AUTHOR==Mike Tyka
METADATA==This document was edited May 25th 2010 by Mike Tyka. This application in mini was created and documented by Mike Tyka, et al.
DESCRIPTION==The "relax" application in Rosetta carries out the task of simple structural refinement of fullatom Rosetta models. It can also read Centroid models, in which case it will convert the model into a fullatom model and pack the sidechains. Relax does not carry out any extensive refinement and only searches the local conformational space neighbourhood.\n\n For virtually all situations it should be sufficient to use either -relax:quick or -relax:thorough and not worry about all the options.
ALGORITHM==The fast relax modes work by running many sidechain repack and minimisation cycles ramping up and down the repulsive weight of the forcefield. This sort of "pulses" the structure in successive collapse and expansion phases which "wiggles" the atoms into a low energy state. No explicit moves are done (this was found not to be useful as most moves are rejected and dont help lowering the nergy). Not that despite that fact, the structure can change up to 2-3 A from the starting conformation during the minimisation cycles.\n\nFastRelax is a more modern version of the initial fast relax algotihm which is more flexible and allows definition of a specific script of relax events (how exactly the repack and minimisation cycles are interlaced and what paramters they should take).
INPUTS==Relax takes as input one or more structures in silent or PDB format. Or Use the PyRosetta Toolkit.  All JD2 options apply (see JD2 Documentation ofr more details)
OUTPUTS==Relax outputs one or more structures in silent or PDB format. All JD2 output options apply (see JD2 Documentation ofr more details) As always -nstruct regulates the number of outputs per input structure.
EXAMPLES==The example with input files can be found in demo/relax/ Just execute the run.sh script.
TIPS==Relax will increase the rmsd of your protein to a high degree.  Use only if you really want to do this.  A better and quicker way to run this application is to use the built in relax applications for loops, domains, subunits, and proteins within the full PyRosetta Toolkit.  See user guide for more details.
ANALYSIS==Typically, one would either cluster similar conformations or simply take the lowest energy score.  You can do this within the toolkit.
LIMITATIONS==Does a great job at minimizing the structure.  button_ be careful.
