Integration with Warp and M
This page describes a method for integration of Dynamo, Warp and M to be able to take advantage of...
Warp's
- streamlined preprocessing
- robust CTF estimation procedures for tilt-series data
Dynamo's
- automated tilt-series alignment
- geometric picking tools
- flexible subtomogram averaging procedures
M's
- multi-particle refinement
- half-map regularisation by denoising
Contents
Overview
- Preprocess from multi-frame micrographs to tilt-series using Warp
- Align tilt-series using [Dynamo]
- Generate downscaled tomograms in warp
- Pick particles in Dynamo and run first alignments
- Reextract unbinned particles in warp using [dynamo2m]
- Run alignments/classifications in dynamo or relion
- Run multi-particle refinements in M
The last steps can be repeated to further improve final reconstruction quality
preprocess
Preprocess your multi-frame micrographs in warp following the guide [here]
Bad images should be deselected in Warp at this stage.
This stage is finished once you have your tilt-series in the imod folder
If you collected your data in Tomo rather than SerialEM and don't have mdoc files, you can try [mdocspoofer]
align tilt-series
Tilt series can either be aligned in IMOD or using dynamo's new tilt series alignment tools
A function to automate the alignment of datasets and convert all necessary metadata for import into warp is provided as [| autoalign_dynamo].
Once you've followed the setup from that page, simply navigate to the imod directory generated by warp and run
dautoalign4warp(<pixel_size_angstrom>, <fiducial_diameter_nm>, <nominal_rotation_angle>, <output_folder>)
