add 3D ctf correction by IMOD

[azazellochg]

suggested by @rdrighetto

[rdrighetto]

Here is a quick how-to generate 3D CTF reconstructions with IMOD. It essentially assumes that all files needed for 2D CTF correction are already present.

First, the following files need to be available to start with:

• the aligned tilt series (.ali stack): run subm newst.com if needed
• the ctfcorrection.com file, which in turn expects the .defocus file to be available
• the usual tilt.com file

Now run the following commands:

# Go into IMOD reconstruction directory:
cd /my/etomo/directory/
 
# Generate all necessary .com files for slabs with thickness of 12 nm:
ctf3dsetup -thick 12 -parallel tilt
 
# Now run 6 parallel jobs on 1 GPU:
processchunks -G localhost:1:1:1:1:1:1 ctf3d
 
# Finally we need to rotate the reconstruction to be in the conventional orientation:
clip rotx tomo_3dctf_full.rec tomo_3dctf.rec
 
# And cleanup the mess
rm *.rec~ *.ali~

For more detail please consult the official Tomography guide from IMOD.

[Vilax]

I agree with this idea. the CTF3D would be a useful protocol

[rdrighetto]

If I may add: support for odd/even stacks in this protocol would be amazing!