Walkthrough on GUI based tilt series alignment - Revision history

Raffaele Coray: /* Data */

2024-12-03T12:47:04Z

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2024-12-02T13:13:47Z

Trail extension

2024-12-02T12:47:07Z

2024-03-15T11:39:08Z

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2024-03-15T11:36:40Z

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2024-03-15T11:36:07Z

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2023-08-17T12:45:00Z

2023-08-17T12:44:34Z

Creating an alignment workflow

2023-08-16T06:44:58Z

2023-08-16T06:35:47Z

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 = Data =
-We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR, then bin it,   [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or simply follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
+We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR, then bin it,   <!--[https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or simply follow this link]-->[{{Template:DownloadLinkAWFHIV1TS}} or simply follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
 = Creating an alignment workflow=

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 ===Trail extension===
 This step aims at locating trails that have been excluded by previous steps of the alignment procedure, or that were never detected as trails because previous, lesser quality stages of the 3d model were not able to analyse the observations correctly.
-[[ File:alignGUI_parametersOfTiltExtensor.png |thumb|center| 600px|parameters of tilt extensor]]
+<!--[[ File:alignGUI_parametersOfTiltExtensor.png |thumb|center| 600px|parameters of tilt extensor]]-->
 [[ File:alignGUI_trailExtensorAddsAFewNewTrails.png |thumb|center| 600px|trail extensor adds a few new trails]]

← Older revision		Revision as of 12:47, 2 December 2024
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		+	[[Category:Walkthroughs]]
		+
	''Dynamo'' includes a package for automated alignment and reconstruction of tilt series. This walkthrough guides users through a series of steps on how to use it in GUI-based mode. The [[Walkthrough on command line based tilt series alignment \| walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line.		''Dynamo'' includes a package for automated alignment and reconstruction of tilt series. This walkthrough guides users through a series of steps on how to use it in GUI-based mode. The [[Walkthrough on command line based tilt series alignment \| walkthrough on command line based tilt series alignment]] shows how to operate this procedure through the command line.

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 = Data =
-We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR   [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or simply follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
+We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR, then bin it,   [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or simply follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
 = Creating an alignment workflow=

@@ Line 3: / Line 3: @@
 = Data =
-We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
+We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). You can download it directly from EMPIAR   [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or simply follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
 = Creating an alignment workflow=

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 Open a new local terminal and navigate to the directory where you just created the tutorial dataset and project.
-  <tt >rsync -av /data/project/bio/tomoworkshop/backup_for_first_day/b001ts001.mrc ./
+  <tt >rsync -av /data/project/bio/tomoworkshop/backup_for_first_day/b001ts001.mrc ./ </tt>
 = Creating an alignment workflow=

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 Start the alignment GUI by typing the command <tt>dtsa</tt> (short form of <tt>dynamo_tilt_series_alignment</tt>) into the ''Dynamo'' command line:
-  <tt>dtsa</tt>
+<tt>dtsa</tt>
 A pop-up window appears. Click on "create a new workflow":

← Older revision		Revision as of 06:35, 16 August 2023
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	We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). Visit the course materials to access the tilt series, download it directly from EMPIAR [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.		We use a binned version of the first tilt series from the EMPIAR entry 10164, depicting a set of virus like particles (VLP). Visit the course materials to access the tilt series, download it directly from EMPIAR [https://drive.google.com/file/d/1EsnKBvbFuWD1njk8dRVLc3SlhdsTHIpY/view?usp=drive_link or follow this link] to download a 600Mb file. You can also follow this tutorial using your own data.
		+
		+	The tilt series has already been prepared and can be found by following the next steps.
		+
		+	Open a new local terminal and navigate to the directory where you just created the tutorial dataset and project.
		+	<tt >rsync -av /data/project/bio/tomoworkshop/backup_for_first_day/b001ts001_15_08_2023.mrc ./

	= Creating an alignment workflow=		= Creating an alignment workflow=