Editing Cealign plugin (section)

====Directions====
# uncompress the distribution file '''cealign-VERSION.tgz'''
# cd cealign-VERSION
# sudo python setup.py install  # if you installed by PyMOL by hand
## python setup.py install --prefix "" --root /DIR/TO/pymol/ext/  # if you are using the precompiled binary download
# insert "run DIR_TO_CEALIGN/cealign.py" and "run DIR_TO_CEALIGN/qkabsch.py" into your '''.pymolrc''' file, or just run the two Python scripts by hand.
# load some molecules
# run, '''cealign molecule1, molecule2'''
# enjoy

=====Pre-compiled Hackish Install=====
For those people that prefer to use the pre-compiled version of PyMOL, here are the basics for your install.  '''This is a poor method of installing Cealign.  I suggest users compile and install their own PyMOL.'''  The final goal is to get 
# '''ccealign.so''' module into '''PYMOL/ext/lib/python2.4/site-packages'''
# numpy installed (get the numpy directory into (or linked into) '''PYMOL/ext/lib/python2.4/site-packages'''
# and be able to run cealign.py and qkabsch.py from PyMOL.
If you can do the above three steps, '''cealign''' should run from the pre-compiled PyMOL.

In more detail, on a completely fictitious machine --- that is, I created the following commands from a fake machine and I don't expect a copy/paste of this to work '''anywhere''', but the commands should be helpful enough to those who need it:
<source lang="python">
# NOTES:
# This is fake code: don't copy/paste it.
#
# PYMOL='dir to precompiled PyMOL install'
# CEALIGN='dir where you will unpack cealign'
# replace lib with lib64 for x86-64
# install numpy
apt-get install numpy

# link numpy to PyMOL
ln -s /usr/local/lib/python2.4/site-packages/numpy PYMOL/ext/lib/python2.4/site-packages

# download and install Cealign
wget http://www.pymolwiki.org/images/e/ed/Cealign-0.6.tar.bz2
tar -jxvf Cealign-0.6.tar.bz2
cd cealign-0.6
sudo python setup.py build
cp build/lib-XYZ-linux/ccealign.so PYMOL/ext/lib/python2.4/site-packages

# run pymol and try it out
pymol
run CEALIGN/cealign.py
run CEALIGN/qkabsch.py
fetch 1cew 1mol, async=0
cealign 1c, 1m
</source>