SPHIRE Workflow
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pipeline:utilities:start
This version (2021/02/19 14:50) was approved by twagner.
Utilities
- Batch Pipeline Execution
- Run jobs that wait with the execution on each other
- Display Data
- Displays images, volumes, or 1D plots.
- PDB File Conversion
- Converts an PDB atomic model into a simulated density map.
- RELION to SPHIRE Conversion
- Convert parameters from RELION to SPHIRE formats.
- SPHIRE to RELION Conversion
- Convert parameters from SPHIRE to RELION formats.
- Separate Into Classes
- Separates stacks of particle images into stacks for each class.
- Compare re-projections
- Compare re-projections to class averages
- 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
- Change Size of Image or Volume
- Change size of image or map
- Window Volume
- Window (pad or clip) volume to the specificy dimension
- Angular Distribution
- Creates a .bild file to display the particle orientation distribution in Chimera.
- crYOLO - boxmanager
- Displays boxfiles on images. Allows creation of new training data for crYOLO
- Balance Angular Distribution
- Balance angular distribution of projection directions by removing excess particles
- PostRefiner (Single Volumes)
- Enhancing the power spectrum of any single volumes (Single Volumes Mode).
- Micrograph Movie Summation
- Create an average micrograph using Summovie http://grigoriefflab.janelia.org/unblur.
- Header Operations
- Perform operations on headers of hdf or bdb image file.
- Create Virtual Stack
- Make a virtual BDB image stack.
- Organize Micrographs/Movies
- Move selected micrographs/movies from source to destination directory.
- CTF refine (Meridien)
- Refine the defocus per particle
- CTF refine (Stack)
- Refine, manual, the defocus per particle
pipeline/utilities/start.txt ยท Last modified: 2019/04/02 12:49 by lusnig
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