3D Builder Panel

Build and edit structures in the Workspace using 3D building tools.

To display this panel:

The panel remains open until manually closed, and always floats above the main window. The main window always has focus.

The 3D Builder panel is the primary structure-editing and building tool of Maestro. It allows you to work directly in the 3D Workspace, selecting atoms and bonds to delete them, add to them, or change their properties.

  • Features
  • Additional Resources

3D Builder Panel Features

The 3D Builder panel has buttons for various tasks related to creating and editing structures. These buttons are grouped into several categories, and are described in the subsections below.

Creating Entries

These buttons create new structures by copying existing structures into new project entries.

Create New Entry. Creates a new blank entry.
Duplicate Entry. Duplicates all entries currently in the Workspace (Duplicate In Place). Each new entry is named for its original entry, with a suffix added.
Copy Selected Atoms. Creates a new entry by copying the atoms selected in the Workspace.
Extract Selected Atoms. Creates a new entry by extracting the selected atoms from the entries in the Workspace.

See Creating Entries from the Workspace for more information.

Basic Edits

Thes buttons perform basic changes to existing atoms: deleting, changing the element or charge.

Delete Atoms. Deletes all selected atoms and their bonds.
Set Element. Changes the element of all selected atoms to what is shown on the label. Click the arrow beside the button to open a palette of common elements. Choosing an element changes the selected atoms to that element and sets the main button to use this element. The “...” button opens another pane with the full periodic table. Recently used elements that are not already shown are preserved in the two empty slots on the palette.
Increase Charge. Increases the charge of all selected atoms by 1.
Decrease Charge. Decreases the charge of all selected atoms by 1.

See Changing Bond Orders, Formal Charges, and Elements for more information.

Bonds

Delete Bonds. Deletes all bonds defined by selected atoms. Leaves atoms.
Add Bond. Adds a bond to the selected pair of atoms.
Increase Bond Order. Increases bond order of all selected bonds by 1, up to 3.
Decrease Bond Order. Decreases bond order of all selected bonds by 1, down to 0.

See Making and Breaking Bonds and Changing Bond Orders, Formal Charges, and Elements for more information.

Moving and Building

Move Atoms. Move the selected atoms to a new location and orientation, with the following actions:

  • Rotate / Translate
  • Sculpt (move and minimize)
  • Adjust (dihedral, angle, length)

Opens a banner with tools for switching to adjustment mode. See Moving Atoms, Adjusting Bond Lengths, Angles, and Dihedrals and Adjusting Peptide and Ring Conformations for more information.

Add Fragments. Add fragments from a palette, which opens when you click the button. Click a fragment to add it to the selected atoms.

The palette contains the following fragments:

  • Rings—a collection of three- to eight-membered rings.
  • Organic—several common groups; click the button if they are not displayed.
  • Metal Centers—several common coordination complex types; click the button if they are not displayed.
  • More—click this button or the "..." button for a full fragment library; opens the Fragments Panel

The Create Enumerated Entries button opens the Custom R-Group Enumeration Panel, which allows you to add multiple fragments to each selected atom and create a new entry for each fragment combination.

See Building Structures from Fragments for more information.

Draw Structure. Draw a structure or add to a structure by drawing in the Workspace. Opens a banner with tools you can use to draw with. See Drawing Structures for more information.

Add Hydrogens. Adds any missing hydrogens to the selected atoms, to complete the valence. If the atom has a specified number of unpaired electrons, the number of hydrogens added is reduced by this number, so that the unpaired electrons are preserved.

Minimize. Minimizes selected atoms (only). Maps to Ctrl+M on keyboard. See Minimizing Structures for more information.

More Editing Options

Other Edits. Perform other edits on the structures.

Invert Chirality. Inverts the chirality of any chiral atoms found among the selected atoms. If all atoms are selected, invert the chirality of the whole molecule.
Flip Spiro. Rotates the smaller ring by 180° around the axis through the spiro atom, for any spiro atoms found among the selected atoms.
Mirror Molecule. Convert the molecules in the Workspace to their mirror images, by reflecting in the xy plane.
Convert Cis/Trans.
  • peptide bond
  • double-bond not in a ring
Select Rotamer. Allows you to step through available rotamers for the selected residue. If the selected atoms represent a single residue, a banner with arrows and other controls opens in the Workspace. If the atoms represent more than one residue, the Rotamers Dialog Box is opened instead. (This dialog can also be opened from the single-residue banner by clicking the 'i' icon.)
Switch Alternate Positions. Allows you to switch to the alternate positions (if any) of the residues represented by the selected atoms. Remains disabled if no alternate positions are found in the selection.
Create Zero-Order Bonds to Metals. Creates zero-order bonds from surrounding atoms to selected metal atoms.
Set Unpaired Electrons. Set the number of unpaired electrons on the selected atoms to 0, 1, or 2. Opens the Change Atom Properties Panel to the Other tab for making the change. Hydrogen addition and adjustment accounts for unpaired electrons, but the number of unpaired electrons is not updated automatically - you must update it manually. Unpaired electrons can also be set in the 2D Sketcher Panel
Change Isotope. Opens a small dialog allowing you to specify the isotope number for the selected atoms. Remains disabled if the selected atoms are not all the same element.
Mutate Residue. Opens a palette of possible residue types, allowing you to change the type of the selected residues. The upper part of the palette has the standard residues; the lower part includes variants of the standard residues.
Change Atom Properties. Opens a dialog with options to change atom or residue properties for the selected atoms. See Change Atom Properties Panel.
Build Peptide from Sequence. Opens a dialog that allows you to build a peptide from a sequence. See Building Biopolymers.
3D Builder Preferences. Set preferences for building 3D structures. Opens the Preferences Panel to the Behavior settings tab of the Builder Preferences.

Undo. Undo the last edit.

Redo. Redo the last undone edit.

Related Topics