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pipeline:meridien:sp_higher_ord_abber [2021/03/16 10:44] aali created |
pipeline:meridien:sp_higher_ord_abber [2021/03/22 16:40] aali |
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~~NOTOC~~ | ~~NOTOC~~ | ||
- | ===== sp_polishing | + | ===== sp_higher_ord_abber |
- | Bayesian | + | CTF Refinement |
===== Usage ===== | ===== Usage ===== | ||
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===== Typical usage ===== | ===== Typical usage ===== | ||
- | sp_polishing | + | sp_higher_ord_abber |
- | The purpose of sp_polishing.py is to : | + | The purpose of sp_higher_ord_abber.py is to : |
< | < | ||
- | : Apply Relion Bayesian Polishing using the stack generated from Meridien. | + | : Apply CTF refinement to estimation different parameters such beam tilt, phase shift, magnification etc. |
- | : The SPHIRE module provides a wrapper around the polishing | + | : The SPHIRE module provides a wrapper around the ctf refinement |
- | motion estimation | + | |
- | : After running the polishing | + | : After running the ctf refinement |
- | | + | |
</ | </ | ||
===== Input ===== | ===== Input ===== | ||
+ | |||
=== Main Parameters === | === Main Parameters === | ||
- | | + | ; ; post_refine_folder : : : Input folder is the directory where the results |
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- | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
- | | + | ; ; < |
- | | + | |
- | ; %%--%%bfac_minfreq : The minimum frequency range which is normally the maximum inner shell to include in enhancement. (default 20) | + | |
- | ; %%--%%bfac_maxfreq : The minimum frequency range which is normally the maximum outer shell to include in enhancement. (default -1) | + | |
- | ; %%--%%mrc_reloc_folder | + | |
===== Output ===== | ===== Output ===== | ||
- | | + | |
- | | + | ; ; particles_ctf_refine.star : : Output star file for ctf refined stack. ; ; bdb:ctfrefine_stack |
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===== ===== | ===== ===== | ||
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< | < | ||
- | module unload sphire (unload the module sphire) | + | module unload sphire (unload the module sphire) |
- | module load sphire/ | + | module load sphire/ |
module load relion | module load relion |