Helical symmetry - Revision history

Daniel Castaño at 13:32, 1 June 2016

2016-06-01T13:32:34Z

Daniel Castaño: /* Helical operator syntax */

2016-06-01T12:40:24Z

Helical operator syntax

Daniel Castaño at 12:40, 1 June 2016

2016-06-01T12:40:04Z

Daniel Castaño: /* Helical operator syntax */

2016-06-01T12:39:49Z

Helical operator syntax

Daniel Castaño at 12:38, 1 June 2016

2016-06-01T12:38:46Z

Daniel Castaño at 12:36, 1 June 2016

2016-06-01T12:36:41Z

Daniel Castaño at 12:35, 1 June 2016

2016-06-01T12:35:10Z

Daniel Castaño at 12:32, 1 June 2016

2016-06-01T12:32:16Z

Daniel Castaño: Created page with " ==Symmetrizing a particle== ===Helical operator syntax=== Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}: `vh = dsym(v,);` w..."

2016-06-01T12:16:50Z

Created page with " ==Symmetrizing a particle== ===Helical operator syntax=== Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}: <tt> vh = dsym(v,<operator>);</tt> w..."

New page

==Symmetrizing a particle==

===Helical operator syntax===
Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}:

<tt> vh = dsym(v,<operator>);</tt>

where {{t|operator}} represents any symmetry operator. The syntax for helical operators is:
<tt>h [<phi>,<dz>,<repetitions[optional]>,<rotational symmetry[optional]>]}} </tt>

Here:
* phi is the angular increment in degrees
* dz is the axial rise in pixels
* the number of repetitions
* additional Cn rotation to account for n-start helices

== Using symmetrization in alignment projects==

The simplest way is to input one operator with the syntax described [[#Helical operator syntax above]] in the {{t|Numerical settings}} area of the [[dcm GUI]].

This allows to impose a given symmetrization. In order to ''estimate'' the symmetry, you will need to create a plugin.

← Older revision		Revision as of 13:32, 1 June 2016
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	This allows to impose a given symmetrization. In order to ''estimate'' the symmetry, you will need to create a plugin.		This allows to impose a given symmetrization. In order to ''estimate'' the symmetry, you will need to create a plugin.
		+
		+	== Estimating the helical symmetry of a density map==
		+
		+	You can use the command {{docfunction\|dynamo_symmetry_scan\| dynamo_symmetry_scan}}.
		+
		+	This command operates by creating a matrix of symmetrization opertors, and comparing the transformed volumes with the original one. The transform that produces the highest cross correlation is considered the best match.

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 * <tt>phi</tt> is the angular increment in degrees
 * <tt>dz</tt> is the axial rise in pixels
-* the number of [[#Number of repetitions | repetitions]] (defaults to the maximum definible for a given volume).
+* the number of [[#Number of repetitions | repetitions]] (defaults to the maximum definible for a given volume). <br /> Can be passed as 0 to force ''Dynamo'' to create a default value.
 * additional Cn rotation to account for n-start helices.

@@ Line 15: / Line 15: @@
 * <tt>dz</tt> is the axial rise in pixels
 * the number of [[#Number of repetitions | repetitions]] (defaults to the maximum definible for a given volume).
-<br /> Can be passed as 0 to force ''Dynamo'' to create a default value.
+;; Can be passed as 0 to force ''Dynamo'' to create a default value.
 * additional Cn rotation to account for n-start helices.

@@ Line 15: / Line 15: @@
 * <tt>dz</tt> is the axial rise in pixels
 * the number of [[#Number of repetitions | repetitions]] (defaults to the maximum definible for a given volume).
-** Can be passed as 0 to force ''Dynamo'' to create a default value.
+<br /> Can be passed as 0 to force ''Dynamo'' to create a default value.
 * additional Cn rotation to account for n-start helices.

@@ Line 11: / Line 11: @@
 Here:
 * <tt>phi</tt> is the angular increment in degrees
 * <tt>dz</tt> is the axial rise in pixels
@@ Line 18: / Line 19: @@
 Example:
   <tt> vh = dsym(v,'h[15.6,4.7]');</tt>
   <tt> vh = dsym(v,'h[15.6,4.7,5]');</tt>       % uses 5 repetitions
   <tt> vh = dsym(v,'h[15.6,4.7,5,8]');</tt>    % uses 5 repetitions and adds a C8 symmetrization
-  <tt> vh = dsym(v,'h[15.6,4.7,0,8]');</tt>    % computes internally the maximum of repetitions and creates a C8 symmetrization
+  <tt> vh = dsym(v,'h[15.6,4.7,0,8]');</tt>    % computes internally the maximal number of repetitions
 == Using symmetrization in alignment projects==
@@ Line 31: / Line 33: @@
 == Number of repetitions ==
-Symmetrization of a volume is computed by applying the transformation (phi,dz) in both directions  to  the original volume a number of times (called ''repetitions'') and then averaging the result.  For instance, 17 repetitions imply 8 subsequent applications of (phi,dz) to the original volume and 8 application of -(phi,dz).
+Symmetrization of a volume is computed by applying onto  the original volume the transformation (phi,dz) repeatedly in both directions a number of times (called ''repetitions'').  The transformed volumes are averaging together.  For instance, 17 repetitions imply 8 subsequent applications of (phi,dz) to the original volume and 8 applications of -(phi,dz).
 Each time (phi,dz) is applied, the transformed volume will have a "bottom" of dz layers of pixels that are undefined: (they correspond to the theoretically part of the infinite helix below our volume). The averaging procedure will discard contributions of such pixels. As a result, the central area of the symmetrized volume will be representing contributions of more transformed volumes, attaining thus a higher SNR.
 If the user does not specify a number of repetitions, ''Dynamo'' will take the maximal number of repetitions for the given volume. If the volume is of size {{t|N}} pixels and the operator carries an axial rise of {{t|dz}} pixels, the maximal number of translations along the z axis is <tt>floor(N/dz)</tt>

@@ Line 13: / Line 13: @@
 * phi is the angular increment in degrees
 * dz is the axial rise in pixels
-* the number of repetitions
+* the number of [[#Number of repetitions | repetitions]] (defaults to the maximum definible for a given volume)
 * additional Cn rotation to account for n-start helices
@@ Line 22: / Line 22: @@
 This allows to impose a given symmetrization. In order to ''estimate'' the symmetry, you will need to create a plugin.

Helical symmetry - Revision history

Daniel Castaño at 13:32, 1 June 2016

Daniel Castaño: /* Helical operator syntax */

Daniel Castaño at 12:40, 1 June 2016

Daniel Castaño: /* Helical operator syntax */

Daniel Castaño at 12:38, 1 June 2016

Daniel Castaño at 12:36, 1 June 2016

Daniel Castaño at 12:35, 1 June 2016

Daniel Castaño at 12:32, 1 June 2016

Daniel Castaño: Created page with " ==Symmetrizing a particle== ===Helical operator syntax=== Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}: vh = dsym(v,); w..."

Daniel Castaño: Created page with " ==Symmetrizing a particle== ===Helical operator syntax=== Symmetrizing a helical particle can be done with the usual tool {{t|dsym}}: `vh = dsym(v,);` w..."