Desmond Tutorial

Learning the Maestro-Desmond Environment
Editing a Molecular Structure
selections on the different tabs of the tool, including SMARTS. Configurations within the
Atom Selection dialog box are translated to an ASL (atom specification language) expression.
The settings shown in the Atom Selection dialog box in Figure 2.5 constrain the
workspace to show residues that are at least 5 Å away from the backbone of polar residues.
Figure 2.5 Atom Selection dialog box
Select arbitrary sets of atoms from
the tabs of this window to show the
desired residues in the Workspace.
Editing a Molecular Structure
Maestro provides a general structure building and editing tool. It can be accessed either
from the main toolbar by clicking the `Hammerʹ button as shown in Figure 2.6, or by selecting
different editing tools from the Edit menu.
When you click the `Hammerʹ button, the most common editing options appear as icons in
the top horizontal toolbar. These tools allow you to hand‐draw structures, set chemical
elements, increment/decrement bond order or formal charge, adjust the position of atoms,
clean up 3D geometry, and add common molecular fragments. View help for each toolbar
icon by slowly moving the cursor over the icons.
Figure 2.6 Opening the Build/Edit Icon Menu
General tools for building
and editing molecular
structures appear when
you click the ‘Hammer’
button.
As shown in Figure 2.7, the Build/Edit menu includes:
• Fragments for adding molecular fragments to your structure.
September 2008 D. E. Shaw Research 23