Using simgen with ZnDraw

Web app

This section describes how to generate structures using the online web app, hosted here. If something breaks, clicking EXIT and reloading the page should fix it. See the in-app help (i button in the top bar) for general ZnDraw controls.

Generation menu

To access the generation menu, click 'Interaction' in the left sidebar and select 'DiffusionModelling' from the 'Method' dropdown menu.

The modifier has three run types:

  • Generate: Generates structures using similarity kernels.
  • Hydrogenate: Adds hydrogen atoms to the active structure.
  • Relax: Uses a pretrained MACE force field to relax/optimize the active structure after hydrogenation.

Clicking "Run modifier" will perform the selected action on the active structure. In addition, a clickable bookmark is created at the start of each run, allowing you to easily revert to the original structure.

Generation Settings

  • Num Steps: Controls the number of integrator steps during generation. 50 is a good starting point.
  • Atom Number: Can be static or determined dynamically based on the length of the guiding curve (see Guided Generation). Select 'PerAngstrom' for dynamic atom number.
  • Guiding Force Multiplier: Adjusts how strongly atoms are attracted to the guiding point cloud. Default of 1 works for simple tasks. Increase if the generated structure is fragmented.

Hydrogenate and Relax Settings

These modes have just one parameter controlling the number of relaxation steps. Defaults are suitable for most uses.

Guided Generation

We can create structures with arbitrary shapes by providing a point cloud prior. To draw a guiding curve:

  1. Press x or the 'Draw' button to enter drawing mode.
  2. Click on atoms to place guiding points.
  3. Press x or the 'Draw' button to exit drawing mode.

A smooth curve that passes through all the guiding points is automatically generated.

The guiding curve is easy to modify:

  • Clicking a point selects it:
    • Move the selected point with the on-screen controls.
    • Delete the selected point by clicking Backspace.
    • Deselect a point by clicking Esc on your keyboard.
  • Clicking the blue midpoint of a segment inserts a new point.

To place points in free 3D space:

  1. Create a canvas using the Drawing option in the left sidebar.
  2. Now in drawing mode, points will snap to the canvas.

To modify the canvas:

  • Press f to enter canvas mode. Now you can rotate and translate the atoms while the canvas stays fixed.
  • Hold shift and scroll to resize the canvas and access on-screen controls.