Release notes for PyRy3D 4.2.0
-------------------------------

(May 2013)
Latest changes include:
- program positions all components randomly inside the density map/SAXS shape; components linked by covalent bonds are moved together
- possibility to include all complex atoms in verification of clashes (new parameter in a configuration file: CLASHES_ALLATOMS)
- radius of dummy atoms can be given as a program parameter (SAXS_RADIUS)
- new parameter added: is_complex_outmap to add additional penalties when one of components is completly outside the density map/ab initio SAXS model
- bug with simulbox shape has been repaired
- symmetry can be used as additional restraint for optimalization of models; programs tries to model structures in such a way that distances defined by the user are of the same lenght
- access restraint was added for defining of single residues or fragments of components that are exposed to solvent (they do not have to be on the surface of a density map as in access_surface restraint)
- exchange mutation has been improved in such a way that program changes positions of two particular components and then performs a series of rotations and translations in order to sample conformational space more effectively
- simulation grid is created only for a density map, not for a whole simulation box to reduce RAM usage and CPU
- clustering procedure and ranking script are now included in the program distribution



(June 2012)
Added features:
- modeling of complexes without defined shape
- possibility to optimize models with PyRy3D from predefined orientations
- possibility to define boundaries of all moves for all components
- possibility to rotate components around covalent bonds (line defined by two points)
- new mutations added: rotate_all, translate_all, rotate_cov (rotation around covalent bond)
- new scoring function element which uses density values during complex scoring
- possibility to define components linked by covalent bonds
- possibility to calculate complex volume based on its sequence and define density map threshold describing complex volume
- new updated CCP4 reader able to read even simulated maps generated automatically
- possibility to generate energy plot of generated complex models
- score complex without running simulations
- sample complex map with one component only


(July 2011)

Program features:

- Simulated annealing / replica exchange /genetic simulation module
- VolumeSimulator a module for random simulation of disordered regions
- further program speedup
- crude models of component for both proteins and nucleic acids available
- history of mutations available
- convinient ways of saving simulation results
- easier way to run program with default parameters
- new simulation paraemters enabling i.e. freezing disorder, 
- scaling parameters during simulation i.e. scoring weights, rotation angles, translation vectors, number of mutated components in a particular iteration
- possibility to define frequencies of all mutations
- possibility to turn on/of simulation parameters scaling
- improved modeling of components with defined boundaries/limitations of movements inside a density map (preoriented components)
- PyRyInputGenerator - a module for automatic creation of PyRy input files
- RankingGenerator - a module for quality assesment of set of structures
- PyRy3D Chimera Extension - a Chimera plugin for testing simulation parameters, running short simulations, run simple program options
