More updates to the superb MayaChemTools.
A new command line script named PyMOLExtractSelection.py to extract an arbitrary PyMOL selection from a macromolecule and write it out to a file.
In addition, the Psi4CalculateEnergy.py and Psi4PerformMinimization.py scripts have been updated to perform these calculations in solution using domain-decomposition-based continuum solvation models. These scripts rely on Psi4 interface to the DDX module to perform the calculations. Two solvation models are supported: COnductor-like Screening MOdel (COSMO) and Polarizable Continuum Model (PCM).
A number of enhancements have been made to the PyMOLVisualizeMacromolecules.py script including identification of arbitrary distance contacts between heavy atoms in pocket residues and docked poses, visualization of solvents and inorganics in the pocket around docked poses, and visualization of B factor values for chains.