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

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>)