Dss

DESCRIPTION

  "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.
  

USAGE

  dss selection, state

  state = state-index or 0 for all states
  

EXAMPLES

  dss

NOTES

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