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DSSP

DSSP is the standard program for identifying secondary structure elements in protein structures.

The home page is: http://swift.cmbi.ru.nl/gv/dssp/

  1. Install the program

    on Ubuntu / Debian Linux:

    sudo apt-get install dssp

    on Mac-OSX:

    brew install brewsci/bio/dssp

  2. 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