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pipeline:meridien:start [2019/04/02 12:20]
lusnig 		pipeline:meridien:start [2021/03/16 10:42]
aali
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 === Commands === === Commands ===
-  ; [[sxmeridien|3D Refinement]] : Perform automatic 3D structure refinement as standard fresh run (default run). 
-  ; [[sxgui_meridien|3D Refinement Assessment]] : GUI tool to assess MERIDIEN 3D Refinement outputs. 
-  ; [[pipeline:utilities:sxprocess|PostRefiner]] : Combine unfiltered halfset volumes, then enhance the power spectrum. 
  
-\\+; ; [[:pipeline:meridien:sxmeridien|3D Refinement]] : : Perform automatic 3D structure refinement as standard fresh run (default run). ; ; [[:pipeline:meridien:sxgui_meridien|3D Refinement Assessment]] : : GUI tool to assess MERIDIEN 3D Refinement outputs. ; ; [[:pipeline:utilities:sxprocess|PostRefiner]] : : Combine unfiltered halfset volumes, then enhance the power spectrum. ; ; [[:pipeline:meridien:sp_polishing|Relion Polishing]] :: Apply Relion Bayesian Polishing on SPHIRE generated stacks from SPHIRE GUI. ; ; [[:pipeline:meridien:sp_higher_ord_abber|Relion CTF Refinement]] :: Apply Relion CTF refinement for higher order aberration correction from SPHIRE GUI. ; ; [[:pipeline:meridien:sp_relion_3dclassifi|Relion 3D classification]] :: Apply Relion 3D classification tool from SPHIRE GUI. 
 === Alternatives === === Alternatives ===
-  ; [[sxmeridien|Local Refinement from Iteration]] : Perform local refinement from the last fully finished 3D refinement iteration. 
-  ; [[sxmeridien|Local Refinement from Stack]] : Perform local refinement from the stack with user-provided orientation parameters. 
-  ; [[sxmeridien|Restart Local Refinement]] : Restart local refinement after the last fully finished iteration of meridian run or local refinement run 
-  ; [[sxgui_meridien|3D Refinement Assessment]] : GUI tool to assess MERIDIEN 3D Refinement outputs. 
-  ; [[sxmeridien|Final 3D Reconstruction Only]] : Do only final 3D reconstruction using a fully finished 3D refinement iteration. 
  
-\\+; ; [[:pipeline:meridien:sxmeridien|Local Refinement from Iteration]] : : Perform local refinement from the last fully finished 3D refinement iteration. ; ; [[:pipeline:meridien:sxmeridien|Local Refinement from Stack]] : : Perform local refinement from the stack with user-provided orientation parameters. ; ; [[:pipeline:meridien:sxmeridien|Restart Local Refinement]] : : Restart local refinement after the last fully finished iteration of meridian run or local refinement run. ; ; [[:pipeline:meridien:sxgui_meridien|3D Refinement Assessment]] : : GUI tool to assess MERIDIEN 3D Refinement outputs. ; ; [[:pipeline:meridien:sxmeridien|Final 3D Reconstruction Only]] : : Do only final 3D reconstruction using a fully finished 3D refinement iteration.
  
 === Utilities === === Utilities ===
-  ; [[pipeline:utilities:e2display|Display Data]] : Displays images, volumes, or 1D plots. + 
-  ; [[pipeline:utilities:sxpipe_moon_eliminator|Volume Adjustment]] : Resamples, clips, and removes disconnected regions from a 3D map. It optionally creates a mask from the resulting volume. +; ; [[:pipeline:utilities:e2display|Display Data]] : : Displays images, volumes, or 1D plots. ; ; [[:pipeline:utilities:sxpipe_moon_eliminator|Volume Adjustment]] : : Resamples, clips, and removes disconnected regions from a 3D map. It optionally creates a mask from the resulting volume. ; ; [[:pipeline:viper:sp_mask|Masking]] : : Mask creation tool for 2D or 3D masks. ; ; [[:pipeline:utilities:sxpipe_angular_distribution|Angular Distribution]] : : Creates a .bild file to display the particle orientation distribution in Chimera. ; ; [[:pipeline:utilities:sxprocess|Balance Angular Distribution ]] : : Balance angular distribution of projection directions by removing excess particles. ; ; [[:pipeline:utilities:sp_batch|Batch Pipeline Execution]] : : Run jobs that wait with the execution on each other. ; ; [[:pipeline:utilities:sp_ctf_refine|CTF refine (Meridien)]] : : Refine the defocus per particle. ; ; [[:pipeline:utilities:sp_ctf_refine_stack|CTF refine (Stack)]] : : Refine, manual, the defocus per particle. ; ; [[:pipeline:meridien:sp_beamtilt|Correct Beam Tilt]] : : Applies beam-tilt correction to particles.. 
-  ; [[pipeline:viper:sp_mask|Masking]] : Mask creation tool for 2D or 3D masks + 
-  ; [[pipeline:utilities:sxpipe_angular_distribution|Angular Distribution]] : Creates a .bild file to display the particle orientation distribution in Chimera. +
-  ; [[pipeline:utilities:sxprocess|Balance Angular Distribution ]] : Balance angular distribution of projection directions by removing excess particles +
-  ; [[pipeline:utilities:sp_batch|Batch Pipeline Execution]] : Run jobs that wait with the execution on each other +
-  ; [[pipeline:utilities:sp_ctf_refine|CTF refine (Meridien)]] : Refine the defocus per particle +
-  ; [[pipeline:utilities:sp_ctf_refine_stack|CTF refine (Stack)]] : Refine, manual, the defocus per particle+
pipeline/meridien/start.txt · Last modified: 2021/03/16 10:42 by aali

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