Per-Model Clipping

Per-Model Clipping example Per-Model Clipping allows different models to be clipped in different ways. Unlike the global clipping planes shown in the Side View, a per-model clipping plane:

acts on only one model
can be placed at any angle relative to the line of sight

While the global clipping planes are a hither-yon (front-back) pair, a per-model clipping plane is a single plane that separates the visible and invisible portions of a model; whether it behaves like a "front" or "back" depends on the direction it is facing. There can be a different per-model clipping plane for each model. For the purposes of Per-Model Clipping, a molecular surface and the structure it is based on are separate models even though they share a model number.

There are several ways to start Per-Model Clipping, a tool in the Graphics category; it can also be started by choosing clipping... from the Model Panel.

The Model pulldown menu shows the current model and allows switching between models. Activating Enable clipping turns on a clipping plane for the current model. The plane's starting position is perpendicular to the line of sight with its center of rotation at the current center of view; the visible portion of the model is behind the plane.

The clipping plane can be moved with the mouse and/or by using:

Orient plane - place the plane perpendicular to the line of sight with its center of rotation at the current center of view, with the visible portion of the model behind the plane
Flip plane - flip the plane so that the previously visible portion of the model is invisible and vice versa
Align plane - align the clipping plane with that of another model (chosen from the pulldown menu); both planes must be enabled

MOUSE MODES

Activating Adjust clipping with mouse as below allows the clipping plane to be moved independently with the mouse. The Clip Motion Assignments determine which buttons are used. Translation moves the plane along its normal without changing the angle; the direction of translation caused by a particular cursor motion depends on the angle of the plane. Rotation changes the angle of the plane, with cursor control similar to that of standard rotation. During such manipulations, the plane's position is illustrated with a semitransparent disk. The plane-controlling mouse modes are shown in the Mouse preferences after Per-Model Clipping has been started.

Changing the current model turns off mouse control of the previous model's clipping plane. When mouse control is turned off for all per-model clipping planes, the mouse buttons return to their previous functions (as shown in the Mouse preferences). During standard rotation and translation operations, each per-model clipping plane will move along with its associated model. If a model is not active, neither it nor its clipping plane will move.

Close closes the Per-Model Clipping interface and turns off mouse control of all per-model clipping planes. Any per-model planes that have been enabled, however, will remain enabled until explicitly disabled (by unchecking Enable clipping). Help opens this manual page in a browser window.

INVISIBLE REGIONS

Portions of a model that are invisible because of clipping (but would otherwise be visible) are considered displayed for the purposes of:

center of rotation determination using the center of models method (default; ~cofr)
center of rotation determination from specified atoms (cofr with an atom-spec argument, focus, and Actions... Focus)
view adjustment with window, focus, and Actions... Focus

Items that are invisible simply because they fall outside the view (for example, off to the side) are also considered displayed.

UCSF Computer Graphics Laboratory / October 2004