Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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Chapter 7: <strong>Prime</strong>–Refinement<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong><br />
Figure 7.5. The Minimize task in the Refinement panel.<br />
7.7 Minimizing Structures<br />
The Minimize refinement task performs a truncated-Newton energy minimization, using the<br />
OPLS_2005 all-atom force field for proteins as well as for ligands and cofactors, and treating<br />
solvation energies and effects via the Surface Generalized Born (SGB) continuum solvation<br />
model.<br />
To minimize all or part of the structure selected:<br />
1. Select Minimize from the Task menu.<br />
Atom selection options are displayed under the heading Atoms for minimization.<br />
2. Click All to minimize all residues, or specify a set of atoms or residues.<br />
For more information on atom selection, see Chapter 5 of the Maestro <strong>User</strong> <strong>Manual</strong>.<br />
3. Click Start to start the minimization job.
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