Relax Mode Application

Rosetta3 makes use of a new strategy for developing applications, a library based approach to creating protocols. The scientific component of the relax protocol is still based on the classical Rosetta relax algorithm. The "relax" mode in Rosetta carries out the task of structural refinement of a monomeric protein. It usually starts from a crude model generated by de novo structure prediction or homology modeling, and uses the Rosetta full-atom energy function refine the structure while searching through conformational space. By adjusting the protein backbone and sidechain torsion angles by relatively small amounts from the starting structure, it can dramatically lower the full-atom energy of a model by correcting local errors and improving interactions significantly. The relax protocol is critical to achieving atomic-level accuracy in structure prediction.

Relax application available at mini/src/apps/public/relax. The name of the application is relax.cc. The programe can invoke a fast mode which can be 5-10 times more efficient than the normal relax mode. You can find the executable of this application in mini/bin after a successful compilation.

Command Lines and Options

• Sample Command Line:

  relax.linuxgccrelease @flags > relax.log 

• Options used by the relax application:

  -database                 Path to rosetta3 databases. [PathVector]
  -s                        Input file paths and name.     [FileVector]
  -relax:fast               Invokes a fast mode, which is almost as effective as
                            a normal relax but 5-10 faster (optional) [Boolean]
  

  Normal I/O and Score Function flags also apply

Result Interpretation

There will be one pdb file and a score file generated. Here are the energy term descriptions.

fa_atr:                   Lennard-Jones attractive
fa_rep:                   Lennard-Jones repulsive
fa_sol:                   Lazaridis-Karplus solvation energy
fa_intra_rep:             Lennard-Jones repulsive between atoms in the same residue
pro_close:                proline ring closure energy
fa_pair:                  statistics based pair term, favors salt bridges
hbond_sr_bb:              backbone-backbone hbonds close in primary sequence
hbond_lr_bb:              backbone-backbone hbonds distant in primary sequence
hbond_bb_sc:              sidechain-backbone hydrogen bond energy
hbond_sc:                 sidechain-sidechain and sidechain-backbone hydrogen bond energy.
dslf_ss_dst:              distance score in current disulfide
dslf_cs_ang:              csangles score in current disulfide
dslf_ss_dih:              dihedral score in current disulfide
dslf_ca_dih:              ca dihedral score in current disulfide
rama:                     ramachandran preferences
omega:                    omega angles
fa_dun:                   internal energy of sidechain rotamers as derived from Dunbrack's statistics.
p_aa_p:                   probability of observing an amino acid, given its phi/psi energy method declaration
ref:                      reference energy for each amino acid
total:                    final score

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