Differences between revisions 12 and 27 (spanning 15 versions)
Revision 12 as of 2009-03-02 20:58:16
Size: 1099
Comment:
Revision 27 as of 2009-11-02 16:44:58
Size: 1387
Editor: gtang
Comment:
Deletions are marked like this. Additions are marked like this.
Line 2: Line 2:
||<<TableOfContents>> || {{attachment:ctf.png}} ||
Line 3: Line 4:
{{attachment:ctf.png}}
Line 5: Line 5:
<<TableOfContents>>
Line 7: Line 6:

To get familiar with how e2ctf.py works, try separating the way you using e2ctf.py into three stages:
To get familiar with how e2ctf.py works, try separating the way you use e2ctf.py into three stages:
Line 11: Line 9:
{{{
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --autofit
}}}
This runs auto CTF parameter determination, storing the result in a local database.
Line 12: Line 14:
=== Fine tuning ===
Line 13: Line 16:
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit e2ctf.py 1.img --gui
Line 15: Line 18:
=== Fine tuning ===

(save any changes you make with the Save Parms button)
{{{
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
Line 23: Line 21:
Line 27: Line 24:
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.
Line 31: Line 27:
Line 35: Line 30:
e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
e2ctf.py *.img --gui
Line 37: Line 34:
Line 39: Line 35:

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:
Line 43: Line 38:
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

e2ctf

ctf.png

CTF processing in 3 stages

To get familiar with how e2ctf.py works, try separating the way you use e2ctf.py into three stages:

Auto fitting

e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --autofit

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

EMAN2/Programs/e2ctf (last edited 2010-06-17 19:16:50 by SteveLudtke)