Difference between revisions of "Pdf tutorials"
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(Created page with " ==Catalogues and particle picking== * General catalogue {{pdftutorial|catalogue_introduction|link}}. * Introduction to particle picking {{pdftutorial|click_particles|link...") |
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| − | + | We have written some detailed walkthroughs for selected specific tasks. Keep in mind that some of them might include commands or GUIs that have been superseded with more modern tools inside ''Dynamo''. We keep these tutorials until we document the new functionalities. | |
==Catalogues and particle picking== | ==Catalogues and particle picking== | ||
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* General catalogue {{pdftutorial|catalogue_introduction|link}}. | * General catalogue {{pdftutorial|catalogue_introduction|link}}. | ||
* Introduction to particle picking {{pdftutorial|click_particles|link}}. | * Introduction to particle picking {{pdftutorial|click_particles|link}}. | ||
| − | * Specific tools for filaments | + | * Specific tools for filaments {{pdftutorial|modelFilament|link}} |
| − | * Specific tools for freely shaped membranes | + | * Specific tools for freely shaped membranes {{pdftutorial|modelMembrane|link}} |
* Model combinations {{pdftutorial|click_particles_with_filaments_as_reference|link}} | * Model combinations {{pdftutorial|click_particles_with_filaments_as_reference|link}} | ||
| + | |||
| + | ==Initial templates== | ||
| + | Some hints for setting up of a project demonstrated for a real data set of subtomograms {{pdftutorial|flagelarMotors|link}}. | ||
==Classification== | ==Classification== | ||
| − | * Introduction to PCA {{pdftutorial| classification_tutorial |link}} | + | * Introduction to PCA {{pdftutorial|classification_tutorial|link}} |
| − | |||
==Subboxing== | ==Subboxing== | ||
By ''subboxing'' we refer to the extraction and realignment of subunits out of aligned subtmograms. | By ''subboxing'' we refer to the extraction and realignment of subunits out of aligned subtmograms. | ||
| − | * General subboxing {{pdftutorial| subboxing |link}} | + | * General subboxing {{pdftutorial|subboxing|link}} |
* Symmetry and subboxing {{pdftutorial| subboxing_symmetry |link}} | * Symmetry and subboxing {{pdftutorial| subboxing_symmetry |link}} | ||
| − | * Subboxing and classification {{pdftutorial| subboxing_multireference_PCA |link}} | + | * Subboxing and classification {{pdftutorial| subboxing_multireference_PCA|link}} |
==Command line operations== | ==Command line operations== | ||
| − | {{pdftutorial| commandline |link}} | + | * For general manipulation of tables and volumes {{pdftutorial|commandline|link}} |
| − | {{pdftutorial| command_line_projects |link}} | + | * in alignment projects {{pdftutorial|command_line_projects|link}} |
| − | {{pdftutorial| commandline_classification |link}} | + | * in classification projects {{pdftutorial|commandline_classification|link}} |
| − | |||
| − | == | + | ==Miscellaneous== |
| − | * Formatting data folders {{pdftutorial| formatting_data |link}} | + | * Formatting data folders {{pdftutorial| formatting_data|link}} |
| − | * Tools to scan convergence: {{pdftutorial| convergence |link}} | + | * Tools to scan convergence: {{pdftutorial| convergence|link}} |
| − | * Writting customized extensions of ''Dynamo'': {{pdftutorial| database_plugins_guidelines |link}} {{pdftutorial| multireference_plugins |link}} | + | * Writting customized extensions of ''Dynamo'': {{pdftutorial| database_plugins_guidelines|link}} {{pdftutorial|multireference_plugins|link}} |
Latest revision as of 12:19, 29 April 2016
We have written some detailed walkthroughs for selected specific tasks. Keep in mind that some of them might include commands or GUIs that have been superseded with more modern tools inside Dynamo. We keep these tutorials until we document the new functionalities.
Contents
Catalogues and particle picking
- General catalogue link.
- Introduction to particle picking link.
- Specific tools for filaments link
- Specific tools for freely shaped membranes link
- Model combinations link
Initial templates
Some hints for setting up of a project demonstrated for a real data set of subtomograms link.
Classification
- Introduction to PCA link
Subboxing
By subboxing we refer to the extraction and realignment of subunits out of aligned subtmograms.
- General subboxing link
- Symmetry and subboxing subboxing_symmetry .pdf link
- Subboxing and classification subboxing_multireference_PCA.pdf link
Command line operations
- For general manipulation of tables and volumes link
- in alignment projects link
- in classification projects link
Miscellaneous
- Formatting data folders formatting_data.pdf link
- Tools to scan convergence: convergence.pdf link
- Writting customized extensions of Dynamo: database_plugins_guidelines.pdf link link
