Main Program
The current version of HullRad for Python (Version 10.1) is available here
The HullRad python script requires either, that your python has numpy and scipy, or the prior installation of qconvex, a program in the qhull suite of programs that implements the Quickhull algorithm for computing the convex hull.
If you have numpy and scipy, you do NOT have to install qconvex from the qhull suite. Further instructions are in the header of the code.
If you are not familiar with using a command line in a terminal window, but would like to run HullRad on your own computer, there are instructions for installing and using a special Python for use with HullRad. Choose one of the links below depending on the type of computer you will be using.
Displaying Convex Hulls
A PyMOL script (Python 2.7) to draw convex hull around a displayed structure is available here
A PyMOL script (Python 3.7) to draw convex hull around a displayed structure is available here
This PyMOL script was adapted from from PyDeT for visualizing a Delaunay triangulation of a protein.
It requires either, that your python has numpy and scipy, or the prior installation of qconvex, a program in the qhull suite of programs that implements the Quickhull algorithm for computing the convex hull. If HullRad works on you machine, this script will work.
Instructions for use are in the header of the code.
Copy the script of your choice to a directory containing a collection of PDB (or mmCIF) files.
Instructions for use are in the header of the script.
Release Notes
Version 5 (The program as described in Fleming and Fleming, BJ, 2018)
Proteins
Nucleic Acids
Version 6 (November, 2019)
Includes many saccharides for glycosylation
Rg is calculated from all atom model, not reduced model as in version 5
Includes option to use numpy and scipy
Asphericity is calculated from gyration tensor (requires numpy)
Option to use either qconvex from qhull or ConvexHull from scipy
(Many thanks to Chad Brautigam for implementation)
Version 7 (July, 2020)
Ported to Python 3 (Python 2 edition of version 7 also available)
Addition of chain ID
Includes several detergents for analysis of protein/detergent micelles.
(Note that hydrodynamic calculations of detergents
is sensitive to partial specific volume of the detergent micelle.
Literature values of detergent partial specific volumes are not consistent.
Solution conditions may also affect partial specific volumes - read the notes in the
code and use with caution.)
Calculation of intrinsic viscosity was removed.
The original implementation was appropriate only for very sperical particles.
This parameter is sensitive to the model used for axial ratio determination and needs further development.
Version 8 (November, 2021)
Accepts mmCIF file format as well as PDB format
Additional error checking for missing backbone atoms
Version 8.1 (March, 2022)
Fixed bugs introduced with mmCIF reader
Version 9 (October, 2022)
Addition of Intrinsic Viscosity
Addition of Non-idealtiy Constant
Version 10 (July, 2024)
Update Non-idealtiy Constant equation for ks (See DOI:https://doi.org/10.1016/j.bpj.2024.05.019)
Note that the sedimentation non-ideality constant (ks) is now calculated using a modified version of the Rowe equation and gives a different (corrected) value compared to HullRad Version 9
Add kd and second virial coeficient
Version 10.1 (Oct, 2024)
Update nucleic acid partial specific volumes.
Many thanks to Brad Chaires and Rob Monsen for pointing out that experimentally the partial specific volumes of all nucleic acids is approximately 0.55.
This is different from that calculated from structure using Voronoi volumes, which HullRad previously used.
Curiously, for proteins the experimentally determined partial specific volumes agree pretty well with those calculated from strucucture using Voronoi volumes. Why this doesn't work for nucleic acids is a mystery.