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INSTALLATION VIA COMPILATION (Generic)
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NOTE: 

These are the general installation instructions for a platform which
has no preinstalled dependencies whatsoever.  These days, that's
pretty rare.  

Most likely, you are on a commmon platform such as RedHat, or OSX, so
look for a INSTALL file which specifically address your platform in
the setup directory.

WARNING: You will need some basic knowledge of Makefiles, compilation
flags, libraries, python, environment variables, and paths in order to
compile PyMOL.  If you don't feel comfortable with this, then try out
the MS-Windows version, which you can download from the web site.

The following instructions assume you are installing PyMOL in your
home directory.  You can of course put it anywhere, but you will need
to replace "$HOME" with an appropriate path.

STEP (1) 

A compiled copy of the external dependencies package ("ext") is
required, but only needs to be downloaded once (20 MB).  This package
contains everything you will need to run PyMOL all in one place so
that you won't have to hunt down the individual components.  

NOTE: 

   If you already have all of the components installed elsewhere on your
   system, then feel free to bypass this step, but note that you will
   probably need to edit some configuration files in order to get that
   to work.

You will need to compile the external dependencies from the sources
(currently in the file "ext-0.99-src.tgz"). See the ext package
release notes for more information.

http://sourceforge.net/project/showfiles.php?group_id=4546

The external dependencies can be installed in an "ext" subdirectory
within the main pymol directory.

   cd $HOME/pymol
   gunzip < ext-0.99-src.tgz | tar -xvf -
   cd ext

  **READ INSTALL in that directory for "ext" building instructions.**

Alternatively, you can put the external dependencies into a different
directory and then use a symbolic link to "ext" in the pymol directory.

   cd $HOME
   gunzip < ext-0.99-src.tgz | tar -xvf -
   cd $HOME/pymol
   ln -s ../ext ext
   cd ext
  **READ INSTALL in that directory for "ext" building instructions.**
   
STEP(2) 

After you have built the external dependencies, copy setup/Rules.<platform>
to "Rules.make" and choose options appropriate for your configuration
(here is where experience counts).

Unless you are planning on doing heavy PyMOL development under Linux,
you should choose to make PyMOL as a Python module and not as a
standalone application.

   cd $HOME/pymol
   cp setup/Rules.<platform> Rules.make
   vi Rules.make

STEP (3) 

"make" to compile.

	cd $HOME/pymol
	make

STEP (4) 
  
Copy "setup/pymol.com.template" to "pymol".

Next, edit pymol so that PYMOL_PATH points to the correct location
on your system.

   cd $HOME/pymol
   cp pymol.com.template pymol
   vi pymol
	
Now you should be all set to run pymol.

   ./pymol

 I suggest putting a link to this file into a directory in your path.

   ln -s $HOME/pymol/pymol /usr/local/bin/pymol

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NOTE: If you ever want to clean up the tree
	"make clean" gets rid of all intermediate objects, etc.
	"make distclean" restores the tree to near "distribution" quality 
    (NOTE: it does not remove pymol, Rules.make, pymol.csh, or the
    "ext" directory/symlink)

