Theory

The Assign helices and Strands option will manually reassign secondary structure to a protein structure. This command does not change the geometry of the model, it only formally assigns secondary structure symbols to residues. f the secondary structure string is not specified, apply ICM modification of the DSSP algorithm of automatic secondary structure assignment (Kabsch and Sander, 1983) based on the observed pattern of hydrogen bonds in a three dimensional structure. The DSSP algorithm in its original form overassigns the helical regions. For example, in the structure of T4 lysozyme (PDB code 103l ) DSSP assigns to one helix the whole region a_/93:112 which actually consists of two helices a_/93:105 and a_/108:112 forming a sharp angle of 64 degrees. ICM employs a modified algorithm which patches the above problem of the original DSSP algorithm. Assigned secondary structure types are the following: "H" - alpha helix, "G" - 3/10 helix, "I" - pi helix, "E" - beta strand, "B" - beta-bridge, "_" or "C" - coil.

To assign secondary structure:

• Load the pdb structure (File/Open or PDB Search}
• Select the structure. You can do this by double clicking on the name of the structure in the ICM Workspace (a selection is highlighted blue in the ICM Workspace and green crosses in the graphical display) or you can use the right-click button and drag it over the whole structure in the graphical display.
• Tools/3D Predict/Assign helices and Strands