User Tools

Site Tools


pipeline:meridien:start

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
Next revision Both sides next revision
pipeline:meridien:start [2019/04/02 12:20]
lusnig
pipeline:meridien:start [2021/03/15 17:04]
aali
Line 2: Line 2:
  
 === 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. 
 === 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