QUICK START INSTRUCTIONS FOR RUNNING CRANK

1) Make sure that you are running CCP4 version 6.3.0 or later, you have sourced the ccp4.setup file.

2) Type ccp4i at your UNIX prompt, or go to directory $CCP4/examples/runnable/crank.exam fo running CRANK
   via a UNIX script.  The rest of the instructions are for the ccp4i interface.

3) Select "Experimental Phasing" module in the Top left hand menu of ccp4i and then the task entitled
   "Crank - automated package".

4) Select your merged mtz file that contains all the intensities for all the data sets of your experiment in
   the MTZ in option and ensure that the intensity labels chosen are correct.  If you wish to input structure
   factor amplitudes instead, choose Amplitudes in the "Input" field.  Select your experiment type in the
   "Setup experiment" option and input the protein sequence for optimal solvent content calculation and 
   sequence docking for automated model building.

5) Tell crank the substructure atom, the number of substructure atoms per monomer, and the f' and f" values
   for the substructure atom.  (all the orange/yellow boxes in the "Crystal" subsection.)

6) If you wish, examine or change the solvent content and number of monomers in the asymmetric unit within the
   "Derived parameters" section - what will be displayed (if the above steps are completed) is the 
   solvent content and most probable number of monomers (based on Kantardjieff-Rupp analysis).  To see the 
   solvent content corresponding to a different number of monomers, change the number of monomers and click 
   on the "Guess Overall B, solvent content" button.  

7) In the "Experimental Pipeline" section, go to the "Pipeline:" menu and change programs for a particular step.
   If you wish to change any program options, click the "Display individual program option" button on.

8) At the bottom left, choose Run and Run Now!

9) To look at the results, see the ccp4i directory $(JOB_NUMBER)_crank directory.  The workdb directory
   contains the mtz and xml substructure files.  While the program specific logfiles are in the 
   $(step)-$(program-name) sub-directory: