Differences between revisions 4 and 11 (spanning 7 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 4 as of 2013-01-03 21:52:03 → 
  Size: 1668
  Editor: StephenMurray
  Comment:
+   ← Revision 11 as of 2013-01-23 21:17:53 → ⇥
  Size: 2290
  Editor: StephenMurray
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-UNDER CONSTRUCTION

This program is normally run via the EMAN2 [[http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2projectmanager|Project Manager]].
+= e2refinetorelion2d =
-Line 6:
+Line 4:
+=== 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.
-Line 8:
+Line 10:
-Options:
||-h ||--help ||bool ||show this help message and exit ||
|| ||--version ||bool ||show program's version number and exit ||
+----
=== Helpful Links: ===

Tutorial is under construction

[[http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page|RELION Webpage]]

----
=== Program Options: ===
||||||||I/O||
|| ||--numclasses ||int ||# of classes ||
||||||||CTF Options||
-Line 14:
+Line 25:
+||||||||Optimisation Options||
|| ||--numiter ||int ||# of iterations to refine ||
|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
-Line 15:
+Line 29:
+|| ||--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 33:
-|| ||--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 35:
-|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
|| ||--solventmask ||string ||Location of the mask to be used ||
+||||||||Running Options||
-Line 25:
+Line 38:
-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||
|| ||--voltage ||float ||Voltage of the Microscope (kV) ||
|| ||--cs ||float ||Spherical Aberration ||
-Line 28:
+Line 42:
-|| ||--cs ||float ||Spherical Aberration ||
-Line 30:
+Line 43:
-|| ||--voltage ||float ||Voltage of the Microscope (kV) ||
+||||||||Default Options||
||-h ||--help ||bool ||show this help message and exit ||
|| ||--version ||bool ||show program's version number and exit ||