External Package requirement of Appion scripts » History » Version 10
Anchi Cheng, 01/23/2018 10:28 AM
| 1 | 1 | Anchi Cheng | h1. Typical Appion workflow package requirement of Appion scripts |
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| 3 | 2 | Anchi Cheng | 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. Note that users may not want to use all functions as programs go out of fashion. |
| 4 | 1 | Anchi Cheng | |
| 5 | 2 | Anchi Cheng | h2. Direct Detector Frame Alignment |
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| 7 | 5 | Anchi Cheng | |appion script name|external package|script/command within the package| |
| 8 | 4 | Anchi Cheng | |makeDDAlignMotionCor2_UCSF.py|MotionCor2|| |
| 9 | |makeDDAlignMotionCorr_Purdue.py|motioncorr v2.0 from Purdue|| |
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| 10 | |makeDEAlignedSum.py|deProcessFrames.py|| |
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| 11 | |makeDEAlignedSum.py|EMAN2|| |
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| 12 | 2 | Anchi Cheng | |
| 13 | h2. Automated CTF Estimation |
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| 15 | |appion script name|external package| |
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| 16 | 3 | Anchi Cheng | |ctffind4.py|CTFFIND4| |
| 17 | 2 | Anchi Cheng | |gctf.py|Gctf| |
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| 19 | h2. Particle Selection |
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| 21 | |templateCorrelator.py|template-based particle selection|FindEM| |
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| 22 | |gAutomatchFast.py|template-based particle selection|Gautomatch| |
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| 24 | h2. Particle Stack Making and manipulation |
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| 26 | 8 | Anchi Cheng | |appion script name|subfunction|package|script/command within the package| |
| 27 | 6 | Anchi Cheng | ||general image manipulation|EMAN1|proc2d| |
| 28 | 2 | Anchi Cheng | |makestack2.py|making Imagic stack|appionlib|| |
| 29 | |makestack2.py|making Relion stack|Relion|relion_preprocess or relion_preprocess_mpi| |
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| 30 | |makestack2.py|CTF correction by Wiener filtering of the full image (Imagic stack only)|ace2|ace2correct.exe| |
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| 31 | |makestack2.py|normalization by edge|appionlib|| |
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| 32 | |makestack2.py/quickstack.py|making montage of stack mean/standard deviation map|ImageMagick|montage| |
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| 33 | |centerParticleStack.py|particle centering in a stack|EMAN1|centeralignint| |
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| 34 | 9 | Anchi Cheng | |boxMaskStack.py|soft masking of helical boxed particles in the stack|Spider|| |
| 35 | 10 | Anchi Cheng | |sortJunkStack.py|sort particle by similarity to average|Xmipp2|xmipp_sort_by_statistics| |