Prime User Manual - ISP

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Chapter 5: Comparative Modeling: Build Structure
If there is an insertion in the query (a template gap) that requires the building of a long loop,
you can instead cut the query sequence and cap it with NMA and ACE, and not build the loop,
by selecting the Insertions (template gaps) option under Omit structural discontinuities, and
enter the maximum length of loops that will be built in the text box. This option could be
useful where there are long insertions that are not in the region of interest.
Likewise, if there are deletions in the query (a query gap), or if there is a junction between two
templates, you can choose to cap the ends of the two pieces and not try to join them in building
the structure. To do this, select Deletions (query gaps) or Template junctions under Omit structural
discontinuities.
When the structure is built with discontinuities, the results appear to be misaligned in the
sequence viewer. To display the correct alignment, right-click in the sequence viewer and
choose Align by Residue Number.
5.3 Running the Build Structure Job
When you click Build, the model-building program begins, and its log is displayed in real time
in the Log file window (see Figure 5.3). It can also be viewed in the Monitor panel (click the job
status icon in the upper right corner of any Prime–SP panel to open the Monitor panel). Finally,
the build log is saved to a log file in the directory where Prime is running.
First, the log lists the chosen templates. If you did not intend to choose more than one template,
or if you neglected to align the templates, stop the job and restart it with the correct template.
Jobs can be stopped, paused, and resumed from the Monitor panel. See Section 2.5 on page 14
for more information on Job Control.
The next part of the log file gives information about the build process for template transition
regions, then for insertions, and then for side chains, followed by non-template regions. The
last line of the log describes the diagnosis and success of model building.
Once the model building calculations are complete, the model is displayed in the Workspace
superimposed on the template, using the color scheme Atom PDB B Factor (Temperature
Factor). Blue atoms are those derived directly from the template; red atoms have been
predicted or modeled. To restore this color scheme, choose Atom PDB B Factor (Temperature
Factor) from the Color all atoms by scheme toolbar button menu in the main window.
Build Structure also creates an atom set named non_template_residues which can be found in
the Sets tab of the Atom Selection dialog box. This set of inserted residues is generally chosen
to undergo refinement.
Prime 2.1 User Manual