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loop file

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loop file

what is skip rate? (the forth column)
and when would you have a 0 at the fifth column?

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Tue, 2013-06-04 13:26

The skip rate is a floating point number in the range of 0 to 1.0, and controls sampling behavior when you want to pick a random loop. If skip rate is non-zero, when picking a random loop, that particular loop will be "skipped" (and another random loop picked) "skip rate" fraction of the time it would otherwise be picked. It's a way to control the relative rate of sampling various loops. (A loop with a skip rate of 0.5 will be picked half as often as one with a skip rate of 0.)

The fifth column is the "extend loop" column. This is a boolean (0 or 1) which determines whether to "extend" the loop (reset to -150phi, 150psi) before remodeling. False means start remodeling from the current configuration.

Not all protocols will obey these designations, however, some having their own notions of how to randomly pick loops and/or how to prepare the loops before remodeling.

Tue, 2013-06-04 14:31

thank you

Wed, 2013-06-05 11:14