Prime User Manual - ISP

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Chapter 5: Comparative Modeling: Build Structure
The Build process includes the following steps:
1. Coordination of the copying of backbone atoms for aligned regions and side chains of
conserved residues
2. Building insertions and closing deletions in the alignment
3. Building tails out to the last residue in the template
The Build process may also include the following steps:
• Side-chain prediction of non-conserved residues
• Minimization of all atoms not derived directly from the template
You can specify which optional steps to perform by clicking Options and making selections in
the dialog box. See Section 5.2.3.
5.2 Preparing to Build
If you want to build a model using multiple templates or including ligands or cofactors, you
must specify how these are to be treated before clicking the Build button to start the building
process.
5.2.1 Multiple Templates (Set Template Regions)
If you intend to use multiple templates to build a model of the query, you will have already
selected them and ensured that they are structurally aligned (i.e., rotated into a common coordinate
frame; see Section 3.2.5). In the Build Structure step, before starting the structure build
by clicking the Build button, you must specify which template to use for each region of the
query. If you do not select regions from other templates, the topmost template in the table will
be used for the entire query.
To enter the mode that allows you to set the template regions, click the Set Template Regions
toolbar button:
Highlight the region of each template in the sequence viewer that you want to use. Click the
Set Template Regions button again to end the selection. (You may need to scroll over and
select again if the desired region is wider than the display window.)
The Set Template Regions tool helps make sure that only one template residue is assigned to a
query residue at one time. Regions of a template not being used to model the query are colored
dark gray (regardless of coloring schemes). When you begin to set template regions, only the
Prime 2.1 User Manual