Prime User Manual - ISP
Prime User Manual - ISP
Prime User Manual - ISP
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7.11 Output of Refinement Jobs<br />
Chapter 7: <strong>Prime</strong>–Refinement<br />
By default, the structures created in <strong>Prime</strong>–Refinement are appended to the Project Table for<br />
the project currently open. If you would prefer the output structure to replace the input structure,<br />
or would rather not incorporate the output structure into the project at all, select the<br />
appropriate option from the Incorporate option menu in the Start dialog box:<br />
• Append new entries as a new group<br />
• Append new entries individually<br />
• Replace existing entries<br />
• Do not incorporate<br />
In addition to returning the structures, the output of a refinement job include several Maestro<br />
properties. The main properties are <strong>Prime</strong> Energy and <strong>Prime</strong> Energy Difference, which reports<br />
the difference in energy between the input and output structures. The energy difference is<br />
cumulative: if the property already exists, the difference is incremented in the current job. For<br />
loop refinement and side-chain prediction jobs, the lipophilic term is reported separately as<br />
<strong>Prime</strong> Lipo; the sum of the <strong>Prime</strong> energy and the lipophilic term is used to rank loop conformations.<br />
<strong>Prime</strong> 2.1 <strong>User</strong> <strong>Manual</strong> 69
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