Difference between revisions of "Integration with Warp and M"
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Preprocess your multi-frame micrographs in warp following the guide | Preprocess your multi-frame micrographs in warp following the guide | ||
[[http://www.warpem.com/warp/?page_id=378 here]] | [[http://www.warpem.com/warp/?page_id=378 here]] | ||
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| + | Bad images should be deselected in Warp at this stage. | ||
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| + | This stage is finished once you have your tilt-series in the ''imod'' folder | ||
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| + | If you collected your data in Tomo rather than SerialEM and don't have mdoc files, you can try [[https://github.com/alisterburt/mdocspoofer mdocspoofer]] | ||
= align tilt-series = | = align tilt-series = | ||
Revision as of 11:03, 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
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]
