Prime User Manual - ISP

Chapter 7: Prime–Refinement
Figure 7.4. The Predict side chains task in the Refinement panel.
7.6 Predicting Side Chains
To predict side-chain conformations:
1. Select Predict side chains from the Task options menu.
The panel displays atom selection options under the heading Residues for side chain
refinement.
2. Use the atom selection options to specify the residues for which you want to predict or
refine side-chain conformations (See Chapter 5 of the Maestro User Manual for information
on selecting atoms).
If you imported a PDB structure that has residues with missing atoms, you can select
those residues by clicking Select Residues with Missing Atoms. The selection is based on
the information generated when the structure was imported, not on the current structure.
The selection therefore includes any residues that were fixed since import.
3. Click Options to change the Number of structures to return from the default, which is to
return a single side-chain prediction.
4. Click the Run button to start the side-chain prediction job.
You can also use this process to add side chains to a backbone structure from Refine Backbone.
For technical details about side-chain prediction, see Section 7.9.3.
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