TM-Align

Install the TM-Align structure alignment program (Zhang and Skolnick 2003).

Program binaries for 64 and 32 bit Linux are provided on the TM-Align home page: http://zhanglab.ccmb.med.umich.edu/TM-align/

Note:: as of May 2012, the new version of TMalign seems to have changed output formats, the Biskit wrapper still needs to be adapted to that.

Download and uncompress the file and make it executable:

cd /tmp
wget http://zhanglab.ccmb.med.umich.edu/TM-align/TMalign.gz
gzip -d TMalign.gz
chmod +x TMalign

Copy it to a system-wide location:
```
sudo mv TMalign /usr/local/bin/
```
...or any other location that is in your search $PATH. As always, you can also configure Biskit to find the program somewhere else:
Adapt biskit settings (optional):

This would only be necessary if the executable has a different name or is not in the search $PATH. Make a local copy of the exe_tmalign.dat configuration file and adapt it accordingly:
```
cd /usr/lib/python2.5/site-packages/Biskit/data/defaults
cp exe_tmalign.dat ~/.biskit/
```
Then edit the "bin=" line in the [BINARY] section of this file.

Test your installation:

cd biskit/Biskit/
python tmalign.py

Should yield:

<....some example data ....>
---------------------------------------
Ran 2 tests in 4.238s

OK

Usage:

Configuration:

see Biskit/data/defaults/exe_tmalign.dat