Differences between revisions 1 and 11 (spanning 10 versions)

e2refinetorelion2d

Information

This program is normally run via the EMAN2 Project Manager.

e2refinetorelion2d.py is typically run after particles have been boxed and particle sets have been created. It can be used as another way to generate class averages in a reference-free manner. When it is run, it will launch Relion to generate class averages with the specified number of classes.

Helpful Links:

Tutorial is under construction

RELION Webpage

Program Options:

I/O
	--numclasses	int	# of classes
CTF Options
	--ctfcorrect	bool	(T/F)Do CTF Correction?
	--dataphaseflipped	bool	(T/F)Has the data been phase flipped already?
	--ignoretofirstpeak	bool	(T/F)Ignore CTF's until the first peak?
Optimisation Options
	--numiter	int	# of iterations to refine
	--regparam	float	Regularization Parameter T (weights experimental data vs. prior
	--imagemaskd	float	Diameter of the image mask
	--maskzeroes	bool	(T/F) For individual particles, the area outside a circle with the radius of the particle will be set to zeros prior to taking the Fourier transform
	--solventmask	string	Location of the mask to be used
Sampling Options
	--inplaneang	float	In-plane angular sampling
	--offsetrange	float	Offset search range (pix)
	--offsetstep	float	Offset search step (pix)
Running Options
	--threads	int	# of threads
	--verbosity	int	Set the level of verbosity for output
Expert Options: used only if this information is not present in the previous EMAN2 reconstruction
	--voltage	float	Voltage of the Microscope (kV)
	--cs	float	Spherical Aberration
	--apix	float	Angstrom per pixel
	--defocus	float	Defocus in Angstroms
Default Options
-h	--help	bool	show this help message and exit
	--version	bool	show program's version number and exit
	--echo	bool	Echo the relion command to the terminal window and exit

EMAN2/Programs/e2refinetorelion2d (last edited 2013-01-23 21:17:53 by StephenMurray)

-  ⇤ ← Revision 1 as of 2013-01-03 21:16:31 → 
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+   ← Revision 11 as of 2013-01-23 21:17:53 → ⇥
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-Describe EMAN2/Programs/e2refinetorelion2d here.
+= e2refinetorelion2d =
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+=== Information ===
This program is normally run via the EMAN2 [[EMAN2/Programs/e2projectmanager|Project Manager]].

''e2refinetorelion2d.py'' is typically run after particles have been boxed and particle sets have been created. It can be used as another way to generate class averages in a reference-free manner. When it is run, it will launch Relion to generate class averages with the specified number of classes.
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+----
=== Helpful Links: ===
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+Tutorial is under construction
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+[[http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page|RELION Webpage]]
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-Options:
||-h ||--help ||bool ||show this help message and exit ||
|| ||--version ||bool ||show program's version number and exit ||
+----
=== Program Options: ===
||||||||I/O||
|| ||--numclasses ||int ||# of classes ||
||||||||CTF Options||
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-|| ||--numclasses ||int ||# of classes ||
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+||||||||Optimisation Options||
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+||||||||Sampling Options||
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+||||||||Running Options||
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-Expert Options: (used only if this information is not present in the previous EMAN2 reconstruction
+||||||||Expert Options: used only if this information is not present in the previous EMAN2 reconstruction||
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+||||||||Default Options||
||-h ||--help ||bool ||show this help message and exit ||
|| ||--version ||bool ||show program's version number and exit ||