Output short

The DSSP code

The output of DSSP is explained extensively under 'explanation'. The very short summary of the output is:

A blank in the DSSP secondary structure determination stands for loop or irregular. Loops and irregular elements are often, very incorrectly, called "random coil" or "coil". Many programs, including the PDBFINDER, replace this blank by a C (doing undue justice to the historical artefactual naming of loops and irregular stretches) because one never knows if a blank means loop or no-output, or something-went-wrong.

Improved π-helix assignment in DSSP 2.0

For about 25 years there was an error in DSSP which caused it to essentially never produce I as output. In the article Wolfgang and Chris write the they first look for H and after that for I. This cause many α-bulges to be marked with HHTHH. By reversing this assignment order Maarten Hekkelman improved DSSP. See our GPCR bulges article if you want to know the impact of this correction.


The WHAT IF software uses DSSP in many ways: a) interactive; b) via the WHAT IF web server ; and c) via the WHAT IF web services . In all three cases WHAT IF simplifies the output. S and B are called loop, and that becomes a blank in most output forms, or a C in cases where a blank is inconvenient. G is converted to 3 to look more like 310, and the occasional π-helix (I in DSSP), that I tend to call an α-bulge, is just counted as normal helix.