The idea is to place a helix more or less “here” (the screen centre) by fitting to the electron density map. The algorithm is straightforward. First we move to the local centre of density, then examine the density for characteristic directions and fit ideal helices (of length 20 residues) to these directions. The helix is then extended if possible (by checking the fit to the map of residues added in ideal helix conformation) and chopped back if not. If the fit is successful, the helix is created in a new molecule called “Helix”. If the fit is not successful, there is instead a message added to the status bar. You can build the majority of a helical protein in a few minutes using this method (you will of course have to assemble the helices and assign residue numbers and sequence later).
This is available as a scripting function (place-helix-here) and
in the GUI (in the “Other Modelling Tools” dialog).