Copying and Pasting Structures

Maestro allows you to copy structures from the Workspace or other locations, and paste them into the Workspace.

Copying or Cutting Workspace Structures

  • To copy the Workspace selection onto the clipboard, you can choose Edit → Copy or press Ctrl+C (⌘C).
  • To cut the Workspace selection, placing it onto the clipboard and removing the atoms from the Workspace structure, you can choose Edit → Cut or press Ctrl+X (⌘X).

The clipboard stores the atoms in the selection in Maestro format and SMILES format. The SMILES string can be pasted into another application; the atoms can be pasted back into the Workspace.

You can also copy the selection as a SMARTS pattern or a SMILES pattern, which you can do with Edit → Copy As → SMARTS or Edit → Copy As → SMILES.

The 3D Builder also has some tools for copying and cutting the Workspace structure:

  • To copy the Workspace selection into a new entry, click the Copy selected atoms to new entry button in the 3D Builder.
  • To cut the Workspace selection and paste it into a new entry, click the Extract selected atoms to new entry button in the 3D Builder.

Pasting Structures into the Workspace

To paste a structure from the clipboard into the Workspace as a separate structure, you can

  • choose Edit → Paste.
  • press Ctrl+V (⌘V).

The structure can be a SMILES string, a structure from ChemDraw or Isis Draw (Windows) or a set of atoms previously cut or copied from the Workspace.

If the structure is a SMILES string, it is converted into a 2D structure. The 2D structure is added to the project as a new entry, with the SMILES string for the structure as the title. No attempt is made at 3D conversion. You should consider running LigPrep to convert the structure to 3D. However, you can perform a 2D to 3D conversion as part of the pasting procedure by choosing Edit → Paste Special → As 3D.

If you paste a set of atoms that were cut or copied from Maestro, they are placed at the coordinates at which they were cut or copied onto the clipboard. If you want to choose the location to paste the atoms, choose Edit → Paste Special → By Placing or press Ctrl+Shift+V (⇧⌘V), then click in the Workspace where you want the centroid of the atoms to be located.

When you paste atoms into the Workspace, they are added to an entry. If there is no entry in the Workspace, a new project entry is created. If there is a single entry in the Workspace, the pasted atoms are added to that entry. If more than one entry is in the Workspace, you are prompted to choose one of the entries or to create a new entry.

Pasting Structures onto Other Structures

If the structure on the clipboard is a fragment, you can paste it onto other structures in a similar way to adding fragments using the 3D Builder Panel. To do this:

  1. Select one or more atoms in the target structures.

    These atoms are replaced by the fragment, along with any attached hydrogens.

  2. Choose Edit → Paste Special → As Added Fragment to replace each of the atoms with the fragment.

A fragment is defined as a structure in which one (and only one) atom has unsatisfied valences (broken bonds). The number of unsatisfied valences must match the number of bonds to non-hydrogen atoms for each target atom.