Differences between revisions 8 and 16 (spanning 8 versions)

This program is normally run via the EMAN2 Project Manager.

e2refinetorelion3d.py 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 could be used to extract the Relion command that could be run on a local machine.

Helpful Links:

Tutorial is under construction

RELION Webpage

Program Options:

I/O
	--randomizemodel	float	Optionally randomize the phases of the initial model to this resolution (in Angstroms)
	--symmgroup	string	Symmetry Group
	--symmnumber	string	Symmetry Number
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
	--lowpass	float	Initial low-pass filter (Ang)
	--imagemaskd	float	Diameter of the image mask
	--solventmask	string	Location of the mask to be used
Sampling Options
	--healpix	string	Angular Sampling Interval (Degrees)
	--auto_healpix	string	Local angular search value
	--offsetrange	float	Offset search range (pix)
	--offsetstep	float	Offset search step (pix)
Run Options
	--threads	int	# of threads
	--maxmemory	float	Maximum memory (in GB) available for each thread
Expert Options
	--amplitudecontrast	float	Amplitude contrast value for the micrographs
	--intensitycorrection	bool	(T/F) Do intensity correction?
	--print_symmetry	bool	Print all symmetry transformation matrices and exit?
	--nearestneighbor	bool	Perform nearest-neighbor instead of linear Fourier-space interpolation
	--oversampling	int	Oversampling Order
	--limit_tilt	int	Limited tilt angle: positive for keeping side views, negative for keeping top views
	--verbosity	int	Set the level of verbosity for output
	--onlyflipphase	bool	(T/F) Only flip phases?
Default Options
-h	--help	bool	show this help message and exit
	--version	bool	show program's version number and exit

EMAN2/Programs/e2refinetorelion3d (last edited 2013-01-23 21:17:34 by StephenMurray)

-  ⇤ ← Revision 8 as of 2013-01-22 20:06:34 → 
  Size: 2220
  Editor: StephenMurray
  Comment:
+   ← Revision 16 as of 2013-01-23 17:48:56 → ⇥
  Size: 3279
  Editor: StephenMurray
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 3:
-e2refinetorelion3d 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 could be used to extract the Relion command that could be run on a local machine.
+''e2refinetorelion3d.py'' 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 could be used to extract the Relion command that could be run on a local machine.
 Line 6:
-Helpful Links:
+= Helpful Links: =
 Line 13:
-Program Options:
I/O:
||set_name||||||||
+= Program Options: =
||||||||I/O||
|| ||--randomizemodel||float||Optionally randomize the phases of the initial model to this resolution (in Angstroms)||
|| ||--symmgroup||string||Symmetry Group||
|| ||--symmnumber||string||Symmetry Number||
||||||||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||
|| ||--lowpass||float||Initial low-pass filter (Ang)||
|| ||--imagemaskd||float ||Diameter of the image mask||
|| ||--solventmask||string ||Location of the mask to be used||
||||||||Sampling Options||
|| ||--healpix||string||Angular Sampling Interval (Degrees)||
|| ||--auto_healpix||string||Local angular search value||
|| ||--offsetrange||float||Offset search range (pix) ||
|| ||--offsetstep||float||Offset search step (pix) ||
||||||||Run Options||
|| ||--threads||int||# of threads ||
|| ||--maxmemory||float||Maximum memory (in GB) available for each thread||
||||||||Expert Options||
|| ||--amplitudecontrast||float||Amplitude contrast value for the micrographs||
|| ||--intensitycorrection||bool||(T/F) Do intensity correction?||
|| ||--print_symmetry||bool||Print all symmetry transformation matrices and exit?||
|| ||--nearestneighbor||bool||Perform nearest-neighbor instead of linear Fourier-space interpolation||
|| ||--oversampling||int||Oversampling Order||
|| ||--limit_tilt||int||Limited tilt angle: positive for keeping side views, negative for keeping top views||
|| ||--verbosity||int||Set the level of verbosity for output ||
|| ||--onlyflipphase||bool||(T/F) Only flip phases?||
||||||||Default Options||
-Line 18:
+Line 46:
-|| ||--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 ||
|| ||--offsetrange ||float ||Offset search range (pix) ||
|| ||--offsetstep ||float ||Offset search step (pix) ||
|| ||--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