Editing Cealign plugin (section)

== Installation ==

===Mac OS X (10.5, 10.6)===
[[Image:Cealign mac os x.png|300px|thumb|center|CEAlign running on Mac OS X (10.5)]]
* Install PyMOL under fink.
* Download and install cealign (download instructions below)
<source lang="bash">
sudo /sw/bin/python setup.py install
</source>
* In PyMOL, run the two scripts needed for cealign: "cealign.py" and "qkabsch.py". These are located in the cealign directory you previously downloaded.
* Voila!
* Note that the above python version must match the same version that is used by PyMOL. If you are using the pre-compiled version of MacPyMOL, the above instructions won't work.
* Note: if you get an error about '''-Wno-long-double''' then your gcc is mismatched.  I fixed this by pointing the symbolic link ''/usr/bin/gcc'' from ''/usr/bin/gcc-4.2'' to ''/usr/bin/gcc-4.0''.  Or, in code,
<source lang="bash">
# These command are commented out to stop people from copy/pasting b/c 
# these are possibly dangerous for your system.  Ensure that /usr/bin/gcc
# is a symbolic link and not a real binary.  If so, I used the following
# to fix the -Wno-long-double error.
# sudo rm /usr/bin/gcc
# sudo ln -s /usr/bin/gcc-4.0 /usr/bin/gcc
</source>

===Windows systems===
====CEAlign 0.9====
This is a Win32 build of CEAlign 0.9 [http://pymolwiki.org/index.php/Cealign#Beta_Version_0.9]
=====Requirements=====
* Christoph Gohlke's latest '''unofficial''' PyMol build: http://www.lfd.uci.edu/~gohlke/#pythonlibs
* "Python 2.6.2 Windows installer" from python.org: http://www.python.org/download/
* '''CEAlign09Win32.zip''' from: http://users.umassmed.edu/shivender.shandilya/pymol/CEAlign09Win32.zip
=====Directions=====
# Download the '''CEAlign09Win32.zip''' file
# Unzip the downloaded file and follow the directions as per the included README.txt
# Enjoy the ''awesomeness'' that is CEAlign!
====CEAlign 0.8====
This is a quick and dirty method to use CEAlign 0.8 on Win32 system with the '''official''' Pymol builds...
=====Requirements=====
* Latest PyMol, installed on your system
* Numpy for python 2.4 -- quick download of just what's needed: http://users.umassmed.edu/shivender.shandilya/pymol/cealign08/numpy.zip
[Note: If this file is corrupt, you may download the latest 'Numpy for Python 2.4' directly from SourceForge.net
* Pre-compiled ccealign.pyd python module: http://users.umassmed.edu/Shivender.Shandilya/pymol/cealign08/ccealign.zip
* Modified pymolrc: http://users.umassmed.edu/Shivender.Shandilya/pymol/cealign08/pymolrc
* cealign.py and qkabsch.py from the Cealign-0.8-RBS package: download below

=====Directions=====
# Unzip the numpy.zip file, which will give you a folder named '''numpy'''
# Move this entire folder to: C:\Program Files\DeLano Scientific\PyMOL\modules\  (or the corresponding location on your system)
# Unzip ccealign.zip, which will give you a file called  '''ccealign.pyd'''
# Move this pyd file to: C:\Program Files\DeLano Scientific\PyMOL\py24\DLLs\  (or the corresponding location on your system)
# Copy the downloaded '''pymolrc''' file to: C:\Program Files\DeLano Scientific\PyMOL\   (or the corresponding location on your system)
# Extract and copy the files cealign.py and qkabsch.py from the Cealign-0.8-RBS package to: C:\Program Files\DeLano Scientific\PyMOL\py24\Lib\   (or the corresponding location on your system)
# Run PyMol and load some molecules
# Run this command in Pymol: '''cealign molecule1, molecule2'''
# Enjoy!

===Gentoo Linux===
Add the science overlay via
 layman -a sci
and emerge the cealign plugin
 emerge pymol-plugins-cealign

===*nix systems===
====Requirements====
* C compiler
* Python 2.4+ with distutils
* Numpy
** for User-compiled PyMOL: <source lang="python">python setup.py install</source>
** for the precompiled version of PyMOL <source lang="python">python setup.py install --prefix "" --root /DIR_TO/pymol/ext/</source>

====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>