Alignment project - Revision history

Daniel Castaño at 07:41, 27 October 2017

2017-10-27T07:41:45Z

2017-09-15T07:45:48Z

In the standalone

2017-09-13T06:31:42Z

Creation of an alignment project

2017-09-13T06:31:12Z

Running from the command line

2017-09-13T06:30:43Z

Output of an alignment project

2017-09-13T06:30:27Z

In the standalone

2017-09-13T06:30:15Z

Running an alignment project

2017-07-06T08:15:45Z

Masks

2016-04-14T08:08:14Z

2016-03-17T11:49:23Z

@@ Line 9: / Line 9: @@
 An alignment project can contain one or several references. In this case, we are running a [[multireference alignment]] project that operates simultaneously alignment and classification.
 == Elements of an alignment project ==
@@ Line 25: / Line 24: @@
 ====Template====
 The initial density (or set of densities in a multiresolution project.), to be rotated multiple times against each one of the particles in the data folder.
 ====Table====
@@ Line 35: / Line 33: @@
 === Numerical Parameters ===
-They define the mathematical part of the project, in terms of sets of angles to scan, shifts to allow, used bandpass or binning options....
+They define the mathematical part of the project, in terms of sets of angles to scan, shifts to allow, used bandpass, [[multilevel refinement | angular refinement policy]] or binning options....
 === Environment Parameters===

@@ Line 78: / Line 78: @@
 <tt>myProject.bat</tt>
-in windows.
+in Windows.
 == Output of an alignment project ==

@@ Line 49: / Line 49: @@
 >> help dcp.new
 </code>
-Additionally, several utilities in ''Dynamo'' give you the option of creating
+Additionally, several utilities in ''Dynamo'' give you the option of creating projects from GUI interfaces.
 == Running an alignment project ==

@@ Line 65: / Line 65: @@
 ==== In Matlab ====
-Write the name of the project in the command line.
+Write the name of the project in the command line:
 <tt>myProject</tt>

← Older revision		Revision as of 06:30, 13 September 2017
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	The main result is the average computed at the last iteration. Besides, ''Dynamo'' stores in the project folder the results ([[table\|alignment parameters]], averages and other intermediate results, as [[Fourier compensation during averaging \| fourier occupancy maps]])		The main result is the average computed at the last iteration. Besides, ''Dynamo'' stores in the project folder the results ([[table\|alignment parameters]], averages and other intermediate results, as [[Fourier compensation during averaging \| fourier occupancy maps]])
−

	== Showing results of an alignment project ==		== Showing results of an alignment project ==

@@ Line 77: / Line 77: @@
 in linux/Mac, or
-<tt>./myProject.bat</tt>
+<tt>myProject.bat</tt>
 in windows.

@@ Line 55: / Line 55: @@
 Projects need to be [[Project checking|checked]] and [[Project unfolding|unfolded]] before they can be run.
-Once they are checked by Dynamo, a simple project script is produced, that can just be invoked in the command line or submitted to a queuing system. As the iterative process advances, many different results are created and stored in the project folder.
+Once they are checked by Dynamo, a simple project script  (''execution script'' ) is produced, that can just be invoked in the command line or submitted to a queuing system. As the iterative process advances, many different results are created and stored in the project folder.
 == Output of an alignment project ==

@@ Line 32: / Line 32: @@
 ====Masks====
-''Dynamo'' uses several masks. The most important is the [[alignment mask]]. The [[classification mask]] is only relevant for multireference analysis. The option for defininf a [[fourier mask on template]] is used in very few special cases. The [[smoothing mask]] is the one used for computing Fourier Shell Correlations.
+''Dynamo'' uses several masks. The most important is the [[alignment mask]]. The [[classification mask]] is only relevant for multireference analysis. The option for defining a [[fourier mask on template]] is used in very few special cases. The [[smoothing mask]] is the one used for computing Fourier Shell Correlations.
 === Numerical Parameters ===

← Older revision		Revision as of 08:08, 14 April 2016
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	Projects need to be [[Project checking\|checked]] and [[Project unfolding\|unfolded]] before they can be run.		Projects need to be [[Project checking\|checked]] and [[Project unfolding\|unfolded]] before they can be run.
	Once they are checked by Dynamo, a simple project script is produced, that can just be invoked in the command line or submitted to a queuing system. As the iterative process advances, many different results are created and stored in the project folder.		Once they are checked by Dynamo, a simple project script is produced, that can just be invoked in the command line or submitted to a queuing system. As the iterative process advances, many different results are created and stored in the project folder.
		+
		+
		+	== Output of an alignment project ==
		+
		+	The main result is the average computed at the last iteration. Besides, ''Dynamo'' stores in the project folder the results ([[table\|alignment parameters]], averages and other intermediate results, as [[Fourier compensation during averaging \| fourier occupancy maps]])

← Older revision		Revision as of 11:49, 17 March 2016
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	The project is also used to design the operations carried on the particles, to select and configure the environment where the actual computations will occur, to start the computations and to access and visualize the results.		The project is also used to design the operations carried on the particles, to select and configure the environment where the actual computations will occur, to start the computations and to access and visualize the results.
		+
		+	An alignment project can contain one or several references. In this case, we are running a [[multireference alignment]] project that operates simultaneously alignment and classification.