Prime User Manual - ISP

Chapter 5: Comparative Modeling: Build Structure
first template is in use. As you select regions in the second template, the tool automatically
deselects the corresponding residues in the first template. If you select regions for use from a
third template, the corresponding regions of the first and second templates are deselected, and
so on.
5.2.2 Including Ligands and Cofactors
Any cofactors and ligands present in the template you have chosen (except HOH) are listed in
the Include ligands and cofactors box. Click in the list to select one or more ligands and cofactors.
Your selections are highlighted in yellow in the Workspace.
5.2.3 Build Options
Click Options to open the Build Structure–Options dialog box and specify which optional
model building steps to perform:
• Retain rotamers for conserved residues—retain side-chain rotamers for conserved residues.
• Optimize side chains—Optimize the side chains.
• Minimize residues not derived from templates—minimize residues that are not derived
from the templates. Only available if Optimize side chains has been selected.
By default, all three of the above options are selected.
5.2.4 Omitting Structural Discontinuities
You can disable the building of structural discontinuities arising from insertions, template
junctions, and deletions. The discontinuities are capped with NMA and ACE, so the final structure
is discontinuous. If you choose any of these options, you should check that your final
structure is reasonable.
Figure 5.2. The Build Structure–Options dialog box.
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