Class Prosa2003

Analyze energies using Prosa2003 for a given PDBModels.

Reference

• http://lore.came.sbg.ac.at/
• http://www.proceryon.com/solutions/prosa.html
• Sippl,M.J. Recognition of Errors in Three-Dimensional Structures of Proteins.Proteins, 17: 355-362 (1993).

Example usage

>>> x = Prosa2003( ref_model, [ m1, m2 ], verbose=1 )
>>> result = x.run()

Settings

• lower_k = |integer| and upper_k = |integer|
  • Pair interaction energies are calculated for residue pairs whose distance k along the sequence is lower_k < k < upper_k. Default values are lower_k = 1, upper_k = 600. For example if you want to see only the short range energy contributions (e.g. sequence separation k < 9) set lower_k = 1, upper_k= 9. These parameters affect pair interactions only.
• pot_lb = |float| and pot_ub = |float|
  • Pair energies are calculated in the distance range [pot_lb, pot_ub] A. Outside this range energies are zero. You can set the desired distance range of pair potential calculations. For example if you are not interested in energy contributions of close contacts, set pot lb = 4. The energy of pair interactions in the intervall [0; pot_lb] is then zero. Default: pot_lb = 0, pot_ub = 15. In addition the upper bound depends on the pair potentials used. The current maximum range is 15A.

Structure of the input file

  pair potential --- read in other than default potential
  surface potential
  pdb_dir --- directory with pdb file
  read pdb |filename| |object name|
  lower_k |int|
  upper_k |int|
  pot_lb |float|
  pot_ub |float|
  analyse energy |object name| 
  print energy |object name| |filename(.ana)|
  exit --- exit without launching graphical mode