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Anchi Cheng, 01/22/2018 11:07 PM
Typical Appion workflow package requirement of Appion scripts¶
Appion python scripts are often wrappers that calls scripts or command from other packages. List here are what is needed by each typically used options.
| appion script name | purpose | subfunction | external package | script/command within the package |
| general image manipulation | EMAN1 | proc2d | ||
| makeDDAlignMotionCor2_UCSF.py | movie frame alignment | MotionCor2 | ||
| makeDDAlignMotionCorr_Purdue.py | movie frame alignment | motioncorr v2.0 from Purdue | ||
| makeDEAlignedSum.py | movie frame aligment | deProcessFrames.py | ||
| makeDEAlignedSum.py | movie frame aligment | EMAN2 | ||
| ctffind4.py | ctf estimation | CTFFIND4 | ||
| gctf.py | ctf estimation | Gctf | ||
| templateCorrelator.py | template-based particle selection | FindEM | ||
| gAutomatchFast.py | template-based particle selection | Gautomatch | ||
| makestack2.py | particle stack making | making Imagic stack | appionlib | |
| makestack2.py | particle stack making | making Relion stack | Relion | relion_preprocess or relion_preprocess_mpi |
| makestack2.py | particle stack making | CTF correction by Wiener filtering of the full image (Imagic stack only) | ace2 | ace2correct.exe |
| makestack2.py | particle stack making | normalization by edge | appionlib | |
| centerParticleStack.py | particle centering in a stack | EMAN1 | centeralignint |
Updated by Anchi Cheng almost 7 years ago · 1 revisions