Differences between revisions 13 and 21 (spanning 8 versions)

e2ctf

Contents

e2ctf

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

-  ⇤ ← Revision 13 as of 2009-03-02 20:59:06 → 
  Size: 1267
  Editor: DavidWoolford
  Comment:
+   ← Revision 21 as of 2009-03-02 21:29:55 → ⇥
  Size: 1409
  Editor: DavidWoolford
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-{{attachment:ctf.png}}
-Line 3:
+Line 2:
-<<TableOfContents>>
-Line 5:
+Line 3:
----- /!\ '''Edit conflict - other version:''' ----
<<TableOfContents>>
+||<<TableOfContents>>||{{attachment:ctf.png}}||
-Line 8:
+Line 5:
----- /!\ '''Edit conflict - your version:''' ----

---- /!\ '''End of edit conflict''' ----
-Line 18:
+Line 12:
-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
-Line 20:
+Line 14:
+This runs auto CTF parameter determination, storing the result in a local database.
-Line 22:
+Line 19:
-(save any changes you make with the Save Parms button)
-Line 24:
+Line 21:
-e2ctf.py  1.img --gui
+e2ctf.py 1.img --gui
-Line 26:
+Line 23:
+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 32:
+Line 31:
-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 40:
+Line 39:
+e2ctf.py *.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
e2ctf.py *.img --gui
-Line 45:
+Line 46:
-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 48:
+Line 49:
-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