Integrate CtfFind5 and add sample thickness parameter

[Poko18]

Hi,

In this pull request, I've incorporated support for CtfFind5 to enhance our local workflow. If this addition could benefit others, please consider merging it.

Related issues

• https://github.com/3dem/relion/issues/1088

Description

• this adds support for CtfFind5 executable with relion (relion_run_ctffind)
• it adds new parameters:
  • is_ctffind5
  • do_determine_thickness
  • do_determine_tilt
  • no_brute_force1d
  • no_refine2d
  • node_lowres_limit
  • node_highres_limit
  • node_rounded_square
  • node_downweight
• saves rlnSampleThickness from CtfFind5 to starfile

Missing

• [x] MPI support

[chewyalvin]

Dear @Poko18 how do i merge your branch to my local workstation? i am really keen to try ctffind5 out in relion ver5

[Poko18]

@chewyalvin You could install relion from my fork. Beware that CtfFind5 is not integrated in GUI, but you can use it from command line

[chewyalvin]

@chewyalvin You could install relion from my fork. Beware that CtfFind5 is not integrated in GUI, but you can use it from command line

Thanks for your quick reply. Apologies I'm a novice at this, I meant to ask for the installation instructions. How do I specify your fork in the git pull request I tried to copy from your git via git fetch https://github.com/Poko18/relion.git ctffind5 Managed to pull but did not successfully see the 4 edited files being downloaded. Did try "git checkout -b ctffind5" and see ctffind5 upon "git branch -a" but hit a wall as well