Desmond Tutorial

Desmond Tutorial
Tutorial Steps
3. Select the type of structure file you will import from the Format field. For this tutorial,
select PDB because we will import a PDB (Protein Databank File).
NOTE Maestro supports many common file formats for structural input. See the Maestro tutorial
(Section 11) or click the Help button for a list of supported formats.
4. Click the Get PDB File button.
The Get PDB File window appears as shown in Figure 1.4.
Figure 1.4 Get PDB File window
Enter the identifier for
the PDB file you want to
import in the ‘PDB ID’
field.
Check the ‘Download
from Web’ option.
Click the Download button.
5. Enter the identifier for the PDB file you want to import into the PDB ID field.
For this example, we will import the small, proteinase (trypsin) inhibitor protein: 4pti.
Therefore, enter 4pti in the PDB ID field.
6. Check the Download from Web option to allow Maestro to download the PDB file from
the PDB website.
7. Click the Download button.
The protein structure appears in the Maestro workspace as shown in Figure 1.5. The
protein structure is displayed using a ribbon representation with colors continuously
varying along the rainbow scale from the N terminus toward the C terminus. The red
dots show the location of the oxygen atoms of the water molecules present in the
X‐ray structure.
September 2008 D. E. Shaw Research 5