Output files from CHI programs:

chi_create

• *.pdb
• *.psf

chi_search

• results/*.pdb
• results/search.out
  • structure - number
  • trial - 1 to ntrials
  • hand - left|right
  • initial omega - initial crossing angle
  • average omega - average final craossing angle
  • energy - total interaction energy
  • initial phi - initial angular rotation about each helix axis
  • final phi - final angular rotation about each helix axis
  • shift - shift (A) wrt to all other helices

chi_rmsd

• results/rmsd.out
  • structure1 structure2 RMSD (A)

chi_cluster

• results/cluster.out
  • cluster # -> structure1 structure2 ... structureN

chi_average

• results/cluster*.pdb
• results/average.out
  • E: Total interaction energy (nonbonded)
  • area: buried surface area between helices
  • omega: crossing angle
  • phi: rotation angle around the long axis of helix (relative to start)
  • shift: Z-shift of helix wrt the other helices
  • close: closest approach distance of helix A to helix B
  • aa1: residue on helix A that is closest to helix B
  • aa2: residue on helix B that is closest to helix A
  • rpt: residues per turn
  • rpr: rise per residue

chi_expand

• results/cluster*.pdb
• results/expand.out
  • lack of closure (A) for each helix

chi_spread

• results/spread.out
  • RMSD for each structure in cluster from average structure in a cluster

chi_plot

• results/plot_all_[left|right].xmgr
• results/plot_cluster_[left|right].xmgr
• results/cluster*.xmgr