3D Builder

3D Building

The 3D Builder palette allows you to edit and build structures in the 3D Workspace.

This small floating pane collects all the most commonly used actions in one place: options for creating new entries, modifying atoms and bonds, moving and adjusting structures, adding common fragments, mutating residues, selecting rotamers, and more. These actions generally work on an existing selection and affect all the selected atoms or bonds. Many common workflows are built into the tools - for instance, hydrogens are adjusted automatically, and each new fragment offers a menu of next steps.

Building in the 3D Workspace

Build button

The Build button on the Selection Toolbar opens the 3D Builder palette. This palette remains open and floats above the Workspace, so it can be dragged to a more convenient location.

Click the Build button again to close the palette, or use the title bar controls.

Tip: Double-clicking the Build button snaps the palette back into view.

Creating a new entry

The palette offers four ways to create new entries:

  • Create an empty entry
  • Duplicate each entry in the Workspace
  • Copy all selected atoms into a new entry
  • Extract all selected atoms from their current entries and put them into a new entry

These actions are confirmed with a banner displaying the new entry name (or suffix). You can change the name and click the green check to apply it, or click the X to keep the default name.

Working in 2D

If your Workspace is empty or contains just a single small molecule, you can click the 2D Sketch… button to create or edit using the 2D Sketcher. (If the Workspace contains a ligand-protein complex, you will get the Ligand Interaction Diagram instead.)

Advanced editing

Click the Other Edits button for a menu of more advanced editing tools. Note that they all operate on your currently selected atoms or bonds. (See the Reference Guide for more details.)

Basic editing

Select the atoms or bonds you want to modify, then click the appropriate button.

  • Delete atoms
  • Delete bonds
  • Add bond between two selected atoms
  • Set element (letter button) / Choose element (arrow)
  • Increment bond order
  • Decrement bond order
  • Increase formal charge
  • Decrease formal charge

Note: The number of hydrogens is automatically adjusted when atoms and bonds are deleted and bond order is changed.

Moving atoms: Translate and Rotate

Click Move Atoms to reposition selected molecules and atoms. A banner will appear with instructions and options (see below). To translate or rotate the atoms, use your standard mouse actions. Only the selected atoms will move.

If you want to move a different set of atoms, simply change selection before pressing and dragging with your mouse. To exit the mode, click OK or Cancel on the banner, or press Enter or Esc on your keyboard. OK (Enter) saves all the changes you made while the banner was up, while Cancel (Esc) discards the last set of changes.

Moving atoms: Sculpt and Adjust

There are other ways to move atoms while in this mode, depending on your selection. They all use the left mouse button:

    • Sculpting. With a single atom selected, press and drag with your left mouse button to move the atom. When you release the mouse, the structure will be minimized.
    • Adjusting dihedrals. Select a dihedral bond, then press and drag with your left mouse button to rotate the atoms at one end. Click the small green arrow at the other end of the bond to rotate those atoms instead.
    • Other adjustments. Choose the desired Quick Adjust setting on the banner, then select the appropriate atoms or bonds. When the markers appear, press with your left mouse button and drag.

Moving atoms: Changing the view

To change the camera view while in Move Atoms mode, hold down the spacebar on your keyboard to bring up the Camera Transformation pane, then click and drag with your left mouse button on the appropriate action button.

Note: this pane is always available, regardless of mode.

Adjusting (only)

To make just a single type of adjustment while keeping your normal camera view controls available, click the arrow next to the Move Atoms button and choose the adjustment from the menu. A banner will appear in the Workspace with instructions and the option to switch to the full Move Atoms mode. Select the atoms or bonds you need, then press and drag with your left mouse button to move the smaller substituent. Click the green arrow to change the direction of the adjustment.

Change your selection at any time to adjust a different portion of the structure. Canceling out of the mode will discard changes to the most recently selected atoms only.

Adding fragments

The Add Fragments button drops down a panel with a choice of rings and other fragments that can be added to your structure. In the Workspace, select the atoms or bonds where you want to add fragments, then click the corresponding button on the panel. The fragment will be added to all selected locations. (Note that if the Workspace is empty, you can simply click one of the fragment buttons to start building.)

Modifying new fragments

If a new fragment is not oriented the way you intended, or if the attachment was made at the wrong side or point, you can fix it by clicking the small Fragment Menu icon that appears when the fragment is added. This opens a menu of fragment-related actions. The specific items depend on the type of fragment and its connection, but they may include:

    • Flip to Alternate H or Flip Orientation
    • Change Connection Point or Change Connection Side
    • Rotate Dihedral
    • Select Fragment
    • Delete Fragment

The Change Connection actions add markers to all bonds or atoms that are valid alternatives to the fragment's current attachment point. Click the appropriate marker to change the connection, then click the green circle or press Enter to complete the action (Esc discards the changes). If multiple orientations are available, use the corresponding Flip action to switch between them.

Filling in hydrogens

Our Builder tries to adjust the hydrogens appropriately after every action. But if you ever need to add missing hydrogens to a structure, just select the relevant atoms (use Control-A for all) and click the Add Hydrogens button.

Minimizing energy

Click the Minimize button to minimize the selected atoms.

Tip: You can use Ctrl+M (or Cmd+M) as a shortcut for this action.

Topics covered in this Webinar:

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