Prime User Manual - ISP

7.2 Using the Refinement Panel
Chapter 7: Prime–Refinement
The four tasks that can be performed in the Refinement panel are single-point energy calculation,
loop refinement, side-chain prediction, and minimization. These tasks are discussed in the
following sections. The general procedure for running a structure refinement is given below.
To run structure refinement tasks:
1. Display the structure you want to refine in the Workspace.
If the structure has alternate positions, choose the desired set of alternate positions.
2. Choose Applications > Prime > Refinement from the main Maestro window.
The Refinement panel is displayed.
3. Select a task from the Task menu.
The default task is Refine loops.
4. If you want to use an implicit membrane model, select Use implicit membrane, then click
Set Up Membrane to define the thickness and orientation of the membrane.
5. Select the region for refinement, as appropriate.
When you have selected a region for refinement, the Start and Write buttons become
available.
6. Click Start.
The Start dialog box is displayed. If you want to run the job later, using refinestruct,
you can click Write to create the input files.
7. Make changes to the job settings, as appropriate.
8. Click Start.
The refinement job begins and the Monitor panel is displayed.
The Start and Write buttons remain dimmed until you have specified some part of the structure
for refinement. When you have made a selection, the Start and Write buttons become available.
The Write button writes the input file for the job, which you can run at a later time
When selecting regions for refinement, you may want to view information about possible
structural problems. This information is available in the Protein Reports panel, which can be
opened from the Tools menu on the main menu bar. For more information on this panel, see
Section 9.5.3 of the Maestro User Manual.
The OPLS_2005 force field is used for all refinement tasks.
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