Structure Solution Software at CHESS

• CCP4 suite (multiple programs for structure solution and refinement) - start the graphical interface by typing "ccp4i". It is advisable to create your own project using the Directories and Project Dir button.

  CCP4 setup is done automatically when you log in as "specuser", so individual programs in the suite can be run directly, or from a script, using just the program name, e.g. "amore". For more information on CCP4 programs, browse to this documentation, also available locally at file:/usr/local/ccp4/html/INDEX.html.

• Shake-and-Bake (find heavy atom positions using SAD data) - type "SnB" to start up the Java interface. For SnB plus additional programs for phasing, etc., type "BnP".

• SOLVE/RESOLVE (find heavy atom positions using SAD or MAD data, phase, generate and improve map, build model) - type "solvehelp" for the manual, including sample scripts.

• SAPI (find heavy atom positions using SAD data) -
  1. Make an MTZ file of SAD data.
  2. "cp $RUNFILES/sapi.com ."
  3. Edit "sapi.com" to read your data file, and change column labels if necessary.
  4. "sapi.com > sapi.log"
  5. Look at peak list in "sapi.log" for an outstanding set of peaks. A huge single peak (usually sitting on a special position) means no good solution was found.

  For more information, browse to http://staff.chess.cornell.edu/~hao/sapi/sapi.html.

• CNS package (multiple programs for structure solution and refinement) - type "cns_web" for Web interface (runs locally), including tutorial as well as tools for use. To run the program itself, type "cns_solve".

• O (map and molecule display, model building) - Type "start_o" and accept all the default answers. For help, look at the O-files. Stereo graphics is only available on some of the machines in the computer room (the ones with emitters on top of their monitors).

• Coot (model building and refinement) - type "coot".

• PyMol (fancy graphics - movies, rendering, and more) - type "pymol".