Multireference alignment - Revision history

Daniel Castaño: /* Random subset averaging */

2018-06-06T20:58:42Z

Random subset averaging

Daniel Castaño: /* Random subset averaging */

2018-06-06T20:58:22Z

Random subset averaging

Daniel Castaño: /* Random subset averaging */

2018-06-06T20:58:03Z

Random subset averaging

Daniel Castaño: /* The process of multireference alignment */

2016-05-23T09:19:14Z

The process of multireference alignment

Daniel Castaño at 10:44, 25 April 2016

2016-04-25T10:44:13Z

Daniel Castaño at 10:36, 25 April 2016

2016-04-25T10:36:58Z

Daniel Castaño: /* The process of multireference alignment */

2016-04-25T10:36:42Z

The process of multireference alignment

Daniel Castaño at 10:26, 25 April 2016

2016-04-25T10:26:28Z

Daniel Castaño at 10:25, 25 April 2016

2016-04-25T10:25:55Z

Daniel Castaño at 10:18, 25 April 2016

2016-04-25T10:18:30Z

@@ Line 43: / Line 43: @@
 ==== Random subset averaging ====
 You can use an avialable table and data folder and construct averages taking N-different subsets of particles. This can be performed with an order like:
   <tt> dynamo_write_multireference(myTable,'table',myFolder,'refs',1:4,'data',myData,'subset',M/4); </tt>
 will create 4 subsets of particles each containing ''M''/4 particles  (''M'' being the number of valid particles in the table), produce 4 averages, store  the files in {{t|myFolder}} and format the individual file names so as to follow the [[#Input format|appropriate convention]]

@@ Line 44: / Line 44: @@
 You can use an avialable table and data folder and construct averages taking N-different subsets of particles. This can be performed with an order like:
-TBI
+ <tt>
 dynamo_write_multireference(myTable,'table',myFolder,'refs',1:4,'data',myData,'subset',M/4);
 </tt>

@@ Line 42: / Line 42: @@
 ==== Random subset averaging ====
-You can use an avialable table and data folder and construct averages taking N-different subsets of particles. This can be performed with an order leike:
+You can use an avialable table and data folder and construct averages taking N-different subsets of particles. This can be performed with an order like:
 TBI
@@ Line 48: / Line 48: @@
 dynamo_write_multireference(myTable,'table',myFolder,'refs',1:4,'data',myData,'subset',M/4);
 </tt>
 will create 4 subsets of particles each containing ''M''/4 particles  (''M'' being the number of valid particles in the table), produce 4 averages, store  the files in {{t|myFolder}} and format the individual file names so as to follow the [[#Input format|appropriate convention]]
 == Output ==

@@ Line 7: / Line 7: @@
 == The process of multireference alignment ==
-If you have R references and N particles, each particle will be aligned against all the R references. The particle will produce R different cross-correlation scores and R different sets of alignment pararameters. Thus, ''Dynamo''will produce R different [[Refined table|refinement tables]], each for one ''reference channel''.
+If you have R references and N particles, each particle will be aligned against all the R references. The particle will produce R different cross-correlation scores and R different sets of alignment pararameters. Thus, ''Dynamo'' will produce R different [[Refined table|refinement tables]], each for one ''reference channel''.
-Each particle will have a single reference yielding the maximal cc score.
+Each particle will thus appear on all tables, but it  will yield a  maximal cross-correlation score in one of them... informally, the particle  ''chooses'' that reference in the current iteration. When computing the averages that will serve as templates for the next iteration, only those particles that "choose" a given reference will contribute to the average in that reference channel.
 == Masks ==

← Older revision		Revision as of 10:44, 25 April 2016
Line 53:		Line 53:
	== Output ==		== Output ==
	You will get a different [[refined table]] and [[iteration average]] for each reference channel and iteration.		You will get a different [[refined table]] and [[iteration average]] for each reference channel and iteration.
		+
		+	===Fast command line access===
		+	The {{t\|ddb}} command is probably the easiest way of accessing the different results in a multireference alignment .
		+
		+	===Swapping history===
		+
		+	It is usually a good idea to check how the particle membership evolves during the iteration procedure. A healthy multireference alignment registers many particle swaps between reference channels in the first iterations. This swapping should decrease gradually until the different channels just evolver independently.
		+	This can be checked through the GUI with ''dcp GUI > show > Multireference''

← Older revision		Revision as of 10:36, 25 April 2016
Line 10:		Line 10:

	Each particle will have a single reference yielding the maximal cc score.		Each particle will have a single reference yielding the maximal cc score.
−

	== Masks ==		== Masks ==

@@ Line 49: / Line 49: @@
 dynamo_write_multireference(myTable,'table',myFolder,'refs',1:4,'data',myData,'subset',M/4);
 </tt>
-will create 4 subsets of particles each containing M/4 particles  (''M'' being the number of valid particles in the table), produce 4 averages, store  the files in {{t|myFolder}} and format the individual file names so as to follow the [[# Input format|appropriate convention]]
+will create 4 subsets of particles each containing M/4 particles  (''M'' being the number of valid particles in the table), produce 4 averages, store  the files in {{t|myFolder}} and format the individual file names so as to follow the [[#Input format|appropriate convention]]
 == Output ==
 You will get a different [[refined table]] and [[iteration average]] for each reference channel and iteration.

@@ Line 19: / Line 19: @@
 == Input format ==
-Introducing project elements (template, tables) for MRA projects is slightly different than introducing them for single reference projects. You can use a .sel file, or pass a folder, where files need to stick to a given naming convention.
+Introducing project elements (template, tables) for MRA projects is slightly different than introducing them for single reference projects. You can use a .sel file, or pass a folder, where individuals files need to stick to a given naming convention. Each reference number is given by a three figure zero padded integer starting with zero.
 <tt>
-   <folder seeds>/template_initial_ref_001.em
+ <folder seeds>/template_initial_ref_001.em
-   <folder seeds>/fmask_initial_ref_001.em
+ <folder seeds>/fmask_initial_ref_001.em
-   <folder seeds>/table_initial_ref_001.em
+ <folder seeds>/table_initial_ref_001.em
 </tt>
 ===Tables===
@@ Line 41: / Line 43: @@
 ==== Random subset averaging ====
-You can use an avialable table and data folder and construct averages taking N-different subsets of particles. This can be performed with the order:
+You can use an avialable table and data folder and construct averages taking N-different subsets of particles. This can be performed with an order leike:
 TBI
 <tt>
-dynamo_write_multireference(myTable,'table',myProject,'refs',1:4,'data',myData,'subset',M/4);
+dynamo_write_multireference(myTable,'table',myFolder,'refs',1:4,'data',myData,'subset',M/4);
 </tt>
 == Output ==
 You will get a different [[refined table]] and [[iteration average]] for each reference channel and iteration.