Ruby-Helix
(
Download v262) for ruby-gsl 1.9 and 1.8
(
Download v262p1) for ruby-gsl 1.10 and later

An implementation of helical image processing based on object-oriented scripting language Ruby.


Ruby-Helix Documentation

Very detailed documentation including installation, commands, and programming interface.

User’s Guide (1.7MB pdf)

written by Andrew Bodey when he studied mitotic kinesin motor at Carolyn Moores’ lab

This is a practical guide to use Ruby-Helix for helical reconstruction.

A sample data can be downloaded from
here

In this sample you can reconstruct following 3D structure from one image (KIF1A-microtubule complex).

Pasted Graphic 1


Installation Guide


Special thanks to:
Masahiro Tanaka, who made
NArray Ruby-Helix heavily depends on this library.

When you use Ruby-Helix or Unbend, please refer to the following publications:

References

Metlagel, Z., Y. S. Kikkawa, and M. Kikkawa
Ruby-Helix : An implementation of helical image processing based on object-oriented scripting language
J. Struc. Biol. 157:95-105, 2007

Kikkawa, M.
A new theory and algorithm for reconstructing helical structures with a seam.
Journal of Molecular Biology, 343:943-955, 2004


List of publications in which Ruby-Helix was used:

Oda T. and M. Kikkawa
Novel Structural Labeling Method using Cryo-electron Tomography and Biotin-Streptavidin System
Journal of Structural Biology, 183:305-11, 2013

Oda T., T. Yagi, H. Yanagisawa, and M. Kikkawa
Identification of the Outer-Inner Dynein Linker as a Hub Controller for Axonemal Dynein Activities
Current Biology, 23:656-64, 2013

Bebeacua C, Lai L, Vegge CS, Brøndsted L, van Heel M, Veesler D, Cambillau C.
Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1
J. of Virology, 87:1061-1068, 2013

Peters C, Brejc K, Belmont L, Bodey AJ, Lee Y, Yu M, Guo J, Sakowicz R, Hartman J, Moores CA.
Insight into the molecular mechanism of the multitasking kinesin-8 motor.
EMBO J. 2010 Oct 20;29(20):3437-47

Kikkawa M, Hirokawa N.
High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations.
EMBO J. 2006 Sep 20;25(18):4187-94.

Mizuno N, Narita A, Kon T, Sutoh K, Kikkawa M.
Three-dimensional structure of cytoplasmic dynein bound to microtubules.
Proc Natl Acad Sci U S A. 2007 Dec 26;104(52):20832-7. Epub 2007 Dec 19.

Oda T, Hirokawa N, Kikkawa M.
Three-dimensional structures of the flagellar dynein-microtubule complex by cryoelectron microscopy.
J Cell Biol. 2007 Apr 23;177(2):243-52. Epub 2007 Apr 16.

Bodey AJ, Kikkawa M, Moores CA.
9-Angström structure of a microtubule-bound mitotic motor.
J Mol Biol. 2009 May 1;388(2):218-24

Peters C, Brejc K, Belmont L, Bodey AJ, Lee Y, Yu M, Guo J, Sakowicz R, Hartman J, Moores CA.
Insight into the molecular mechanism of the multitasking kinesin-8 motor.
EMBO J. 2010 Oct 20;29(20):3437-47