HOWTO.txt

 HOWTO:
 
- Check if your installation is ok. First setup as described in REAME.txt in this directory.
    Then type:
    cing --test -v 0
    
- Run procheck on a small example.
    cing -n 1brv --nosave --ipython --initPDB $CINGROOT/Tests/data/cyana/1brv/1brv.pdb
    project.procheck()
    
- Convert some cyana data to cing:
    python -u $CINGROOT/python/cing/Scripts/cyana2cing.py --pdbFile $CINGROOT/Tests/data/2hgh_small
    
- Print the first model's chi 1 as reported by procheck of residue 77 in chain A.
    format project.molecule.A.GLU77.procheck.CHI1[0]
    Not very useful as it's already part of cing itself; just like PHI, etc.
    format project.molecule.A.GLU77.CHI1[0] or:
    formatall( project.molecule.A.residues[0].CHI1 )
    more useful might be:
    format project.molecule.A.GLU77.procheck.secStruct
    
    NB. 
    format object
    is equivalent with 
    print object.format()
    format is a method that most of cing's objects have and that give more user friendly
    output (sometimes over multiple lines)
    
- Print list of parameters:- print list of parameters:
    formatall( project.plotparameters.PHI )
    formatall( project.molecule.A.residues[0].C.coordinates )
    formatall( project.molecule.A.residues[0].procheck )
    formatall( project.molecule.A.VAL171.C )

- Reload a plugin after you recoded it:
    from cing.core.importPlugin import importPlugin
    importPlugin("procheck")
    
- Configure local settings:
    Create a file localConstants parallel to the setup.py file and add definitions that
    get imported from the parallel __init__.py code. Just one setting at the moment.