Idealization Application

This application rebuilds molecules using ideal bond lengths, bond angles, and torsion angles. It is at is at mini/src/apps/public/. The name of the application is idealize.cc

Command Lines and Options

• Command Lines:

  idealize.linuxgccrelease @flags > idealize.log 

• Options:

  -database                 Path to rosetta databases. [PathVector]
  -s                        Input file paths and name.     [FileVector]
  -no_optH                  Do not change positions of Hydrogen atoms!
                            (default true, specify false if you want optH). [Boolean]
  -ignore_unrecognized_res  Do not abort if unknown residues are found in PDB file;
                            instead, ignore them. default='false'. [Boolean]
  

Result Interpretation

There is a pdb file generated from this application with ideal bond lenghths, bond angles and torsion angles.Please note, few features have not been implemented in this application since the protocol is still under development. 1. A scoring function, other than the atom-pair and coordinate constraints. So it may generate structures with bad clashes. The only criterion is similarity to the input structure. 2. Tethers to the starting torsion angles. Right now the torsion angles are completely free, which is probably not the best thing. In Rosetta++ harmonic constraints hold the torsions in their starting values.

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