Starters guide (workshop version) - Revision history

Raffaele Coray at 13:51, 2 December 2024

2024-12-02T13:51:12Z

← Older revision		Revision as of 13:51, 2 December 2024
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			[[Category:WalkthroughsSpecific]]

	This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide \| starters guide]] that was adapted for the use in ''Dynamo'' workshops.		This tutorial shows how to manually pick particles in a tomogram, extract them, align and classify them. This tutorial is a shortened version of the original [[Starters_guide \| starters guide]] that was adapted for the use in ''Dynamo'' workshops.

Stefano Scaramuzza: /* Alignment projects */

2021-09-03T17:27:47Z

Alignment projects

← Older revision		Revision as of 17:27, 3 September 2021
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	[[File:StartersGuideFigure10.png\|thumb\|center\|600px\|]]		[[File:StartersGuideFigure10.png\|thumb\|center\|600px\|]]

	Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version during a workshop). Set ''CPU cores'' to the maximum available (e.g., 24). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project		Click on ''Computing environment'' and select your computing environment (choose ''standalone'' if you are working on the standalone version during a workshop). Set ''CPU cores'' and ''parallelize averaging step'' to the maximum available (e.g., 24). Leave the rest as it is and click ''ok''. In the alignment GUI click ''check'' and ''unfold''. To run the project

	* in a Matlab session, you can just click on “run”.		* in a Matlab session, you can just click on “run”.

Stefano Scaramuzza: /* Alignment projects */

2021-09-03T17:21:36Z

Alignment projects

← Older revision		Revision as of 17:21, 3 September 2021
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	In thw new window, do the following:		In thw new window, do the following:
	# Add the project name ''drun1''.		# Add the project name ''drun1'', press the ''enter'' key and select ''create a new project'' in the pop-up window.
	# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.		# Click on ''particles'' and provide the particle folder name ''thermosomeParticles.Data''. Click ok.
	# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.		# Click on ''table'' and provide the table name ''thermosomeParticles.Data/crop.tbl''. Click ok.

Stefano Scaramuzza: /* Initial reference generation */

2021-09-03T17:17:53Z

Initial reference generation

← Older revision		Revision as of 17:17, 3 September 2021
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	==Initial reference generation==		==Initial reference generation==
	We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dgallery</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all ''Dynamo'' windows and type into the ''Dynamo'' command line:		We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dgallery</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all open ''Dynamo'' windows and type into the ''Dynamo'' command line:

	<tt>dgallery('data','thermosomeParticles.Data');</tt>		<tt>dgallery('data','thermosomeParticles.Data');</tt>

Stefano Scaramuzza: /* Initial reference generation */

2021-09-03T17:17:40Z

Initial reference generation

← Older revision		Revision as of 17:17, 3 September 2021
Line 73:		Line 73:

	==Initial reference generation==		==Initial reference generation==
	We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dgallery</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all 'Dynamo' windows and type into the 'Dynamo' command line:		We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dgallery</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all ''Dynamo'' windows and type into the ''Dynamo'' command line:

	<tt>dgallery('data','thermosomeParticles.Data');</tt>		<tt>dgallery('data','thermosomeParticles.Data');</tt>

Stefano Scaramuzza: /* Initial reference generation */

2021-09-03T17:16:54Z

Initial reference generation

← Older revision		Revision as of 17:16, 3 September 2021
Line 73:		Line 73:

	==Initial reference generation==		==Initial reference generation==
	We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dgallery</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference:		We want to align the extracted tomograms to a common reference. For that, we need an initial reference (which will later be refined during the iterative alignment). Here, we create such an initial reference by manually align a few particles and average them. We use the command <tt>dgallery</tt> to generate initial orientations for some of our particles that will be used to generate the initial reference. Close all 'Dynamo' windows and type into the 'Dynamo' command line:

	<tt>dgallery('data','thermosomeParticles.Data');</tt>		<tt>dgallery('data','thermosomeParticles.Data');</tt>

Stefano Scaramuzza: /* An alternate visualization: orthogonal projections */

2021-09-03T17:15:51Z

An alternate visualization: orthogonal projections

← Older revision		Revision as of 17:15, 3 September 2021
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	==An alternate visualization: orthogonal projections==		==An alternate visualization: orthogonal projections==

	Clicking in the menu on ''Projection -> project full shown fragment along z'' and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.		Clicking in the menu on ''Projection -> project full shown fragment along z'' (still in dtmslice) and you will get a screen where the x-y projection of the tomogram is shown. Use the secondary click on it to launch the orthogonal views of x-z and y-z planes that traverse that point. These views can also be used to click particles, in case the standard view is not sufficient.

	{\|style="margin: 0 auto;"		{\|style="margin: 0 auto;"

Stefano Scaramuzza: /* Viewing tomograms */

2021-09-03T17:07:29Z

Viewing tomograms

← Older revision		Revision as of 17:07, 3 September 2021
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	==Viewing tomograms==		==Viewing tomograms==
	Select the first tomogram in the list ~~with a secondary mouse click~~ and go to ''View volume>Full tomogram file in tomoslice''.		Select the first tomogram in the list and go to ''View volume>Full tomogram file in tomoslice''.

	[[ File:StartersSelectTomoSliceInCatalogue.png \|thumb\| center \|600px\| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]		[[ File:StartersSelectTomoSliceInCatalogue.png \|thumb\| center \|600px\| Figure 2: Selecting a volume in the catalogue manager to be inspected in <tt>dpreview</tt>]]
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	[[ File:StartersTomoSlice.png \|thumb\| center \|600px\|]]		[[ File:StartersTomoSlice.png \|thumb\| center \|600px\|]]


	==Picking and extracting particles in tomograms==		==Picking and extracting particles in tomograms==

Stefano Scaramuzza: /* Subtomogram classification */

2021-08-18T10:57:53Z

Subtomogram classification

← Older revision		Revision as of 10:57, 18 August 2021
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	[[File:StartersGuideResultsClassification2.png\|thumb\|center\|400px\|]]		[[File:StartersGuideResultsClassification2.png\|thumb\|center\|400px\|]]

	Choose the same computing environment as in the previous alignment project and run the project in the same way too. ~~This project will~~ run ~~twice as long~~ because each particle will be aligned to two references. Monitor the progress of the project ~~sam~~ as before:		Choose the same computing environment as in the previous alignment project and run the project in the same way too. MRA projects usually run longer, because each particle will be aligned to two references. Here, however, we chose the parameters in a way that the process is still fast (e.g., small dimensions). Monitor the progress of the project same as before:

	<tt>dvstatus drun2</tt>		<tt>dvstatus drun2</tt>

Stefano Scaramuzza at 10:54, 18 August 2021

2021-08-18T10:54:52Z

← Older revision		Revision as of 10:54, 18 August 2021
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	# Click on ''numerical parameters'' and set the following parameters. Click ok.		# Click on ''numerical parameters'' and set the following parameters. Click ok.

			[[File:StartersGuideResultsClassification2.png\|thumb\|center\|400px\|]]

			Choose the same computing environment as in the previous alignment project and run the project in the same way too. This project will run twice as long because each particle will be aligned to two references. Monitor the progress of the project sam as before:

	# Choose the same computing environment as in the previous alignment project and run the project in the same way too. This project will run twice as long because each particle will be aligned to two references.

	Monitor the progress of the project sam as before:

	<tt>dvstatus drun2</tt>		<tt>dvstatus drun2</tt>