Prime User Manual - ISP

60
Chapter 7: Prime–Refinement
6. To designate this loop for refinement, select the check box in the Run column.
The Start and Write buttons becomes available.
7. Repeat Step 3 through Step 6 for each loop you want to refine.
8. (Optional) Set up and enable an implicit membrane model.
9. Click Start.
The Start dialog box opens.
10. Make any job settings, then click Start.
The loop refinement job is started.
When you choose several loops for refinement, they are refined in series. The first selected
loop is refined, the best scoring structure for that loop is determined, that structure is used in
refining the next loop, and so on. When all loops have been refined, one final structure is
returned. If only one loop is refined, the four highest scoring structures are returned by default.
If you want to refine two loops cooperatively, you should replace Step 3 through Step 7 above
with the following steps:
1. Click the Run column for the two loops you want to refine cooperatively.
2. If necessary, shorten the loop region to be refined by changing the first and last residue
numbers (Res1 and Res2).
3. Click Options to open the Structure Refinement Options dialog box.
4. Select Cooperative loop sampling in the Loop refinement section.
5. Set any other options, then click OK.
For technical details about loop refinement, see Section 7.9.1.
When a loop refinement begins, a validation program checks the loop features of the structure.
Apparent errors are reported in a warning dialog box. You may choose Run All Features, Run
Only Valid Features,orCancel. It is recommended that you make a note of the invalid features,
click Cancel, and correct the structure if appropriate.
Prime 2.1 User Manual