Difference between revisions of "Integration with Warp and M"

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(preprocess)
(align tilt-series)
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= align tilt-series =
 
= align tilt-series =
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Tilt series can either be aligned in IMOD or using dynamo's new [[Walkthrough on command line based tilt series alignment | tilt series alignment tools]]
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A function to automate the alignment of datasets and convert all necessary metadata for import into warp is provided as [[https://github.com/alisterburt/autoalign_dynamo | autoalign_dynamo]].
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Once you've followed the setup from that page, simply navigate to the imod directory generated by warp and run
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<nowiki>dautoalign4warp(<pixel_size_angstrom>, <fiducial_diameter_nm>, <nominal_rotation_angle>, <output_folder>)</nowiki>
  
 
= generate downscaled tomograms =  
 
= generate downscaled tomograms =  

Revision as of 12:10, 13 August 2020

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>)

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