Differences between revisions 2 and 11 (spanning 9 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 2 as of 2013-01-03 21:49:06 → 
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+   ← 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.
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-This program is normally run via the EMAN2 [[http://blake.bcm.edu/emanwiki/EMAN2/Programs/e2projectmanager|Project Manager]].

e2refinetorelion is run after an EMAN2 refinement has been completed. When it is run, it will take the input particle set and convert it to many normalized .mrcs files, each of which represents a single micrograph with all particles from that micrograph in it, stacked along the z-axis. It creates the "all_images.star" file which contains all of the information about the particles on a per-particle basis (CS, Defocus, Microscope Voltage, etc). It will take the input EMAN2 3D map and convert it to a Relion-style formatted map called 3DRefMap.mrc. One final thing this program does is created a directory, run01, that contains an submission script for submitting an MPI Relion job (on our clusters specifically. It will likely need to be modified to specfically address the computing environment you have). Because of the nature of Relion and of Cryo-EM itself, it is unwise to attempt to do these reconstructions on a local machine. Distributed computing works very well in these situations though the submission script can be used to extract the Relion command one could run on their local machine.
+= e2refinetorelion2d =
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+=== Information ===
This program is normally run via the EMAN2 [[EMAN2/Programs/e2projectmanager|Project Manager]].
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-Options:
||-h ||--help ||bool ||show this help message and exit ||
|| ||--version ||bool ||show program's version number and exit ||
+''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

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

----
=== Program Options: ===
||||||||I/O||
|| ||--numclasses ||int ||# of classes ||
||||||||CTF Options||
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+||||||||Optimisation Options||
|| ||--numiter ||int ||# of iterations to refine ||
|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
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+|| ||--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||
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-|| ||--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 ||
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-|| ||--regparam ||float ||Regularization Parameter T (weights experimental data vs. prior ||
|| ||--solventmask ||string ||Location of the mask to be used ||
+||||||||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||
|| ||--voltage ||float ||Voltage of the Microscope (kV) ||
|| ||--cs ||float ||Spherical Aberration ||
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-|| ||--cs ||float ||Spherical Aberration ||
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-|| ||--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 ||