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
Program Options:
I/O |
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--numclasses |
int |
# of classes |
CTF Options |
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--ctfcorrect |
bool |
(T/F)Do CTF Correction? |
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--dataphaseflipped |
bool |
(T/F)Has the data been phase flipped already? |
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--ignoretofirstpeak |
bool |
(T/F)Ignore CTF's until the first peak? |
Optimisation Options |
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--numiter |
int |
# of iterations to refine |
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--regparam |
float |
Regularization Parameter T (weights experimental data vs. prior |
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--imagemaskd |
float |
Diameter of the image mask |
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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 |
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--solventmask |
string |
Location of the mask to be used |
Sampling Options |
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--inplaneang |
float |
In-plane angular sampling |
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--offsetrange |
float |
Offset search range (pix) |
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--offsetstep |
float |
Offset search step (pix) |
Running Options |
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--threads |
int |
# of threads |
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--verbosity |
int |
Set the level of verbosity for output |
Expert Options: used only if this information is not present in the previous EMAN2 reconstruction |
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--voltage |
float |
Voltage of the Microscope (kV) |
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--cs |
float |
Spherical Aberration |
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--apix |
float |
Angstrom per pixel |
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--defocus |
float |
Defocus in Angstroms |
Default Options |
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-h |
--help |
bool |
show this help message and exit |
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--version |
bool |
show program's version number and exit |
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--echo |
bool |
Echo the relion command to the terminal window and exit |