Difference between revisions of "Averaging of subtomograms"
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From the operative point of view, the particles are stored in a [[data folder]], which are indexed by a [[table]]. | From the operative point of view, the particles are stored in a [[data folder]], which are indexed by a [[table]]. | ||
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== Through the command line == | == Through the command line == | ||
To operate manually averages of particles (given an available [[table|metadata]]), use the {{t|daverage}} command, or its GUI version {{t|dvarage_GUI}}. {{docfunction|dynamo_average|daverage}} | To operate manually averages of particles (given an available [[table|metadata]]), use the {{t|daverage}} command, or its GUI version {{t|dvarage_GUI}}. {{docfunction|dynamo_average|daverage}} | ||
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== Inside an alignment project == | == Inside an alignment project == | ||
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There are different project parameters that can be used to modify the default behaviour of the {{t|daverage}} command used inside an alignment project. | There are different project parameters that can be used to modify the default behaviour of the {{t|daverage}} command used inside an alignment project. | ||
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| + | ===Parallelism=== | ||
| + | It is possible to select the number of cores that will be used during the ''averaging''. The project parameter is called <tt>matlab_workers_average</tt> (shortform <tt>mwa</tt>), and can be modified also in [[dcp GUI]] (in the section of environment variables). | ||
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| + | This option is available for computations on a single server with several cores. It will not work for the current MPI implementation. | ||
Revision as of 12:05, 27 October 2017
Averaging of subtomograms means applying an available set of alignment parameters onto a set of data particles and adding them together. Because of the missing wedge, a compensation in the Fourier space is operated during this step.
From the operative point of view, the particles are stored in a data folder, which are indexed by a table.
Through the command line
To operate manually averages of particles (given an available metadata), use the daverage command, or its GUI version dvarage_GUI. daverage
Inside an alignment project
At the end of each iteration, the refined table generated by Dynamo is used to produce an average, which will be used as starting template in the next iteration.
There are different project parameters that can be used to modify the default behaviour of the daverage command used inside an alignment project.
Parallelism
It is possible to select the number of cores that will be used during the averaging. The project parameter is called matlab_workers_average (shortform mwa), and can be modified also in dcp GUI (in the section of environment variables).
This option is available for computations on a single server with several cores. It will not work for the current MPI implementation.
