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Recipe: Hiding Rebuild V2
Created by spvincent 62 34
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Name: Hiding Rebuild V2
ID: 37872
Created on: Tue, 01/24/2012 - 15:05
Updated on: Tue, 01/24/2012 - 23:05
Description:

Optimizes for a specific score component (default is hiding) . See first comment for more details.



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spvincent's picture
User offline. Last seen 3 hours 19 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
This script is not intended

This script is not intended to improve the score, although it may indeed have that happy side effect.

Rather the aim is to improve a specific component of the score like hiding or bonding at the likely expense of the total score: subsequent scripts like Quakes or Rebuilders can then be used to tidy up or you can adjust things manually. The default component to improve is hiding (other styles of script generally seem to have a problem with this component) but this can readily be changed (see component_to_optimize at start). It's probably best to confine the scripts effects to a specific region of the protein like a large loop: see min_residue and max_residue at start.

This script runs for a specific time: the default is one hour. If you stop it before then you may have to step back through the undo graph to find the end product of the script.

It looks for the "best" score after multiple rebuild/shakes: rejecting rebuild results that have unduly kinked backbones. It then takes that structure, wiggles, shakes, wiggles at lower CI, ands wiggles again.

Joined: 08/30/2011
components

Am I right that the component option can be changed to clashing, packing, hiding, bonding and sidechain?

And how did you manage that the script runs for 1hr? Is there a way to change that?

spvincent's picture
User offline. Last seen 3 hours 19 min ago. Offline
Joined: 12/07/2007
Groups: Contenders
Yes to question 1. Hiding's

Yes to question 1. Hiding's the default because it's my general impression that that's the component hardest to improve with other types of script.

Q2: Use the os library in Lua. Something like this.

start_time = os.time ()

.. Do something. Call it X.

end_time = os.time ()

time_taken = os.difftime ( end_time , start_time )

print ( "Seconds to do X " .. time_taken * 3600 )

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons