Subboxing - Revision history

Daniel Castaño: /* Icosahedral symmetry */

2017-10-26T15:54:26Z

Icosahedral symmetry

Daniel Castaño at 13:01, 26 October 2017

2017-10-26T13:01:36Z

Daniel Castaño at 11:01, 26 October 2017

2017-10-26T11:01:18Z

Daniel Castaño: Created page with "Subboxing is the technique of locating the position of subunits inside ''data'' particles. When an average is available, is possible to express the positions of the subunits..."

2017-10-26T10:31:08Z

Created page with "Subboxing is the technique of locating the position of subunits inside ''data'' particles. When an average is available, is possible to express the positions of the subunits..."

New page

Subboxing is the technique of locating the position of subunits inside ''data'' particles.
When an average is available, is possible to express the positions of the subunits of interest with relation to the center of the average. Then, the alignment [[table]] that produced the average can be used to produce a ''subboxed table'' that locates the subunits in the data. This subboxed table can be used to recrop a new [[data folder]], in which each particle file will contain a subunit.

== Orientation of subboxed particles ==

Each subboxed particle file will contain a subunit. The density map particle itself is stored (as always in ''Dynamo'') without any rotation: the fact the different subunits will (possibly) have different orientations will always be expressed through the metadata, that is, it will be reflected in the subboxed table.

== Creation of subboxed tables ==

The fundamental command is <tt>dsubboxing_table</tt>

<tt>sbt = dynamo_subboxing_table(table',centeredPoint); </tt>

Here, the <tt>centeredPoint</tt> point is expressed in relation to the [[Volume center | center point]] of the average.

← Older revision		Revision as of 15:54, 26 October 2017
Line 43:		Line 43:

	<tt> subboxedTable = dynamo_subboxing_table(table, locationPenton,'sym','ico_vertex'); </tt>		<tt> subboxedTable = dynamo_subboxing_table(table, locationPenton,'sym','ico_vertex'); </tt>
		+
		+	=== Custom symmetry ===
		+	It is possible to pass a text file containing all symmetry operators, expressed as matrices.

← Older revision		Revision as of 13:01, 26 October 2017
Line 20:		Line 20:
	<tt>subboxedTable = dynamo_subboxing_table(table,centeredPoint,'sym',symmetryOperator); </tt>		<tt>subboxedTable = dynamo_subboxing_table(table,centeredPoint,'sym',symmetryOperator); </tt>

−	There are different values that can be used as symmetry operator: <tt>'Cn'</tt>, <tt>'Dn'</tt>,<tt>'ico'</tt>,<tt>'ico_vertex'</tt>.	+	There are different values that can be used as symmetry operator: <tt>'Cn'</tt>, <tt>'Dn'</tt>,<tt>'ico'</tt>,<tt>'ico_vertex'</tt>. The position of the symmetry axes is fixed by convention on each case.
		+
		+	=== Cn symmetry ===
		+
		+	The symmetry axis goes along the direction ''z'' and passes through the [[Volume center \| center of the volume ]]
		+
		+	=== Icosahedral symmetry ===
		+
		+	==== Pentons ====
		+
		+	Pentons are centered on the C5 symmetry axes of the particle. As the orientation is defined by the convention, it is only necessary to provide the distance of a reference penton to the center.
		+
		+	The 12 orientations can be computed as:
		+
		+	<tt>pentonNormals = dpkgeom.symmetry.ico.directionsC5Axises();</tt>
		+
		+	Then, the location of a penton situated <tt>r</tt> pixels away is simply given by
		+
		+	<tt>locationPenton = r*pentonNormals(1,:);</tt>
		+
		+	for position 1 (arbitrarily chosen). Then, the subboxed table can be computed:
		+
		+	<tt> subboxedTable = dynamo_subboxing_table(table, locationPenton,'sym','ico_vertex'); </tt>

@@ Line 10: / Line 10: @@
 The fundamental command is <tt>dsubboxing_table</tt>
-  <tt>sbt = dynamo_subboxing_table(table',centeredPoint); </tt>
+  <tt>subboxedTable = dynamo_subboxing_table(table,centeredPoint); </tt>
 Here, the <tt>centeredPoint</tt> point is expressed in relation to the [[Volume center | center  point]]  of the average.