Diff for "EMAN2/Programs/e2refinetorelion2d"

Differences between revisions 1 and 3 (spanning 2 versions)

This program is normally run via the EMAN2 Project Manager.

Options:

-h	--help	bool	show this help message and exit
	--version	bool	show program's version number and exit
	--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?
	--imagemaskd	float	Diameter of the image mask
	--inplaneang	float	In-plane angular sampling
	--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
	--numclasses	int	# of classes
	--numiter	int	# of iterations to refine
	--offsetrange	float	Offset search range (pix)
	--offsetstep	float	Offset search step (pix)
	--regparam	float	Regularization Parameter T (weights experimental data vs. prior
	--solventmask	string	Location of the mask to be used
	--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

--apix	float	Angstrom per pixel
--cs	float	Spherical Aberration
--defocus	float	Defocus in Angstroms
--voltage	float	Voltage of the Microscope (kV)
--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 3 as of 2013-01-03 21:50:12 → ⇥
  Size: 1646
  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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+Line 11:
+|| ||--ignoretofirstpeak ||bool ||(T/F)Ignore CTF's until the first peak? ||
|| ||--imagemaskd ||float ||Diameter of the image mask ||
|| ||--inplaneang ||float ||In-plane angular sampling ||
|| ||--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 ||
-Line 15:
+Line 16:
-|| ||--ignoretofirstpeak ||bool ||(T/F)Ignore CTF's until the first peak? ||
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-|| ||--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 ||
|| ||--inplaneang ||float ||In-plane angular sampling ||
-Line 24:
+Line 19:
+|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
|| ||--solventmask ||string ||Location of the mask to be used ||
-Line 28:
+Line 25:
+|| ||--apix ||float ||Angstrom per pixel ||
|| ||--cs ||float ||Spherical Aberration ||
|| ||--defocus ||float ||Defocus in Angstroms ||
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-|| ||--cs ||float ||Spherical Aberration ||
|| ||--apix ||float ||Angstrom per pixel ||
|| ||--defocus ||float ||Defocus in Angstroms ||