motioncor	Align image movie stack using motioncor2

 


USAGE:	motioncor

	.Input mrc stack: stackmrc/corstack000.mrc
	[Enter the name of the non-aligned image stack. This should be the
	 gain and darkimage corrected stack with bad pixels removed. The 
	 program was implemented to process the data from the FSU cryo-EM
	 consortium. Their setup requires separate handling of the 
	 normalization files, at least for the DE64 camera.]
	
	.Output aligned image (real): outaligned0001.mrc
	[Name of image created from the aligned stack.]
         
	 If requested, output stack will be named 
_Stk.mrc: 
	.Create aligned stack (Y/N): y
	[If you answer Y also the aligned stack will be saved. This may allow
	 you to test which frames to take out to reduce blurring.]

	.Output list file containing shifts: motioncorshiftfile0001
	[This file will create a file with the list of image shifts. It is the
	 log-file defined in motioncor.Unfortunately the moticor program 
	 modifies this ile name and the real file name afterwards will be 
	 0-FULL.log.
	 You may want to rename this to something usable. This file, can be read
	 in emira using the readlist command.]
	
	.Maximum iterations (def:5): 7
	[Enter the maximum interations desired.]

	.Maximum tolerance (def:0.5 pixels): 0.5
	[Specify tolerable fitting error.]

	.Initial, Last frames to remove (def 0,0): 0,0
	[Specify the frames you like to leave out at either or both ends of the
	image stack.]
	
NOTES:	If you need more optioins, please edit em_motioncor.py
	
	THIS PROGRAM REQUIRES MOTIONCOR TO BE INSTALLED,WHICH IS NOT PART OF THE
 	EMIRA DISTRIBUTION. MOTIONCOR IS NOT OPEN SOURCE (unfortunately).

	To run this module you need to install a version of motioncor, enter 
	the directory into the path of EMIRA (edit the file emira),For eample 
	enter: export PATH=$PATH:/mnt/tools/production/motioncor  
	In the directory of motioncor, link the version of motioncor you 
	are using to motioncor (ln -s  motioncor).	

	UCSF MotionCor2 is licensed for noncommercial use at no cost by the 
	Regents of the University of California.
	See also:
	Xueming Li, Paul Mooney, Shawn Zheng, Chris Booth, Michael B. Braunfeld,
	Sander Gubbens, David A. Agard and Yifan Cheng (2013) Electron counting
	and beam-induced motion correction enables near atomic resolution 
	single particle cryoEM. Nature Methods, 10, 584-590.