External Package requirement of Appion scripts » History » Version 1
Anchi Cheng, 01/22/2018 11:07 PM
| 1 | 1 | Anchi Cheng | h1. Typical Appion workflow package requirement of Appion scripts |
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| 3 | 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. |
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| 5 | |appion script name|purpose|subfunction|external package|script/command within the package| |
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| 6 | ||general image manipulation||EMAN1|proc2d| |
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| 7 | |makeDDAlignMotionCor2_UCSF.py|movie frame alignment||MotionCor2| |
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| 8 | |makeDDAlignMotionCorr_Purdue.py|movie frame alignment||motioncorr v2.0 from Purdue| |
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| 9 | |makeDEAlignedSum.py|movie frame aligment|deProcessFrames.py|| |
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| 10 | |makeDEAlignedSum.py|movie frame aligment|EMAN2|| |
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| 11 | |ctffind4.py|ctf estimation||CTFFIND4|| |
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| 12 | |gctf.py|ctf estimation||Gctf|| |
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| 13 | |templateCorrelator.py|template-based particle selection||FindEM| |
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| 14 | |gAutomatchFast.py|template-based particle selection||Gautomatch| |
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| 15 | |makestack2.py|particle stack making|making Imagic stack|appionlib|| |
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| 16 | |makestack2.py|particle stack making|making Relion stack|Relion|relion_preprocess or relion_preprocess_mpi| |
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| 17 | |makestack2.py|particle stack making|CTF correction by Wiener filtering of the full image (Imagic stack only)|ace2|ace2correct.exe| |
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| 18 | |makestack2.py|particle stack making|normalization by edge|appionlib|| |
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| 19 | |centerParticleStack.py|particle centering in a stack||EMAN1|centeralignint| |