DSSP

The home page with license and download links is: http://swift.cmbi.ru.nl/gv/dssp/

To install the program...

1. Print and fill out license the form at http://swift.cmbi.ru.nl/gv/dssp/license.html and fax it to +31 243652977

2. Download / Uncompress / Compile the source code:

   wget ftp://ftp.cmbi.ru.nl/pub/molbio/software/dsspcmbi.zip
   unzip dsspcmbi.zip
   
   cd dssp
   ./DsspCompileGCC
   

   Note:

   Under Mac-OSX, first try ./DsspCompileCC

3. Install it system-wide

   For example:

   cd ..
   sudo mv dssp /usr/local/src/
   cd /usr/local/bin
   sudo ln -s ../src/dssp/dsspcmbi .
   

4. Test the Biskit / DSSP interface:

   cd biskit/Biskit
   python DSSP.py
   

   Should yield something like:

   Loading PDB...
   Starting DSSP
   Running DSSP
   Sequence : AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIRKKAVINGEQIRSISDLHQTLKKELALPEYYGENLDALWDALTGWVEYPLVLEWRQFEQSKQLTENGAESVLQVFREAKAEGADITIILS
   Secondary: .....SHHHHHHHHHHHSS..TTEE.HHHHHHHT..GGGT.HHHHSTT.EEEEEEE..TT..S...TT..EEEEE.S..SSS..S.EEEEETT..EEEESSSSSS.EE...EEEEETTT..SHHHHHHHHHHHHT..TT..SSHHHHHHHHHHT..SSEEEEEE.HHHHHHHTTTTHHHHHHHHHHHHHHT..EEEEE.
   

Usage:

see PDBDope.addSecondaryStructure()

Custom configuration:

see biskit/data/Biskit/defaults/exe_dsspcmbi.dat