Desmond Tutorial

Desmond Tutorial
Preparing Proteins with Missing Residues or Side Chains
Figure 3.9 Prime Build Structure window
Click the ‘Options’ button to
set build parameters for the
structure builder.
h. Click Options.
The Build Structure–Options window appears as shown in Figure 3.10.
Figure 3.10 Prime Build Structure – Options window
Check the ‘Retain rotamers for
conserved residues’ option.
Check the ‘Optimize side
chains’ option.
Click OK.
i. Check the Retain Rotamers for conserved residues option to ensure that none of the
atoms in the X‐ray structure (the self‐template structure) are allowed to move
since the self‐template residues are considered to be conserved residues by definition.
j. Check the Optimize side chains option to allow the structure builder to optimize
rotamers of side chains as it builds them.
k. Click OK.
l. Back in the Structure Prediction window, click the Build button as shown in
Figure 3.11.
36 D. E. Shaw Research September 2008