Desmond Tutorial

Desmond Tutorial
Tutorial Steps
11. Click Preprocess to execute the first phase of the protein preparation tasks. The Analyze
only button simply fills the tables in the wizard panel, but changes are not applied to
the structure.
Setup takes only a few seconds to complete. The Protein Preparation Wizard displays
the chains, waters, and het groups as shown in Figure 1.8.
Figure 1.8 Protein Preparation Wizard — Preprocessing stage
Double-click
the ‘Display Only
Selected Atoms’
button to show
the added
hydrogen atoms.
Residue chains
and water
molecules are
listed here.
HET groups (if
any) are listed
in this table.
As shown, the top table lists residue chains and water molecules, and the bottom table
lists HET groups such as metal ions, enzyme cofactors, ligands, and so on (in this
example this table is empty).
The added hydrogen atoms are not shown by default. To display them, double‐click
the Display Only Selected Atoms button as shown in Figure 1.8. You can also use the
options in the Protein Preparation Wizard panel to display hydrogen atoms. Also note
that the added capping groups can be seen in the circled area, shown in wire frame
representation.
You can select any item in the table by clicking its row as shown in Figure 1.9. Notice
that when you select an item in the table, the Workspace view focuses on the selection
and highlights it with a contrasting color scheme; hydrogen bonds are also displayed.
Use CTRL‐Click to return to the original view. On Figure 1.9 a single water molecule
is selected, which is shown with the red oxygen atom in the middle of the Maestro
Workspace.
September 2008 D. E. Shaw Research 9