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| attachment:ctf.png | ||<<TableOfContents>>||{{attachment:ctf.png}}|| || Table of Contents || The EMAN2 ctf icon || == CTF processing in 3 stages == |
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| == Auto fitting == | === Auto fitting === |
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| e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit | e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit |
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| == Fine tuning == | |
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| (save any changes you make with the Save Parms button) | This runs auto CTF parameter determination, storing the result in a local database. === Fine tuning === |
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| e2ctf.py 1.img --gui | e2ctf.py 1.img --gui |
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| == Write output == | Now that you have determined the parameters with the first command, have a look at the results in the interface. Tweak if necessary. Save any changes you make with the Save Parms button === Write output === |
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| The output will be in the particles directory. Also, you can supply more than one image as input to e2ctf.py. |
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| You can combine more than command would have worked if you had used a command like this: | Finally generate output. The output will be in the particles directory. |
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| e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui | == Processing multiple images simultaneously == e2ctf takes multiple images as input, so you can use commands like this: {{{ e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit e2ctf.py *.img --gui e2ctf.py *.img --phaseflip --wiener }}} == Combining stages into a single command == You can combine more than one of the e2ctf processing stages into a single command. For instance you can run automated fitting and open the GUI with a single command like this: {{{ e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui }}} |
e2ctf
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Table of Contents |
The EMAN2 ctf icon |
CTF processing in 3 stages
To get familiar with how e2ctf.py works, try separating the way you using e2ctf.py into three stages:
Auto fitting
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
This runs auto CTF parameter determination, storing the result in a local database.
Fine tuning
e2ctf.py 1.img --gui
Now that you have determined the parameters with the first command, have a look at the results in the interface. Tweak if necessary. Save any changes you make with the Save Parms button
Write output
e2ctf.py 1.img --phaseflip --wiener
Finally generate output. The output will be in the particles directory.
Processing multiple images simultaneously
e2ctf takes multiple images as input, so you can use commands like this:
e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit e2ctf.py *.img --gui e2ctf.py *.img --phaseflip --wiener
Combining stages into a single command
You can combine more than one of the e2ctf processing stages into a single command. For instance you can run automated fitting and open the GUI with a single command like this:
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui