Crop Structure

Description

Crop a structure and the optional volume data inside a given geometry.

Input Ports

structure_in MoleculeType Molecular structure data.
fld_in Field_Unif The volume data. Beware that the uniform field has been skewed, using xform, to match the unit cell.

Parameters

Select crop center radio buttons Select how the unit cell borders are rendered on screen:
Specific atom
Select one atom as the crop center. Below the "Select atoms" widget is visible.
Fractional coordinates
Select the fractional coordinates of the crop center. Below the three sliders "a fraction", "b fraction" and "c fraction" are visible.
Select atoms atoms selection widget The list of atoms contained in the input structure. The list could show individual atoms or element types. A buttom permits clearing the selection. The freeze toggle disable the selection and make possible saving the selection in the application.
a (or b or c) fraction slider Position of the crop center respect to the unit cell base vector.
Select crop shape list Select the cropping geometry:
Sphere
A sphere of a given radius.
Tube XYZ
A cylinder of a given radius oriented along one of the XYZ axis (set by radio buttons).
Tube abc
A cylinder of a given radius oriented along one of the unit cell vectors (set by radio buttons).
Slab XYZ
A slab of a given tickness perpendicular to one of the XYZ axis (set by radio buttons).
Slab abc
A slab of a given tickness perpendicular to one of the unit cell vectors (set by radio buttons). The extent along the other two vectors is limited to the unit cell extent.
Axis aligned block
A block of given sides perpendicular to the XYZ axis.
Block
A block of given sides rotated by given angles from XYZ axis.
Show toggle Make visible the geometry on the obj output.
Crop toggle Enablin the cropping action.
Reverse toggle Reverse inside and outside.
Shape parameters various fields Set the geometry parameters specific for each shape (see above).

Output Ports

structure_out MoleculeType The cropped molecular structure data.
fld_out Field_Unif The cropped volume data.
obj DefaultObject The cropping geometry.
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