Prime User Manual - ISP

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Chapter 3: Prime–Structure Prediction: Initial Steps
3.2.4 Search Results
Prime 2.1 User Manual
Figure 3.4. The Find Homologs–Options dialog box.
The output from the homolog search appears in the table labeled Homologs: (N found, n
selected). For each potential template, the row contains the ID, the name, score, expectation
value, % identities, % positives, % gaps, and header information (if taken from a PDB file). All
percentages are rounded to the nearest whole number, which may be zero. A description of the
table columns is given in Table 3.1.
You can view the complete text of each table cell as a tooltip by pausing the pointer over the
cell. Columns can be sorted by clicking on the column heading. Click once to sort in
descending order, and click twice to sort in ascending order. The column widths can be
adjusted using the left mouse button to drag the column border.
If no structural coordinates are available for a template, that row is dimmed and cannot be
selected.
If a chain ID is given for a homolog (e.g., Chain A in 1EMS_A), then that chain, not the entire
protein, is the potential template. When aligning multiple templates with multiple chains, you
may need to extract single chains using the getpdb utility, as described in Section D.2.3 of the
Maestro User Manual.
Once homologs are found, click on a row to view the structure of that template in the Maestro
workspace. If no structural coordinates are available for selection, the row is dimmed.
Selecting a template will also bring the sequence alignment of the template and the query
sequence into the sequence viewer. Click on another template to deselect the first one and
display the selection in the Workspace window.
After you review the alignments, select the template that you want to build on by clicking on
its row in the table. To select multiple templates, see Section 3.2.5.