Difference between revisions of "mrc3Dto2D"

Revision as of 06:08, 15 July 2014 (view source) Kinoshita (Talk | contribs) (Created page with "'''mrc3Dto2D''' is Eos's Command that creates 2D Image from 3D Image. In this case, 3D image refers to the reference image mainly, 2D image refers ...")		Latest revision as of 05:09, 30 July 2014 (view source) Kinoshita (Talk | contribs) (→‎Rotation Order details)
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	<td>-EulerMode</td>		<td>-EulerMode</td>
	<td>Optional</td>		<td>Optional</td>
−	<td>Rotaion mode of [[Euler angle]]</td>	+	<td>Rotaion mode of [[Euler Angle]]</td>
	<td>ZOYS</td>		<td>ZOYS</td>
	</tr>		</tr>
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	</table>		</table>
	<br>		<br>
−		+
	=== -m details ===		=== -m details ===
	<table border="1">		<table border="1">
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	<br>		<br>
−	=== [[Rotation Order]] details ===	+	=== [[Euler Angle|Rotation Order]] details ===
	<pre>		<pre>
	1st digit: Setting the rotation axis of the first		1st digit: Setting the rotation axis of the first
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	== Execution example ==		== Execution example ==
−	===Input file image===	+	===Input file's image===
	[[File:121p.png]]		[[File:121p.png]]
−	Details of the input file as seen by [[pdbInfo]].	+	Details for the input file by [[pdbInfo]].
	[[File:121p-Info.png]]		[[File:121p-Info.png]]
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	<br>		<br>
−	<div>Setting at 0 180 30 to Rot of all later.</div>	+	<div>In the following, Setting at 0 180 30 to Rot of all.</div>
	<br>		<br>

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Latest revision as of 05:09, 30 July 2014

mrc3Dto2D is Eos's Command that creates 2D Image from 3D Image. In this case, 3D image refers to the reference image mainly, 2D image refers to the projected image mainly. It is possible to acquire the projected image of the various angles from the crystal structure (PDB file) or similar structure. Projected image output is used to determine the angle of the particles in a single particle analysis.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: mrcImage(3D)	NULL
-o	Essential	Output: mrcImage(2DSet)	NULL
-Rot1	Optional	1st Rotation	0.0 360.0 10
-Rot2	Optional	2nd Rotaion	0.0 360.0 10
-Rot3	Optional	Last Rotaion	0.0 360.0 10
-EulerMode	Optional	Rotaion mode of Euler Angle	ZOYS
-InterpolationMode	Optional	Interpolation mode	1
-AreaMode	Optional	AreaMode：Form of the whole space to be projected 0: square 1: sphere	0
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0	Projection by the number of all.
1	Reducing the number of projections in accordance with the rotation angle. Axis nRot3=1 and Rot2 if is perpendicular to the 2D image plane, it is possible to reduce the number of projections.

-InterpolationMode details

Setting of Interpolation Mode.

Value	Description
0	Nearest neighbor method
1	Bi-linear interpolation method
2	Cubic convolution method
3	Polynomial interpolation method

Rotation Order details

1st digit: Setting the rotation axis of the first
2nd digit: Setting the order-1 of the rotation axis
	O: Order Z -> Y-> X 
	E: Order Z -> X-> Y 
3rd digit: Setting the order-2 of the rotation axis
	Y: Keep the order
	N: Reverse the order
4th digit: Setting rotation method
	S: Rotate the object
	N: Move the coordinates

Execution example

Input file's image

Details for the input file by pdbInfo.

Converting to mrcImage file(3D) by pdb2mrc.

XY-plane	YZ-plane

Example of options only essential

Min Max Mean SD SE

0 0.186008 0.00302756 0.0128325 7.12722e-07

Option -Rot1 -Rot2 -Rot3

XY-plane	YZ-plane
		Min Max Mean SD SE	0 0.175 0.00302838 0.0129759 8.75794e-06

Option -EulerMode

XY-plane	YZ-plane
		Min Max Mean SD SE	0 0.175 0.00303008 0.0129694 8.75351e-06

Option -InterpolationMode

InterpolationMode: 0

Min Max Mean SD SE

0 0.2125 0.00301082 0.0137354 9.27052e-06

InterpolationMode: １

Min Max Mean SD SE

0 0.175 0.00302838 0.0129759 8.75794e-06

InterpolationMode: 2

Min Max Mean SD SE

-0.0325619 0.213961 0.00302793 0.0137247 9.26332e-06

InterpolationMode: 3

Min Max Mean SD SE

-5.4667 184.383 3.28548 13.7206 0.00926055