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Recipe: Manual Rebuild 1.0.1 -- Brow42
Created by brow42 78 381
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Name: Manual Rebuild 1.0.1 -- Brow42
ID: 41950
Created on: Sat, 05/26/2012 - 01:55
Updated on: Tue, 06/12/2012 - 01:32
Description:

Replacement for the built in GUI Rebuild...prints scores, does shake, sets 1 rebuild per undo, each rebuild is different.



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brow42's picture
User offline. Last seen 3 days 23 hours ago. Offline
Joined: 09/19/2011
Groups: None
For better manual rebuilding

I find manual rebuilding really difficult. I can't tell which spot in the undo track is a better score, I have to fiddle with quicksaves to try out different rebuilds, and I'm convinced the GUI rebuild just sits there wiggling but producing no rebuilds at all far longer than rav3n_pl DRW, which finds a new shape almost instantly.

This script replaces the usual right-click rebuild function. You have to tell it where to rebuild by either selecting with the selection interface, or making two frozen segments around the section where you want to rebuild. It will rebuild between the frozen places, or between the first and last selection (including the endpoints).

The script will do the following:

For each rebuild, it prints the score (which identifies each rebuild), and the change in energy subscores.

A single shake is done at the end of each rebuild to fix up the clashing and sidechain scores. This should be very fast in most cases.

At the end of the script, each rebuild is given one spot in the undo menu, up to the last 25 rebuilds (the current length of the undo). The undo key will move backwards in the rebuild list as you'd expect.

It still does this if you hit cancel. If you don't hit cancel, it will do 50 rebuilds and exit.

Rebuilds that are identical to the previous rebuild are not included in the final undo list.

Quicksave slots 76-100 are used for the undo buffer.

It does not change the secondary structure, the clash importance, or look for the worst spots to rebuild. This is for manual rebuilding, it's just giving you the rebuilds in better way.

There is no dialog...it's just click-and-run.

brow42's picture
User offline. Last seen 3 days 23 hours ago. Offline
Joined: 09/19/2011
Groups: None
Small update 1.0.1

By request, the script now looks at only the rebuilt segments' energy total instead of the protein total score when determining if the rebuild call actually changed the protein. This is because sometimes the score is stuck at -99999999.999.

Joined: 04/11/2013
Great

This is great
Brow Would you mind adding an option to shake and wiggle at a chosen Ci? It would really help at the beginning of a puzzle.
Thanks for this script
porky :)

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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