HIV1 workshop - Revision history

Raffaele Coray at 13:38, 2 December 2024

2024-12-02T13:38:23Z

AlmaVivas: /* Subtomogram averaging */

2024-03-06T12:27:54Z

Subtomogram averaging

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AlmaVivas: /* Dynamo models and particles */

2024-03-06T12:27:34Z

Dynamo models and particles

AlmaVivas: /* Extraction of coarse half maps */

2024-03-06T12:26:52Z

Extraction of coarse half maps

AlmaVivas: /* Dynamo models and particles */

2024-02-29T15:00:00Z

Dynamo models and particles

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AlmaVivas: /* Outputs */

2024-02-26T12:44:46Z

Outputs

AlmaVivas: /* Outputs */

2024-02-26T12:42:53Z

Outputs

AlmaVivas: /* Outputs */

2024-02-26T12:42:31Z

Outputs

AlmaVivas: /* Outputs */

2024-02-26T12:42:27Z

Outputs

AlmaVivas at 12:41, 26 February 2024

2024-02-26T12:41:58Z

← Older revision		Revision as of 13:38, 2 December 2024
Line 1:		Line 1:
		+	[[Category:WalkthroughsSpecific]]

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

@@ Line 621: / Line 621: @@
-Once you have decided the oversampling configuration, open the script via
+Once you have decided the oversampling configuration, the time for scripting has come. Get out the catalogue directory to the workspace and:
 <pre style="color: blue">
 open model_workflow.m
 </pre>
-Remember, you will find a '''[!!]''' and sometimes an '''NaN''' wherever scripts need to be completed.
+Remember, you will find a '''[!!]''' and/or an '''NaN''' wherever scripts need to be completed.
 Is time for to fill in the quantities missing to:
@@ Line 652: / Line 656: @@
 run model_workflow.m
 </pre>
 This will create a regular lattice of coordinates (about 800 to 1,000 per tomogram) on the surface. These coordinates will be the center of the extracted subvolumes. For each tomogram and the associated set of dipoles a regular lattice of cropped subvolumens, the output will be a crop table, and a template of the initial average of those oriented particles (subvolumes).  Technically, the so-called particle extraction process involves the creation of a merged table with <code>dynamo_table_merge</code>. Then, the cropping of sub-volumes with <code>dtcrop</code>. It will not only crop the table but it will also manage the sub-volume tagging. Finally, templates generate averaging all the particles with <code>daverage</code>. While the user can implement its own version, the recommendation is to use the in-house version given that it accounts for missing wedge compensation.

@@ Line 1,090: / Line 1,090: @@
 <pre style="color: blue">open coarse_gold_standard_alignment.m</pre>
-From the last project, the tables will be gathered. Column 10 stores the CC between each aligned subvolume and the final average. The exclusion process is done by fitting a Gaussian mixture model (GMM) to the such  distribution. The MATLAB function fitgmdist will help to classify them into a combination of two populations. The one with the lower CC score is assumed to be the “bad” class (i.e., particularly bad quality or subvolumes containing pure noise). Therefore, it  needs to be excluded from the processing. The threshold is then defined by taking the minimum between the 2 Gaussian peaks and by adding an empirically defined constant of 0.01.
+From the last project, the tables will be gathered. Column 10 stores the CC between each aligned subvolume and the final average. The exclusion process is done by fitting a Gaussian mixture model (GMM) to the such  distribution. The MATLAB function fitgmdist will help to classify them into a combination of two populations. The one with the lower CC score is assumed to be the “bad” class (i.e., particularly bad quality or subvolumes containing pure noise). Therefore, it  needs to be excluded from the processing. The threshold is then defined by taking the minimum between the 2 Gaussian peaks and by adding an empirically defined constant of 0.01.
-While the table get filtered, to visualise the results:
+While the table get filtered, to visualise the results add the following lines in the loop:
-<pre style="color: blue">
+<pre style="color: blue">figure;
 hold on;
 histogram(t(:,10), 'Normalization', 'pdf', 'EdgeColor', 'none')
@@ Line 1,104: / Line 1,103: @@
 legend('CC distribution','GMM fit','Threshold')
 stackName{idx} = D{1,2}{idx,1}(end-7:end-4);
-title(['Stack: ' stackName{idx}])
+title(['Stack: ' stackName{idx}])</pre>
 Tips:
-<pre style="color: blue">To terminate debug mode and continue execution, use the dbcont command.
+'''Tips:'''
 To terminate debug mode and exit the file without completing execution, use the dbquit command.</pre>
@@ Line 1,115: / Line 1,123: @@
-[[File:gmm-population-clasification.png|centre|thumb|950px| GMM fit to the CC score distribution of the particles from each tomogram and the automatically defined threshold for particle exclusion.]]
+[[File:gmm-population-clasification-sta.png|centre|thumb|950px| GMM fit to the CC score distribution of the particles from each tomogram and the automatically defined threshold for particle exclusion.]]
@@ Line 1,129: / Line 1,137: @@
-[[File:Synthetic-height-reference.png|centre|thumb|550px|Synthetic reference for alignment to common height. Mask computed from membrane object X-View, left; Z-view, right. ]]
+[[File:Synthetic-height-reference-sta.png|centre|thumb|550px|Synthetic reference for alignment to common height. Mask computed from membrane object X-View, left; Z-view, right. ]]
@@ Line 1,151: / Line 1,159: @@
 The configuration of the 2 independent alignment projects using the starting references that have been created before is displayed below. A total of 3 rounds with 3 iterations each are set up. The parameter search space is reduced after each round. The low-pass filter is increased to 32 pixels (8.1 Å), and the last 2 rounds are run on full-sized particles.
-[[File:coarse-half-maps-alignment-configuration.png|centre|thumb|600px|  Numerical parameters configuration for coarse half maps alignment project. ]]
+[[File:coarse-half-maps-alignment-configuration-sta.png|centre|thumb|600px|  Numerical parameters configuration for coarse half maps alignment project. ]]
-The estimated times are, for registration, and re-cropping, 20  min (8 workers). The coarse even/odd project is around 48 hour per half-set (8 gpus). Therefore, as expected, the files simulating the full execution of the script will be copied to the workspace you are working on when launching it.
+<pre style="color: blue">run coarse_gold_standard_alignment.m</pre>
 To check the resulting maps:
-<pre style="color: blue">prEO = 'pr_EO';
+<pre style="color: blue">aEPath = ddb([pr_EO{1} ':as']);
-aPaths = ddb([prEO ':as:ite=last:ref=*']);
+aOPath = ddb([pr_EO{2} ':as']);
-dshow([dread(aPaths{1}); dread(aPaths{2})])</pre>
+dshow([dread(aEPath); dread(aOPath)])</pre>
-[[File:last-average-for-coarse-half-maps.png|centre|thumb|900px| Last average from coarse gold standard alignment project. ]]
+[[File:last-average-for-coarse-half-maps-sta.png|centre|thumb|900px| Last average from coarse gold standard alignment project. ]]
 === Extraction of refined half maps ===

← Older revision		Revision as of 12:44, 26 February 2024
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	- the high-resolution average RELION.<br>		- the high-resolution average RELION.<br>
	- the aligned particle positions in RELION.<br>		- the aligned particle positions in RELION.<br>
−
−
−
−	~~[[File:hello-world.png\|centre\|thumb\|600px\| ]]~~

← Older revision		Revision as of 12:42, 26 February 2024
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−	[[File:hello.png\|centre\|thumb\|600px\| ~~TEST~~ ]]	+	[[File:hello-world.png\|centre\|thumb\|600px\| ]]

← Older revision		Revision as of 12:41, 26 February 2024
Line 1,440:		Line 1,440:
	- the high-resolution average RELION.<br>		- the high-resolution average RELION.<br>
	- the aligned particle positions in RELION.<br>		- the aligned particle positions in RELION.<br>
		+
		+
		+
		+	[[File:hello.png\|centre\|thumb\|600px\| TEST ]]