Prime User Manual - ISP

64
Chapter 7: Prime–Refinement
Seed
Specify the seed for the random-number generator used in side-chain predictions. The seed is
used for side-chain prediction in both the loop refinement and the side-chain prediction tasks.
The options are:
• Random: use a random seed.
• Constant: use the integer given in the text box as the seed. The default is 0.
Use crystal symmetry
If crystal symmetry is known for this protein, apply periodic boundary conditions so that the
crystal symmetry is satisfied.
7.8.2 Dielectric Options
The Dielectric section allows you to set the dielectric constants used in the calculations, in the
following text boxes.
Internal dielectric
Set the dielectric constant used for the interior of the protein and any implicit membrane.
External dielectric
Set the dielectric constant for the (continuum) solvent.
7.8.3 Loop Refinement Options
The Loop Refinement section provides options for selecting the sampling method, job options,
output options, and some general options.
Prime can perform cooperative loop sampling as well as serial loop sampling. Both the size of
the loop and the sampling options chosen affect the time needed for loop refinement. The
options are:
Cooperative loop sampling
Select this option to refine two loops together. Each loop is refined in turn until the refinement
has converged for both loops. You must have only two loops selected to use this option.
Serial loop sampling
Select this option to refine each loop independently. The option menu provides five levels of
sampling accuracy: Default, Extended Low, Extended Medium, Extended High, Ultra Extended.
Prime 2.1 User Manual