Superimposing structures (SUPPOS)

• Introduction.
• Options to do matrix administration
  • Transformation file format
  • Put a matrix/vector in the database (PUTMAT)
  • Get a matrix/vector from the database (GETMAT)
  • List the matrix/vector database (LSTMAT)
  • Delete a matrix/vector from the database (DELMAT)
  • Looking in transformation database (DIRMAT)
  • Reading external matrices in (GETOLD)
  • Show the presently active matrix (SHOMAT)
• Atom/residue selection
  • Select the atoms on which to superimpose (RANGE1)
  • Select the atoms to be superposed (RANGE2)
  • Picking pairs of atoms to superimpose (PICKIN)
  • Showing the sets (SHORNG)
  • Saving sets in a file (SAVRNG)
  • Retrieving sets (RESRNG)
• Manual superimposing
  • The superimposing step (DOSUP)
  • Applying a transformation (APPLY)
  • Undoing an applied transformation (UNDO)
  • Optimisation of superposition (SUPOPT)
• Evaluation options
  • Alpha carbon distances (CADIFF)
  • Residue center distances (CENDIF)
  • Statistics (SUPSTS)
  • Tabulating the superpositioning result (COMPAR)
  • Analyze a transformation (ANAFIT)
  • Comparing two covalently identical molecules (EQUAL)
  • Comparing two almost covalently identical molecules (EQUALF)
• Automatic 3-D alignment
  • Aligning two molecules/domains (MOTIF)
  • (MOTIV)
• Superpositioning parameters (PARAMS)
  • Minimal fragment length in motivs (MINLEN)
  • Maximal error in superposition (MAXERR)
  • Root mean square error in superposition (RMSERR)
  • Length of equivalenced stretches (LENHOM)
  • Skipping helix-helix superpositions (NONHEL)
• Other superposition related options
  • (Re-)initialization (INISUP)
  • Color as function of the misfit (COLDIF)
  • Apply matrix to mol-items (APLITM)
  • Manual diagonal plot (CABOX)
  • Averaging molecules (SFUDGE)
  • Averaging molecules (SFUDG2)
  • Detecting hinges (ISBEND)
• Activating more commands (MORE)