These scripts are used for calculating the free-hand test for single particles in electron microscopy images, implementing protocols developed by Rosenthal &  Henderson, 2003, J. Mol. Biol.  

Free-hand scripts were given to the Nogales lab from John Rubinstein at University of Toronto. 

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Executable files (compiled on ubuntu) provided by John Rubinstein:
'lib/fastfreehand_v1_01.csh' - C-Sell script that calls 'fastfreehand_v1_01.exe,' to run free-hand test
'lib/totsumstack.csh' - C-Shell script that calls 'totsumstack.exe' to create average free-hand plot image
'lib/npo_CC.csh' - C-Shell script that calls CCP4 commands to create free-hand contour plot

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Higher-level scripts that wrap everything together:

Particle extraction:
'ctftilt.py' - For leginon micrographs with .box files, estimate defocus and angle with ctftilt.exe and extract particles.

Assign euler angles & run free-hand test:
'freeHand_wrapper.py' - Using EMAN2/Sparx scripts, assign euler angles and perform free-hand test
'freeHand_from_spi.py' - Using SPIDER angular & shifts files, perform free-hand test
'freeHand_from_Frealign.py' - Using FREALIGN refinement input files, perform free-hand test
'freeHand_from_EMAN2_param.py - Using EMAN2 parameter file, perform free-hand test

Calculate average free-hand plot:
'freeHand_calc_plot.py' - Generate average free-hand plot and consolidate files into an output folder 

Input parameter info:
'free_param.par' - necessary input file for 'freeHand_wrapper.py' and 'freeHand_calc_plot.py' 

Visualize per-particle angle assignment
'lib/fhplot.m' - MATLAB script to plot individual particle free-hand angles

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Information on compiling 'fastfreehand' can be found in /compile

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Information for picking tilting particles and calcualting tilt angles can be found in /extract