Integration with Warp and M - Revision history

Raffaele Coray at 13:04, 2 December 2024

2024-12-02T13:04:36Z

2020-08-19T11:47:50Z

align tilt-series

2020-08-19T11:43:40Z

2020-08-19T10:39:29Z

align tilt-series

2020-08-19T08:27:11Z

run alignments/classifications in dynamo or relion

2020-08-19T08:26:27Z

rerun alignments/classifications in dynamo or relion (optional)

2020-08-19T08:21:36Z

rerun alignments/classifications in dynamo or relion

2020-08-19T08:21:21Z

2020-08-19T08:20:37Z

Overview

2020-08-13T10:49:01Z

run multi-particle refinements in M

← Older revision		Revision as of 13:04, 2 December 2024
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		+	[[Category:Walkthroughs]]
		+
	This page describes a method for integration of Dynamo, Warp and M to be able to take advantage of...		This page describes a method for integration of Dynamo, Warp and M to be able to take advantage of...

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 = align tilt-series =
-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]]
+'''Without Fiducials'''
 A function to automate the alignment of datasets with fiducials and convert all necessary metadata for import into warp is provided as [https://github.com/alisterburt/autoalign_dynamo autoalign_dynamo].

@@ Line 5: / Line 5: @@
 * robust CTF estimation procedures for tilt-series data
 Dynamo's
-* automated tilt-series alignment
+* automated fiducial based tilt-series alignment
 * geometric picking tools
 * flexible subtomogram averaging procedures

@@ Line 39: / Line 39: @@
 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]]
-A function to automate the alignment of datasets with fiducials and convert all necessary metadata for import into warp is provided as [[https://github.com/alisterburt/autoalign_dynamo | autoalign_dynamo]].
+A function to automate the alignment of datasets with fiducials and convert all necessary metadata for import into warp is provided as [https://github.com/alisterburt/autoalign_dynamo autoalign_dynamo].
 Once you've followed the setup from that page, simply navigate to the imod directory generated by warp and run

@@ Line 75: / Line 75: @@
 When warp exports subtomograms it provides a STAR file for the output. This can be used to run refinements in RELION.
-If we want to import particles back into Dynamo, we run the ''warp2dynamo'' script from [[https://github.com/alisterburt/dynamo2m]] on this STAR file.
+If we want to import particles back into Dynamo, we run the ''warp2dynamo'' script from [https://github.com/alisterburt/dynamo2m dynamo2m] on this STAR file.
 This script creates a table file and corresponding tomogram-table map file, this table file should be used for refinements with the Warp particles.

← Older revision		Revision as of 08:26, 19 August 2020
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	= rerun alignments/classifications in dynamo or relion (optional) =		= rerun alignments/classifications in dynamo or relion (optional) =
		+
		+	If you want to re-refine or re-classify particles after running multi-particle refinements in M export your particles from within M directly as described [[http://www.warpem.com/warp/?page_id=1631 here]]
		+
		+	If you would like to import these particles into dynamo please use the ''m2dynamo'' script from [[https://github.com/alisterburt/dynamo2m dynamo2m]]

← Older revision		Revision as of 08:21, 19 August 2020
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	Then, follow the guide for running [[http://www.warpem.com/warp/?page_id=827 multi-paricle refinements]] in M		Then, follow the guide for running [[http://www.warpem.com/warp/?page_id=827 multi-paricle refinements]] in M

−	= rerun alignments/classifications in dynamo or relion =	+	= rerun alignments/classifications in dynamo or relion (optional) =

← Older revision		Revision as of 08:21, 19 August 2020
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	Then, follow the guide for running [[http://www.warpem.com/warp/?page_id=827 multi-paricle refinements]] in M		Then, follow the guide for running [[http://www.warpem.com/warp/?page_id=827 multi-paricle refinements]] in M
		+
		+	= rerun alignments/classifications in dynamo or relion =

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 * 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

← Older revision		Revision as of 10:49, 13 August 2020
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	= run multi-particle refinements in M =		= run multi-particle refinements in M =
		+	M expects two independently refined half-maps, a mask and a corresponding ''_data.star'' file, as well as the settings file from the directory you used to process your frames in Warp.
		+
		+	We assume here that you have run a [[Adaptive_bandpass_filtering \| gold standard]] alignment project in Dynamo, and thus have two tables and two half maps in the results of your alignment project.
		+
		+	Run the ''dynamo2m'' script in this directory, providing the two tables and the corresponding [[tomogram-table map file]]. This will give you a ''_data.star'' file which can be used in M.
		+
		+	Then, follow the guide for running [[http://www.warpem.com/warp/?page_id=827 multi-paricle refinements]] in M