
+  `ccmake` instead of `cmake`.
 
-Author
-  Dmitriy Morozov <morozov@cs.duke.edu>
+  When compiling on a 64 bit platform (with Boost 1.34) add
+  `-DBOOST_NO_INTRINSIC_INT64_T` to `CMAKE_CXX_FLAGS`.
+
+## Author
+  Dmitriy Morozov <dmitriy@mrzv.org>