Skip to main content

User interaction and Controls

Main buttons:​

1. + New Experiment ​

interaction 1
  • Creates a new experiment within the current project.
  • Allows you to work with a protein using different approaches and settings.

2. Start​

interaction 2
  • Launches the current stage, initiating the selected computational process.
  • Must be pressed after setting up parameters to begin execution.

3. Stage Settings​

interaction 3
  • Allows users to customize the process by adjusting various parameters before execution.
  • After a stage is completed, it can also be used to review the applied settings.

4. Next Stage​

interaction 4
  • Moves the experiment forward through the pipeline to the next stage.
  • Available only after the current stage is successfully completed.

5. Recreate Stage​

interaction 5
  • Provides the ability to re-run a stage with modifications.
  • All existing experiments will be saved, and data will not be lost. A new copy of the experiment will be created instead.

Offers two options:​

  • Different step results – Creates a new experiment where you can select a different result from this step.
  • Different starting parameters – Creates a new experiment where you can modify starting parameters before execution.

6. Stage Results​

interaction 7
  • Saves the results of the current stage to your computer.
  • Downloads the output in a ZIP format for further analysis or storage.

7. Stage Settings (Post-execution)​

interaction 8
  • Displays the applied settings for the completed stage.
  • Allows users to review how the stage was configured after execution.

3D Workspace Interaction guide​

  1. Right-click (RMB) and drag to rotate the 3D scene around the center of workspace.

  2. Left-click (LMB) and drag to pan the view horizontally or vertically.

  3. Adjust fog intensity/Depth cueing – Hold mouse wheel (MMB) and move the cursor up or down to increase or decrease the fog effect in the 3D scene.

  4. Scroll the mouse wheel to zoom in and out smoothly.

  5. Switch between three visualization modes for different structural representations:

    • Cartoon – ligand and surrounding residues are shown in ball and stick while other residues shown in secondary structure representation.
    • Ball + Stick – all atoms shown in ball and stick.
    • Electrostatic – surface charge visualization.

  6. Toggle different molecular elements through the "Elements" panel for a customized view.

  1. To display a molecule in the 3D Workspace, click on its row or the eye icon.
  1. Double-click the eye icon to pin the structure, keeping it visible while navigating other molecules.