; ; 3D Refinement : : Perform automatic 3D structure refinement as standard fresh run (default run). ; ; 3D Refinement Assessment : : GUI tool to assess MERIDIEN 3D Refinement outputs. ; ; PostRefiner : : Combine unfiltered halfset volumes, then enhance the power spectrum. ; ; Relion Polishing :: Apply Relion Bayesian Polishing on SPHIRE generated stacks from SPHIRE GUI. ; ; Relion CTF Refinement :: Apply Relion CTF refinement for higher order aberration correction from SPHIRE GUI. ; ; Relion 3D classification :: Apply Relion 3D classification tool from SPHIRE GUI.
; ; Local Refinement from Iteration : : Perform local refinement from the last fully finished 3D refinement iteration. ; ; Local Refinement from Stack : : Perform local refinement from the stack with user-provided orientation parameters. ; ; Restart Local Refinement : : Restart local refinement after the last fully finished iteration of meridian run or local refinement run. ; ; 3D Refinement Assessment : : GUI tool to assess MERIDIEN 3D Refinement outputs. ; ; Final 3D Reconstruction Only : : Do only final 3D reconstruction using a fully finished 3D refinement iteration.
; ; Display Data : : Displays images, volumes, or 1D plots. ; ; Volume Adjustment : : Resamples, clips, and removes disconnected regions from a 3D map. It optionally creates a mask from the resulting volume. ; ; Masking : : Mask creation tool for 2D or 3D masks. ; ; Angular Distribution : : Creates a .bild file to display the particle orientation distribution in Chimera. ; ; Balance Angular Distribution : : Balance angular distribution of projection directions by removing excess particles. ; ; Batch Pipeline Execution : : Run jobs that wait with the execution on each other. ; ; CTF refine (Meridien) : : Refine the defocus per particle. ; ; CTF refine (Stack) : : Refine, manual, the defocus per particle. ; ; Correct Beam Tilt : : Applies beam-tilt correction to particles..