pdbTrans

pdbTrans is Eos's Command that that performs Affine Transform of PDB file.

List of option

Main option

Option	Essential/Optional	Description	Default
-i	Essential	Input: PDB	NULL
-o	Essential	Output: PDB	NULL
-M	Optional	Matrixfile: ASCII(4x4 Matrix)	NULL
-EA	Optional	Euler Angle	Mode　0.0　0.0　0.0
-c	Optional	ConfigurationFile	NULL
-m	Optional	Mode	0
-h	Optional	Help

-m details

Value	Description
0

-M format

data(0, 0) data(0, 1) data(0, 2) data(0, 3)
data(1, 0) data(1, 1) data(1, 2) data(1, 3)
data(2, 0) data(2, 1) data(2, 2) data(2, 3)
data(3, 0) data(3, 1) data(3, 2) data(3, 3)

You can create by using matrix3DFromEulerAngle.

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

*If both -M and -EA are set, -M is run at first, and -EA is run at next.

Execution example

Input file image

Input file details by pdbInfo

*There isn't difference between input and output by default.

Option -M

Example1: coordinate transformation by Shear at x-axis

Matrix file data

       1.000000        1.000000        1.000000        0.000000
       0.000000        1.000000        0.000000        0.000000
       0.000000        0.000000        1.000000        0.000000
       0.000000        0.000000        0.000000        1.000000
			

Output image

Example2: coordinate transformation by Reflecting at XY-plane

Matrix file data

       1.000000        0.000000        0.000000        0.000000
       0.000000        1.000000        0.000000        0.000000
       0.000000        0.000000        -1.000000        0.000000
       0.000000        0.000000        0.000000        1.000000
			

Output image

Example3: coordinate transformation by Rotation at x-axis

Matrix file data

       1.000000        0.000000        0.000000        0.000000
       0.000000        0.707107        -0.707107        0.000000
       0.000000        0.707107        0.707107        0.000000
       0.000000        0.000000        0.000000        1.000000
			

Output image

Example4: coordinate transform by parallel transformation along x-axis

Matrix file data

       1.000000        0.000000        0.000000        1.000000
       0.000000        1.000000        0.000000        0.000000
       0.000000        0.000000        1.000000        0.000000
       0.000000        0.000000        0.000000        1.000000
			

Output image

Option -EA

Option -EA ZONS 30 30 30

*White…Input image, Pink…Output image