Diff for "EMAN2/Programs/e2refinetorelion2d"

Differences between revisions 4 and 5

UNDER CONSTRUCTION

This program is normally run via the EMAN2 Project Manager.

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 4 as of 2013-01-03 21:52:03 → 
  Size: 1668
  Editor: StephenMurray
  Comment:
+   ← Revision 5 as of 2013-01-23 17:24:35 → ⇥
  Size: 1841
  Editor: StephenMurray
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 8:
-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||
-Line 14:
+Line 15:
+||||||||Optimisation Options||
|| ||--numiter ||int ||# of iterations to refine ||
|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
-Line 15:
+Line 19:
+|| ||--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||
-Line 16:
+Line 23:
-|| ||--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 ||
-Line 21:
+Line 25:
-|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
|| ||--solventmask ||string ||Location of the mask to be used ||
+||||||||Running Options||
-Line 25:
+Line 28:
+||||||||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 ||
-Line 26:
+Line 38:
-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 ||