Crop a structure and the optional volume data inside a given geometry.
||Molecular structure data.
||The volume data. Beware that the uniform field has been skewed, using xform, to match the unit cell.
|Select crop center
||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.
||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
||Position of the crop center respect to the unit cell base vector.
|Select crop shape
||Select the cropping geometry:
- 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.
- A block of given sides rotated by given angles from XYZ axis.
||Make visible the geometry on the obj output.
||Enablin the cropping action.
||Reverse inside and outside.
||Set the geometry parameters specific for each shape (see above).
||The cropped molecular structure data.
||The cropped volume data.
||The cropping geometry.