Workshop exercises - Revision history

Raffaele Coray at 13:46, 2 December 2024

2024-12-02T13:46:50Z

2016-09-01T08:30:02Z

Ribosomes from noise

2016-09-01T08:29:46Z

Ribosomes from noise

2016-09-01T08:28:19Z

2016-08-18T15:27:56Z

2016-08-16T15:31:15Z

2016-08-16T15:30:56Z

2016-08-16T15:23:34Z

2016-08-16T14:31:39Z

General tools

2016-08-16T14:28:12Z

Importing annotations for a single tomogram

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 You have access to a supercomputer (GPU). Generate a data set of particles containing pure noise (around 1K should be ok) and align them against a ribosome template.... can you reproduce the famouse "Einstein from noise"  example out of these pure data particles?
-A (low resolution) ribosome template is available as file <tt>'ribosome32.em'</tt>
+A (low resolution) ribosome template is available as file <tt>ribosome32.em</tt>
 Suggested tools: <tt>rand</tt>, <tt>dwrite</tt>.

← Older revision		Revision as of 08:29, 1 September 2016
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	You have access to a supercomputer (GPU). Generate a data set of particles containing pure noise (around 1K should be ok) and align them against a ribosome template.... can you reproduce the famouse "Einstein from noise" example out of these pure data particles?		You have access to a supercomputer (GPU). Generate a data set of particles containing pure noise (around 1K should be ok) and align them against a ribosome template.... can you reproduce the famouse "Einstein from noise" example out of these pure data particles?
		+
		+	A (low resolution) ribosome template is available as file <tt>'ribosome32.em'</tt>

	Suggested tools: <tt>rand</tt>, <tt>dwrite</tt>.		Suggested tools: <tt>rand</tt>, <tt>dwrite</tt>.

← Older revision		Revision as of 08:28, 1 September 2016
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	Task:		Task:
	Reproduce with the command line the [[Walkthrough model worfklow reuse \| technique ]] of addressing sets of models that already contain points to [[https://wiki.dynamo.biozentrum.unibas.ch/w/index.php?title=Filament_model#Programmatically\| operate]] on them the same geometric computation.		Reproduce with the command line the [[Walkthrough model worfklow reuse \| technique ]] of addressing sets of models that already contain points to [[https://wiki.dynamo.biozentrum.unibas.ch/w/index.php?title=Filament_model#Programmatically\| operate]] on them the same geometric computation.
		+
		+	== Alignment ==
		+
		+	=== Ribosomes from noise ===
		+
		+	You have access to a supercomputer (GPU). Generate a data set of particles containing pure noise (around 1K should be ok) and align them against a ribosome template.... can you reproduce the famouse "Einstein from noise" example out of these pure data particles?
		+
		+	Suggested tools: <tt>rand</tt>, <tt>dwrite</tt>.

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 Use subboxing tools to produce a ''subboxing table'' that can crop the directly the subboxes from the original tomograms.
-==Models manipulation==
+==Model manipulation==
 === Command line manipulation of sets of models ===

← Older revision		Revision as of 15:23, 16 August 2016
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	Task:		Task:
	Use subboxing tools to produce a ''subboxing table'' that can crop the directly the subboxes from the original tomograms.		Use subboxing tools to produce a ''subboxing table'' that can crop the directly the subboxes from the original tomograms.
		+
		+	== Models ==
		+
		+	=== Command line manipulation of sets of models ===
		+
		+	This is a very common situation: you want to apply a set of predefined actions onto a set of predefined models. We know that we can do it with the approach of saving a ''Model workflow'' and applying them later on a set of models defined inside the ''Catalogue'' manager <tt>dcm</tt>. This technique may proof inflexible in some situations, as its foresee model workflows as predefined sets of actions onto a model.

@@ Line 1: / Line 1: @@
 == General tools ==
-=== Average ===
 Create an average given a table and a data folder, programmatically.
 == Particle extraction==

← Older revision		Revision as of 14:28, 16 August 2016
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	=== Importing annotations for a single tomogram===		=== Importing annotations for a single tomogram===

		+	You have a tomogram and a text file with 3D coordinates. It's a simple situation, so you don't want to use the ''Catalogue'' to crop particles from the tomogram in the positions indicated by the file.
		+
		+	* How can you create a data folder and a table?
		+	* What if the coordinates in your file correspond to a binned tomogram?
		+	* What if you have a second file indicating an euler triplet of orientations for each particle?

	=== Importing annotations for several catalogued tomograms===		=== Importing annotations for several catalogued tomograms===