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Dept. Biochemistry & Molecular Biology
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Software


RSRef

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

  • Stand-alone program for unrestrained real-space rigid-group and/or restrained B-factor refinement and for optimization of EM imaging parameters vs. an atomic model, all by least-squares gradient-descent.
  • Extension module for other optimizers (eg. CNS) enabling stereochemically-restrained real-space refinement by gradient descent or simulated annealing using Cartesian or torsion angle coordinate systems.

This 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.
This is an extension of an approach first described in Chapman, M. S. (1995) Acta Crystallographica A51, 69-80 (1995).

RSRef is documented and distributed as part of the PaStO package, see below.


Superpose:

For the superimposition of protein structures, moving and target. The pairing of atoms is through user-specified combinations of order and type. The moving molecule can be treated as one or more rigid groups, and/or flexibly with variable backbone dihedral angles throughout or in selected regions, optionally adding a parsimony restraint for minimalist changes. This allows the characterization of hinge regions from pairs of crystal structures, the method having been cross-checked against NMR measures of dynamics.

The approach is described in Chapman, B.K., Davulcu, O, Skalicky, J.J., Bruschweiler, R.P. & Chapman, M.S. (2015) Parsimony in Protein Conformational Change, Structure, in press; http://dx.doi.org/10.1016/j.str.2015.05.011

Superpose is documented and distributed as part of the PaStO package, see below.


PaStO - Parsimonious Structure Optimization:

This is a package of programs that share a need for optimization of protein structures using models with optionally reduced parameterization to minimize overfitting, particularly when working with data of limited resolution.

Documentation

  • Installation / new user README.txt.
  • On-line documentation.
  • Documentation is also distributed with the package (as web pages or a single pdf) for local access.

Download (version: 0.5.6; August 2016)

Licensing (free for academic use) can be initiated at http://www.ohsu.edu/tech-transfer/portal/technology.php?technology_id=1004881. Upon receipt, instructions will be provided for accessing the distribution. RSRef is coded in Python and is compatible with diverse platforms.

Right click and save target: Encrypted tar distribution; (Instructions for decryption, when you have the password.)

PaStO will soon also be available through SBGrid.


DeIce:

Pre-processor for the subtraction of ice rings from diffraction images (Chapman, M. S. & Somasundaram (2010), T. De-icing: recovery of diffraction intensities in the presence of ice rings. Acta Crystallogr D Biol Crystallogr 66, 741-744,
http://dx.doi.org/10.1107/S0907444910012436.).  A self-documenting Python script can be saved (deice.py), together with example control input (run), input data (AKAp_1_001.img) and output (di_AKAp_1_001.img)
.  Deice.py is currently configured for ADSC Quantum 4 & like detectors, but is extendable to others.  For full documentation use "pydoc deice" and "deice.py -h".  Imports modules from NumPy.


At http://www.sb.fsu.edu/~rsref

The following programs are no longer actively supported, but continue to be available as-is from Chapman's former institution, Florida State University.

RoadMap:

A program to display the surface of a macromolecule, and its properties. (UNIX).

ssNMR:

Module for refinement of macromolecular structures using orientational data from solid-state NMR. (UNIX).

Hbond2002:

Module for including an angle-dependent hydrogen bond restraint in crystallographic refinement of macromolecules. (UNIX and Linux).

PBrestraint:

Module for including an electrostatic Poisson-Boltzmann restraint in crystallographic refinement of macromolecules. (Linux).

Rfree2005:

Module for calculating less bias R-free by excluding neighboring reflections of test set reflections based on G-function. (Linux).

Last updated: 06/09/15