PaStO – Parsimonious Structure Optimization:

This is a package for macromolecular structure refinement and superimposition.  It is named for the option of component programs to work with reduced parameterization, limiting overfitting when using data of limited resolution.  Modules are summarized below:

RSRef

For the “real space” fitting of atomic models into density maps derived from x-ray crystallography or electron microscopy (EM). Can be used in two modes:

  • Stand-alone, for gradient descent optimization of atomic coordinates (all-atom or rigid-group), B-factors and EM imaging parameters.
    • The latest version restrains stereochemistry using Amber forcefields through OpenMM.
    • This will be the usual mode of usage.
  • PaStO exposes python, C and FORTRAN APIs for embedding as an extension module within other packages, thereby supporting other modes of refinement (torsion angle, simulated annealing, etc.).  The interface to CNS is being deprecated and its unique features will be replaced.

In comparing an atomic model to a map, RSRef is uniquely rigorous in its accounting for experimental resolution, as described in Chapman, M. S. (1995) Acta Crystallographica A51, 69-80 (1995).  The module is a completely new implementation described in: Chapman, M. S., Trzynka, A., and Chapman, B. K. (2013) Atomic modeling of cryo-electron microscopy reconstructions – Joint refinement of model and imaging parameters, J Struct Biol 182, 10-21.

Superpose:

For the superimposition of protein structures, moving and target. There is great flexibility in both designation of corresponding atoms and parameterization as rigid or and morphing (phi/psi) regions.  It allows identification of hinges from pairs of crystal structures, as validated with NMR dynamics.  (Chapman, B.K., Davulcu, O, Skalicky, J.J., Bruschweiler, R.P. & Chapman, M.S. (2015) Parsimony in Protein Conformational Change, Structure, Structure 23: 1190-8; http://dx.doi.org/10.1016/j.str.2015.05.011)

SymExp:

For the expansion of lattice and local (non-crystallographic) symmetry in macromolecular structures.

Documentation

Download

PaStO is available under GPLv3 copyleft license (open source & no cost).  The latest version is available for alpha testing, please e-mail: chapmanms@missouri.edu.  It will soon be available from the PyPI repository (https://pypi.org/) for installation using pip.