Introduc)on to Appion and Leginon tools Chi-yu Fu (ICOB) NRAMM/AMI - - PowerPoint PPT Presentation

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Introduc)on to Appion and Leginon tools Chi-yu Fu (ICOB) NRAMM/AMI - - PowerPoint PPT Presentation

Dec 07, 2022 102 likes •453 views

Introduc)on to Appion and Leginon tools Chi-yu Fu (ICOB) NRAMM/AMI at New York Structural Biology Center h=p://emg.nysbc.org/redmine/projects/ leginon/wiki/Leginon_Homepage h=p://emg.nysbc.org/redmine/projects/ appion/wiki/Appion_Home

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Introduc)on to Appion and Leginon tools

Chi-yu Fu (ICOB)

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h=p://emg.nysbc.org/redmine/projects/ leginon/wiki/Leginon_Homepage h=p://emg.nysbc.org/redmine/projects/ appion/wiki/Appion_Home

NRAMM/AMI at New York Structural Biology Center

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Leginon/Appion pipeline

Installed in cryoEM core Special thanks to Anchi Cheng (AMI) Shin-bo Cheng (ICOB computer center)

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Atlas collec)on

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Square targe)ng

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Hole targe)ng

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Exposure targe)ng

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Alignment of different resets

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Beam shiR and image shiR in preset alignment

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Z-focusing

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Focusing

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Coma-free alignment

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Camera gain correc)on

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Appion Image assessment

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DD frame alignment

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CTF correc)on

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CTF correc)on

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CTF correc)on

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Par)cle picking

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Assess par)cle sizes

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Par)cle picking

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Manual picking

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Clean up par)cle picks

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Stack crea)on

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Stack crea)on

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Assessment of par)cle picks

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2D classifica)on and 3D refinement

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Import par)cle stack to Frealign

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[user1@fulab frealign_recon1]$ ls files_to_remote_host initmodel0001.mrc note params.000.par prepRefineFrealign.log start.mrc thread000.log thread001.log [cyfu@pcf00243 refinement]$ ls frealign.log mparameters pdh_2_r1.mrc pdh_2_r1.par pdh_stack.mrc scratch

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[user1@fulab frealign_recon1]$ ls all_par)cles.star initmodel0001.mrc params.000.par start.mrc thread000.log files_to_remote_host note prepRefineFrealign.log start.mrcs thread001.log [user1@fulab frealign_recon1]$

Import par)cle stack to Relion

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Import par)cle coordinates to Relion

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Import CTF star file to Relion

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