Differences between revisions 2 and 25 (spanning 23 versions)

e2ctf.py

Contents

e2ctf.py

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 --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 2 as of 2009-03-02 17:55:21 → 
  Size: 638
  Editor: DavidWoolford
  Comment:
+   ← Revision 25 as of 2009-07-24 00:46:10 → ⇥
  Size: 1408
  Editor: 10
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-= e2ctf =
+= e2ctf.py =
 Line 3:
-To get familiar with how  e2ctf.py works, try separating the way you using e2ctf.py into three stages:
+||<<TableOfContents>>||{{attachment:ctf.png}}||
== CTF processing in 3 stages ==
-Line 5:
+Line 6:
-== Auto fitting == 
e2ctf.py  1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
+To get familiar with how  e2ctf.py works, try separating the way you use e2ctf.py into three stages:
 Line 8:
-== Fine tuning ==
+=== Auto fitting ===
 Line 10:
-(save any changes you make with the Save Parms button)
e2ctf.py  1.img --gui
+{{{
e2ctf.py 1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit
}}}
-Line 13:
+Line 14:
-== Write output ==
+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 ===

{{{
-Line 15:
+Line 29:
+}}}
-Line 16:
+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 19:
+Line 33:
-You can combine more than command would have worked if you had used a command like this:
+== Processing multiple images simultaneously ==
-Line 21:
+Line 35:
-e2ctf.py  1.img --voltage=200 --apix=2 --cs=3.2 --auto_fit --gui
+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
}}}