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Image Processing Software for Helical Crystals

This software also originated at the Laboratory of Molecular Biology in Cambridge, UK, but has been substantially modified and adapted by several groups:  e.g., Chikashi Toyoshima, Nigel Unwin, and David DeRosier.

Chikashi Toyoshima's programs explicitly determine the repeat distance for the helix and interpolate the image to ensure that layer lines fall exactly on integer pixels.  Also, they have developed methods for alignment of maps in real space either for averaging or for calculation of difference maps.  These programs are based on the original MRC programs, but have been rewritten in C.

Outline of Toyoshima's standard programs
Graphical flow-chart of the process (PostScript)
Toyoshima's detailed description of his programs
Outline of steps for aligning maps and calculating a difference map
Outline of steps for aligning and averaging maps in real space
Software developed by Nigel Unwin are based on Toyoshima's programs, but have been translated back into Fortran.  In addition, Rameen Bekouim developed a series of scripts to detect and compensate for distortions in the tubes.  This "unbending" substantially improves the S/N ratio along the layer lines.
Outline of Nigel's programs
Rameen's detailed description of the programs and scripts and their parameters

More recently, scripts have been developed in our laboratory for more automated processing using Unwin's strategy. Also, methods for averaging little g's have been implemented, for cases where very many helical symmetries are obtained. In particular, little g averaging was implemented by Bill Rice for use on Na,K-ATPase tubes, which have p1 symmetry.

Outline of steps used for processing tubes with p1 symmetry.
Correction of ctf for p1 tubes using little g averaging.
Image Processing Software for 2D or thin 3D Crystals

This software originated in the 1960's from the Laboratory of Molecular Biology
in Cambridge, UK. If you are interested in obtaining the latest version of this software,
I would recommend you contact Judy Smith or Richard Henderson. This software relies on file handling routines and Fourier syntheses written for x-ray crystallography and this software can be obtained from the CCP4 project in Daresbury, UK (try ccp4@ccp4.dl.ac.uk).

Documentation for our implementation of this software

MRC Package documentation
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