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bjh_dissertation

cablam_data

Contour data for CaBLAM validation in cctbx and MolProbity

disulfide_research

Tools, scripts, and results for research on disulfide bond geometry

identify_dna_decoys

Code to identify potential purid decoys id DNA, i.e. purines that need to flip from syn to anti or viser versa.

javadev

Java programs (including KiNG) for protein visualization and analysis

kincontours

Tools for creating 2D or 3D kinemage visualizations from contour tables

lab_scripts

Repository for Q&D lab scripting projects; primarily a repository of scripts not history

mage

3d molecular visualization tool

magekinjas

javascript viewer for kinemage files, to replace java-based KiNG for web apps

molprobity

Protein and nucleic acid validation service

mon_lib

pdb_mongodb

This is a repository for a python program that does individual runs on deposited pdbs.

phenix_king_binaries

This hosts static binaries of KiNG for PHENIX. KiNG code is in the javadev repository.

prekin

Prepare molecular kinemages from protein PDB files

probe

Evaluate and visualize protein interatomic packing

probe_analysis

Tools for analysis and interpretation of Probe output

protocol-captures

Archive of lab protocols

quantitate_density_fit

This tool quantifies density fit.

reduce

Reduce - tool for adding and correcting hydrogens in PDB files

reference_data

This repository contains reference data from the Richardson Lab at Duke.

rna11

RNA11 dataset PDBs and related files

rna_precis

Scripts for RNA parameterization. To be folded into cctbx_project when complete.

rotarama_data

Contour data for Ramachandran and rotamer validation in cctbx and MolProbity

suitename

Categorize each suite in an RNA backbone as belonging to either one of 53 defined types or as outlier