Prime User Manual - ISP

Chapter 7: Prime–Refinement
The text below the option and menu displays the recommended loop length for the selected
accuracy.
Extended sampling samples loop conformations more thoroughly, using a series of loop
constraint settings. Up to eight processors can be used simultaneously to perform loop refinement.
Extended sampling can be run at four different sampling levels: Low, Medium, High, and
Ultra. If you select Ultra Extended, you can only refine one loop at a time.
Job
These options allow you to set a limit on the number of processors over which to distribute the
loop sampling subjobs. Each sampling method runs in several stages, and each stage can use a
different number of processors. The maximum number of processors that can be used by the
different sampling methods are:
Default 1
Extended Low 2
Extended Medium 4
Extended High 8
Ultra Extended 8*L (L is the loop length)
• To make use of as many processors as are available, select Distribute subjobs over maximum
available processors.
• To set the maximum number of processors, select Distribute subjobs over and enter a
value in the text box.
Output for single loop feature
These options determine how many structures are returned:
• Maximum number of structures to return: Select this option to return more than one structure
for each loop specified for refinement. The default when this option is selected is to
return 4 structures for each loop.
• Energy cutoff: Select this option to prevent higher-energy structures from being returned.
Structures whose energy is higher than that of the lowest-energy structure by more than
this amount are not returned. The default cutoff when this option is selected is 10 kcal/
mol.
The following settings are applied to the loops you have selected for refinement.
• Maximum CA movement: To limit the extent to which alpha carbon atoms can move from
their original positions, select this option, and enter a limit in the text box. The default
distance is 3.0 Å. The extended sampling procedure tests multiple values for Maximum
CA movement, so this option is unavailable when extended sampling is selected.
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