Release notes for PyRy3D 4.6.0
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(April 2014)
Lates changes include:
- possibility to verify discrepancy between experimental and theoretical SAXS/SANS curve calculated from the model. Calculations include chi2 and RGE values and are performed with CRYSOL tool from ATSAS package. Remember to obtain CRYSOL code and licence from program's authors.
- new representation type added: sphere. Here components are described by centre of mass and radius only. Program apart from available scoring function elements, calculates clashes between spheres and violation of distances between cetres of mass

(March 2014)
Latest changes include:
- program takes much less RAM when modeling without a density map
- scaling of angles and translation vectors is tuned up
- new mutations appear: rotate_whole, exchange_and_sample
- max_pool_size parameter can be set up in configuration file
- identify_disorder parameter added; it allows to speed up a program by omitting disorder detection (which requires calculation of sequence alignments for all components)
- program can work with residue modifications now
- clustering can be now done based on RMSD values for centres of mass only (to speed up analysis and avoid problems with high RMSDs for rotated components)

(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 optimization 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
