Surface Zone restricts the display of surface models and their caps to zones around selected atoms or markers. For Volume Viewer surfaces, the Zone feature in the volume dialog is more efficient; it limits contouring calculations to the region containing the zone. Surface Zone information is included in saved sessions. See also: Color Zone, bondzone, zonesel
There are several ways to start Surface Zone, a tool in the Surface/Binding Analysis category. It is also implemented as the command sop zone.
The Surface of interest should be chosen from the list of available surface models. Surfaces from Multiscale Models will be named for the PDB file from which the surfaces were generated.
Clicking Zone limits the display of the chosen surface to areas within a specified distance (Radius) of any selected atoms. Surfaces are composed of triangles; only triangles with all three vertices in the zone will be shown.* By default, a zone is based only on distances to any selected atoms (and Volume Tracer markers); the bondzone command indicates that points along any selected bonds (and Volume Tracer links) should also be used.
The Radius can be adjusted by moving the slider or by typing in a new value. There is no way to use different radii for different atoms. Although the maximum radius attainable by moving the slider is 30.0, larger values can be typed. If the set of selected atoms is changed, Zone must be clicked again to move the zone accordingly. Otherwise, the zone will remain centered on the formerly selected atoms. Clicking Zone will not update the surface display when no atoms are selected.
Clicking No Zone unlimits the display of the chosen surface model (shows the entire surface).
Close dismisses the dialog, and Help opens this manual page in a browser window.
* To hide the visual clutter of disconnected patches of surface that fall within the zone, try the maxComponents option of sop zone.