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"dss" defines secondary structure based on backbone geometry and hydrogen bonding patterns. With PyMOL, heavy emphasis is placed on cartoon aesthetics, and so both hydrogen bonding patterns and backbone geometry are used in the assignment process. Depending upon the local context, helix and strand assignments are made based on geometry, hydrogen bonding, or both. This command will generate results which differ slightly from DSSP and other programs. Most deviations occur in borderline or transition regions. Generally speaking, PyMOL is more strict, thus assigning fewer helix/sheet residues, except for partially distorted helices, which PyMOL tends to tolerate. WARNING: This algorithm has not yet been rigorously validated.
dss selection, state state = state-index or 0 for all states
If you dislike one or more of the assignments made by dss, you can use the alter command to make changes (followed by "rebuild"). For example:
alter 123-125/, ss='L' alter pk1, ss='S' alter 90/, ss='H' rebuild