MOptima
Chapter 02

Interface and Navigation

Source: docs/manual/02-interface-and-navigation.md

Main window layout

The main window is divided into four practical areas:

The MOptima main window is organized around menus, a workflow sidebar, the 3D viewer, and task or result tabs.
The MOptima main window is organized around menus, a workflow sidebar, the 3D viewer, and task or result tabs.

1. Menu bar

The top menu bar is the fastest way to reach high-level actions. The main menus are:

  • Project
  • Edit
  • Single Task
  • Process Task
  • Tools
  • Settings
  • About

Use the menu bar when you want to start a new action from scratch, especially project management, import, and task entry points.

2. Left sidebar

The left sidebar changes according to the active workflow. It contains task-specific controls such as:

  • Edit mode selection.
  • Parameter fields.
  • Apply or run buttons.
  • Clear-selection controls.
  • Progress-related controls for some workflows.

The sidebar is the main place where you tell MOptima what you want to do with the current structure.

3. Central 3D viewer

The center of the window contains the molecule viewer. This is where you:

  • Inspect geometry.
  • Pick atoms.
  • Rotate, pan, and zoom.
  • Preview task results.
  • Compare optimization states and scan structures.

The viewer is interactive, but its behavior depends on the active panel. For example, atom clicks in the Editor tab can populate edit selections, optimization constraints, or scan targets.

4. Tab area

The main tab bar starts with the Editor and grows as you run tasks. New calculation results are opened as additional tabs so you can compare steps without replacing the current editor state.

QM-related content is grouped in a container-style tab so multiple QM jobs can stay organized inside one section.

Typical navigation pattern

Most operations follow the same pattern:

  1. Choose the task from the menu or switch to the matching panel.
  2. Use the viewer to select atoms if the task requires geometry targets.
  3. Set parameters in the left panel.
  4. Click the run or apply button.
  5. Read the generated result tab.

Result tabs vs Editor tab

Use the Editor tab when you want to change the working structure. Use result tabs when you want to inspect calculation outputs without overwriting the current editor state immediately.

This distinction matters because MOptima is built to preserve workflow history. A result tab is not just a picture of the molecule; it is a step in the project record.

Editor status 1
Energy 1Optimize 1
Editor status 2
Optimize 2Gen 1
Editor status 3
LowE Conf 1
The Editor tab is used for interactive structure work, while result tabs preserve calculation outputs for later comparison.

Light and Dark Themes

Use Settings -> Themes to switch between Light(Default) and Dark.

The theme change affects the main window, menu styling, sidebar panels, tabs, and the integrated 3D viewer. If you change themes while working, review the viewer contrast and panel readability before continuing a detailed selection step.

MOptima includes both Light(Default) and Dark themes, and the change applies across the main interface and 3D viewer.

Batch Mode

MOptima also supports Batch Mode for multi-structure input. The interface behavior changes when Batch Mode is active, so read Batch Mode before running multi-molecule workflows.