Differences between revisions 12 and 22 (spanning 10 versions)

e2ctf

Contents e2ctf CTF processing in 3 stages Auto fitting Fine tuning Write output Processing multiple images simultaneously Combining stages into a single command
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

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|| Table of Contents || The EMAN2 ctf icon ||
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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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+This runs auto CTF parameter determination, storing the result in a local database.
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-(save any changes you make with the Save Parms button)
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-e2ctf.py  1.img --gui
+e2ctf.py 1.img --gui
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+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
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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.
+Finally generate output. The output will be in the particles directory.
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+e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
e2ctf.py *.img --gui
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-You can combine more than one of the e2ctf processing stages into a single command. For instance you can run automated fitting and force the opening of the GUI in a with a single command like this:
+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:
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-e2ctf.py  1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui
+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