Directory listing of protocols file

boxtyp20.pdb water box
calibrate.cns calibration module
calib.inp calibration and assignment input file
cop.inp ramachandran plot
define_methyls_all.cns define equivalent protons
define_methyls_ini.cns generate methyl group table
energy.inp calculate energy (elec + vdw)
errset.cns set error bounds
flags_new.cns set energy flags
generate.inp generate MTF file
generate_homology.inp generate homology model (not updated)
generate_template.inp generate template structure
generate_water.cns generate water shell
h2orefine.cns refine in explicit water
initialize.cns initialise variables
make_tensor.inp generate tensor for sani
merge.inp merge several data sets
noe_violations.inp print noe violations of final structures (not updated)
noe_violations_sml.inp print noe violations of final structures (not updated)
parmread.cns read energy parameters (not used)
planarf.cns define planar restraints (not used)
planar.cns define planar restraints (not  used)
pmrefine2.inp probability map refinement (not used)
pmrefine.inp probability map refinement (not used)
print_coorheader.cns generate coordinate header
print_coup.inp print violations for coupling restraints
print_dih.inp print violations for dihedral angle restraints
print_geom.inp print violations for covalent energy terms
print_noe.inp print noe violations of final structures
read_data.cns read experimental data
refine.inp calculate / refine a structure
re_h2o.inp refine in h2o
rmsave.inp calculate average rms from average structure
rotares.cns rotate symmetric residues
run.cns general include file
sa_ls_cool2.cns 2nd cartesian cooling stage
sa_ltad_cool1.cns  1st tad cooling stage 
sa_ltad_hightemp4.cns tad high temperature stage
sa_l_cool1.cns 1st cartesian cooling stage
sa_l_hightemp.cns cartesian high temperature stage
sa_l_randomchain.cns randomize peptide chain
sa_l_reduced.cns select atoms for reduced vdw 
setup_swap_init.cns setup floating assignment
swap.cns swap swap groups in floating assignment
swap_back.cns (not used)
swap_back.inp (not used)
torsiontop.cns setup torsion angle topology
wellordered.inp average structure and wellordered region
xplortodiana3.inp switch to IUPAC notation
