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:: Later versions of TMalign (since 2012) have changed output formats. The Biskit wrapper has been adapted to TMAlign.f (Fortran version) as downloaded from the Zhang lab website 04/2013.

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