Diff for "EMAN2/Programs/e2refinetorelion2d"

Differences between revisions 1 and 6 (spanning 5 versions)

This program is normally run via the EMAN2 Project Manager.

Helpful Links:

Tutorial is under construction

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 → 
  Size: 1575
  Editor: StephenMurray
  Comment:
+   ← Revision 6 as of 2013-01-23 17:28:44 → ⇥
  Size: 1950
  Editor: StephenMurray
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-Describe EMAN2/Programs/e2refinetorelion2d here.
+This program is normally run via the EMAN2 [[http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2projectmanager|Project Manager]].
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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 ||