Integration with Warp and M

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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]

align tilt-series

generate downscaled tomograms

pick particles in dynamo

reextract unbinned particles in warp

run alignments/classifications in dynamo or relion

run multi-particle refinements in M