HIV1 Walkthrough (PSI 2023) - Revision history

Raffaele Coray at 13:15, 2 December 2024

2024-12-02T13:15:15Z

AlmaVivas: /* Subtomogram averaging */

2024-03-06T12:28:08Z

Subtomogram averaging

AlmaVivas: /* Subtomogram averaging */

2024-03-05T15:53:51Z

Subtomogram averaging

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AlmaVivas: /* Dynamo models and particles */

2024-03-05T15:53:32Z

Dynamo models and particles

AlmaVivas: /* Dynamo models and particles */

2024-02-29T15:01:01Z

Dynamo models and particles

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AlmaVivas: /* Extraction of refined half maps */

2023-08-14T15:11:44Z

Extraction of refined half maps

AlmaVivas: Created page with "= Goal = This walkthrough was designed to describe and discuss the steps necessary to go from the raw microscope data of a cryo-electron tomography experiment to a high-reso..."

2023-08-14T15:10:16Z

Created page with "= Goal = This walkthrough was designed to describe and discuss the steps necessary to go from the raw microscope data of a cryo-electron tomography experiment to a high-reso..."

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← Older revision		Revision as of 13:15, 2 December 2024
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		+	[[Category:WalkthroughsSpecific]]
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	= Goal =		= Goal =

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 stackName{idx} = D{1,2}{idx,1}(end-7:end-4);
 title(['Stack: ' stackName{idx}])</pre>
 Similarly to the subboxing section, is interesting to see how the filtering strategy worked. So:

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-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 594: / Line 598: @@
 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.

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 Et voilà! The latest results have been obtained. And with them, we have finished the subtomogram averaging projects. The computation time of this for the refinement project is estimated to be 24 hours per half-set (8 gpus).
-[[File:final-result-from-refined-gold-standard-sta.png|centre|thumb|600px| HIV-1 immature Gag structure, shown as cryoET final subtomogram averaging map though two orthogonal views via <code>dshow</code>, top left.]]
+[[File:final-result-from-refined-gold-standard-sta.png|centre|thumb|550px| HIV-1 immature Gag structure, shown as cryoET final subtomogram averaging map though two orthogonal views via <code>dshow</code>.]]
 Finally, the resulting odd/even maps are reformatted and prepared. To this end, the even half-map is aligned to the odd half-map with the usual function <code>dalign</code>. The resulting transformation parameters are used to transform the table corresponding to the even half-map though <code>dynamo_table_rigid</code>. The table is then used to re-average the even particles using<code>daverage</code> imposing a '''c6''' symmetry, <code>dynamo_csym</code>.