High resolution walkthrough with HIV1 - Revision history

Raffaele Coray: /* Extraction of first per tomogram average */

2025-02-14T12:15:19Z

Extraction of first per tomogram average

← Older revision		Revision as of 12:15, 14 February 2025
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	From here, copy and open the <code>first_aligment_per_tomogram.m</code> script.		From here, copy and open the <code>first_aligment_per_tomogram.m</code> script.

	style="color: blue"~~></pre~~> movefile([pathToDownloads '/Subtomogram_averaging/scripts_wc/*'], './scripts')		<pre style="color: blue"> movefile([pathToDownloads '/Subtomogram_averaging/scripts_wc/*'], './scripts')
	open first_aligment_per_tomogram.m</pre>		open first_aligment_per_tomogram.m</pre>

Raffaele Coray: /* Extraction of first per tomogram average */

2025-02-14T12:13:55Z

Extraction of first per tomogram average

← Older revision		Revision as of 12:13, 14 February 2025
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	Let us start by preparing the last average by running the <code>prepare_average_for_chimera.m</code> script.		Let us start by preparing the last average by running the <code>prepare_average_for_chimera.m</code> script.

	<pre style="color: blue">< movefile([pathToDownloads '/Subtomogram_averaging/scripts/*'], './scripts')		<pre style="color: blue"> movefile([pathToDownloads '/Subtomogram_averaging/scripts/*'], './scripts')
	prepare_average_for_chimera(pr_0)</pre>		prepare_average_for_chimera(pr_0)</pre>

Raffaele Coray: /* Extraction of first per tomogram average */

2025-02-14T12:13:47Z

Extraction of first per tomogram average

← Older revision		Revision as of 12:13, 14 February 2025
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	Let us start by preparing the last average by running the <code>prepare_average_for_chimera.m</code> script.		Let us start by preparing the last average by running the <code>prepare_average_for_chimera.m</code> script.

	re style="color: blue"><~~/pre>~~ movefile([pathToDownloads '/Subtomogram_averaging/scripts/*'], './scripts')		<pre style="color: blue">< movefile([pathToDownloads '/Subtomogram_averaging/scripts/*'], './scripts')
	prepare_average_for_chimera(pr_0)</pre>		prepare_average_for_chimera(pr_0)</pre>

Raffaele Coray: /* Structure of the walkthrough */

2024-12-03T12:31:03Z

Structure of the walkthrough

← Older revision		Revision as of 12:31, 3 December 2024
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	= Structure of the walkthrough =		= Structure of the walkthrough =

	The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in: <!--https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing~~<br>~~-->{{Template:DownloadLinkHighResHIV1presentation}}		The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in: <!--https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing-->{{Template:DownloadLinkHighResHIV1presentation}}<br>
	<br>		<br>
	<br>		<br>
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	\| The 'data' section has been made available from a physical memory.		\| The 'data' section has been made available from a physical memory.
	\|-		\|-
	\| The 'script' section can be downloaded from https://drive.google.com/file/d/1sM8OBQ7LF7OfhMPU0WwfJ31hVeXwTbCh/view?usp=drive_link.		\| The 'script' section can be downloaded from <!--https://drive.google.com/file/d/1sM8OBQ7LF7OfhMPU0WwfJ31hVeXwTbCh/view?usp=drive_link-->{{Template:DownloadLinkHighResHIV1scripts}}.
	\|-		\|-
	\| The script generally do not need modification.		\| The script generally do not need modification.
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	\| Intended for individual practical use.		\| Intended for individual practical use.
	\|-		\|-
	\| The 'data' section starts by being mostly empty. The 'data' section can be downloaded from https://drive.google.com/file/d/1k4bLLswsacYdIGcNRc76YcbAiycxyPuX/view?usp=drive_link.		\| The 'data' section starts by being mostly empty. The 'data' section can be downloaded from <!--https://drive.google.com/file/d/1k4bLLswsacYdIGcNRc76YcbAiycxyPuX/view?usp=drive_link-->{{Template:DownloadLinkHighResHIV1lightData}}.
	\|-		\|-
	\| The 'script' section can be downloaded from https://drive.google.com/file/d/1sM8OBQ7LF7OfhMPU0WwfJ31hVeXwTbCh/view?usp=drive_link.		\| The 'script' section can be downloaded from <!--https://drive.google.com/file/d/1sM8OBQ7LF7OfhMPU0WwfJ31hVeXwTbCh/view?usp=drive_link-->{{Template:DownloadLinkHighResHIV1scripts}}.
	\|-		\|-
	\| The scripts will need modifications.		\| The scripts will need modifications.

Raffaele Coray: /* Structure of the walkthrough */

2024-12-03T12:29:28Z

Structure of the walkthrough

← Older revision		Revision as of 12:29, 3 December 2024
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	= Structure of the walkthrough =		= Structure of the walkthrough =

	The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in: https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br>		The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in: <!--https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br>-->{{Template:DownloadLinkHighResHIV1presentation}}
	<br>		<br>
	<br>		<br>

Raffaele Coray: /* Structure of the walkthrough */

2024-12-03T10:54:21Z

Structure of the walkthrough

← Older revision		Revision as of 10:54, 3 December 2024
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	\| Intended for individual practical use.		\| Intended for individual practical use.
	\|-		\|-
	\| The 'data' section starts ~~has~~ mostly empty. The 'data' section can be downloaded from https://drive.google.com/file/d/1k4bLLswsacYdIGcNRc76YcbAiycxyPuX/view?usp=drive_link.		\| The 'data' section starts by being mostly empty. The 'data' section can be downloaded from https://drive.google.com/file/d/1k4bLLswsacYdIGcNRc76YcbAiycxyPuX/view?usp=drive_link.
	\|-		\|-
	\| The 'script' section can be downloaded from https://drive.google.com/file/d/1sM8OBQ7LF7OfhMPU0WwfJ31hVeXwTbCh/view?usp=drive_link.		\| The 'script' section can be downloaded from https://drive.google.com/file/d/1sM8OBQ7LF7OfhMPU0WwfJ31hVeXwTbCh/view?usp=drive_link.

Raffaele Coray: /* Structure of the walkthrough */

2024-12-02T13:53:48Z

Structure of the walkthrough

← Older revision		Revision as of 13:53, 2 December 2024
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	= Structure of the walkthrough =		= Structure of the walkthrough =

	The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in~~: HIV1 presentation~~:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br>		The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in: https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br>
	<br>		<br>
	<br>		<br>

Raffaele Coray at 12:53, 2 December 2024

2024-12-02T12:53:51Z

← Older revision		Revision as of 12:53, 2 December 2024
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			[[Category:Walkthroughs]]

	= Goal of the walktrough =		= Goal of the walktrough =

Raffaele Coray: /* Structure of the walkthrough */

2024-11-14T09:34:23Z

Structure of the walkthrough

← Older revision		Revision as of 09:34, 14 November 2024
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	= Structure of the walkthrough =		= Structure of the walkthrough =

	The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection.<br>		The full HIV1 walkthrough pipeline has been split into multiple sequential steps. Each of these steps corresponds to a subsection of this wiki page. It is possible to reach an average with about ~4 A of resolution starting from 5 tilt series by following all of the steps described in this walkthrough. The only exception is the process to create a tilt series from the microscope movies, which is only discussed in the "Motion correction and dose weighting" subsection. The walkthrough is paired with a presentation giving context on each step. The presentation can be found in: HIV1 presentation:https://drive.google.com/file/d/1em6wWQUaB3mwIyL9LTnDyPG4Ks43quBK/view?usp=sharing<br>
	<br>		<br>
	<br>		<br>

Raffaele Coray: /* Practical notes: alignment */

2024-05-13T07:59:52Z

Practical notes: alignment

← Older revision		Revision as of 07:59, 13 May 2024
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	The alignment will be generated using the script <code>make_AWF.m</code>. This script will programmatically initialize and run the dynamo automatic fiducial-based tilt series alignment but skipping the CTF handling and the reconstruction.		The alignment will be generated using the script <code>make_AWF.m</code>. This script will programmatically initialize and run the dynamo automatic fiducial-based tilt series alignment but skipping the CTF handling and the reconstruction.

	The algorithm only requires as parameters the gold bead radius, the gold bead mask, the ~~template~~ sidelength and the binning to apply. These parameters are determined by inspecting a tilt series. Open the first tilt series by running:		The algorithm only requires as parameters the gold bead radius, the gold bead mask, the patch sidelength and the binning to apply. These parameters are determined by inspecting a tilt series. Open the first tilt series by running:

	<pre style="color: blue">dshow([root,'data/TS_not_dose_weighted/01.mrc']);</pre>		<pre style="color: blue">dshow([root,'data/TS_not_dose_weighted/01.mrc']);</pre>
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	This procedure allows to estimate the radius of the gold bead and the binning to apply. This is because the AWF will initially detect the gold beads using template matching on the visually binned tilt series just as it was done manually now.<br>		This procedure allows to estimate the radius of the gold bead and the binning to apply. This is because the AWF will initially detect the gold beads using template matching on the visually binned tilt series just as it was done manually now.<br>

	The next figure present ~~visaully~~ the relationship between parameters gold bead radius, the gold bead mask radius and the ~~template~~ sidelength.		The next figure present visually the relationship between parameters gold bead radius, the gold bead mask radius and the patch sidelength.

	[[File:AWF_GB_definitions.png\|centre\|thumb\|600px\| Schematic representation of the AWF gold bead parameters.]]		[[File:AWF_GB_definitions.png\|centre\|thumb\|600px\| Schematic representation of the AWF gold bead parameters.]]

	Generally we suggest to set the mask radius parameter as about 50% bigger than the beads radius and then set the ~~template~~ sidelength as the smallest that can contain the mask diameter.		Generally we suggest to set the mask radius parameter as about 50% bigger than the beads radius and then set the patch sidelength as the smallest that can contain the mask diameter.

	<pre style="color: blue">Use this rule of thumb to estimate the gold bead radius and sidelength parameters</pre>		<pre style="color: blue">Use this rule of thumb to estimate the gold bead radius and sidelength parameters</pre>