Prime User Manual - ISP

Figure 7.3. The Refine loops task in the Refinement panel.
2. Click Load from Workspace.
Chapter 7: Prime–Refinement
The loop features of the Workspace structure appear in the Loops table. For each loop, the
table includes a Run check box, a feature name such as loop1, and the numbers of the first
(Res1) and last (Res2) residues in the loop. When you click a row in the table to select a
loop, the Workspace shows the loop residues highlighted in yellow. Note that loops of
one or two residues are not listed, as they are unsuitable for the refinement protocol.
3. Select a loop by clicking its name in the Feature column.
The loop row is highlighted in yellow. The default settings for the loop are displayed.
4. If necessary, shorten the loop region to be refined by changing the first and last residue
numbers (Res1 and Res2).
The time required to refine a loop scales approximately linearly with the length of the
loop, and the sampling options recommended for loops longer than five residues are also
more time-intensive.
5. (Optional) Click Options to select a sampling method and make settings for this loop in
the Structure Refinement Options dialog box.
If the loop is longer than five residues, you should select a sampling method other than
the default.
See Section 7.8.3 for information on the loop refinement options.
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