Atom selection groups

Create and edit groups

Open Selections and click Add group, or select atoms to create the first group automatically. Choose Click atoms to pick individual atoms or Drag a box to select atom centers inside a rectangle. Changes apply immediately; no separate save step is needed. Each group has an editable name, color and Show group atoms checkbox.

After selecting atoms, click Hide selected atoms to hide the current group's atoms together with their attached bonds and arrows. The button changes to Show selected atoms to restore them. Hidden atoms continue to participate in analyses and remain in exported CSV data. Automatic scalar color limits exclude atoms hidden by a selection group; manually fixed limits remain unchanged. The button is available when the current group contains atoms present in the open frame.

Select a group in the list to edit it. Add atoms retains its existing members, Remove atoms subtracts the picked IDs, and Replace atoms replaces all members with the new selection. Clear members keeps an empty editable group; Delete group removes the group and its display overrides. Up to 64 groups and 1,000,000 stored member IDs are supported.

Member IDs and manual edits shows a preview of the group's IDs and accepts space- or comma-separated IDs. The selected Add, Remove or Replace operation also applies to these entries. This allows editing hidden atoms and IDs absent from the current frame. Alternatively, check Show group atoms before picking members again. Group counts distinguish IDs present in the current frame from absent IDs.

Viewport controls

Group picking is active while Selections is open. In Click mode, dragging still rotates the camera. In Box mode, dragging with the primary mouse button or one finger draws the selection rectangle; right-drag, the wheel or two fingers navigate the view. Escape cancels the rectangle. Switching tools or closing Selections restores normal picking and camera controls while keeping group colors and visibility.

A box selects projected atom centers throughout the viewing depth, including atoms behind the front layer. Visibility masks and clipping planes still apply. The selection operation yields during large scans and is cancelled if the source, frame, camera or selection mode changes before completion.

IDs, display and persistence

Groups store stable atom IDs rather than row indices. They therefore follow reordered trajectory frames; IDs absent from a frame remain in the group for later frames. Display replicas refer to their source atom, so selecting several copies adds that ID once. With Replicate atoms for analysis enabled, physical copies have independent IDs and can belong to different groups.

Group colors override the selected element/scalar/crystal palette. Later groups take color precedence when an atom belongs to several groups; a specific per-atom appearance override takes precedence over group color. Membership in any hidden group hides the atom, even if another group containing it is visible. Existing legend filters, individual visibility settings and clipping planes also apply. A group's color does not change the underlying analysis values or legend ranges.

JSON configuration export/import saves group names, colors, visibility, member IDs and the selected group. Click/Box mode and Add/Remove/Replace are temporary editing controls. A new source clears groups; importing its saved configuration restores them after the matching files are opened. Older configurations start with no groups.

Implementation

Selection data model, group controls, box projection, appearance precedence, configuration.