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Recipe: Power Shift 1.0.1 - Brow42
Created by brow42 83 422
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Name: Power Shift 1.0.1 - Brow42
ID: 44189
Created on: Wed, 09/19/2012 - 04:37
Updated on: Mon, 09/24/2012 - 06:09
Description:

Thread a group of segments like you can in the alignment tool. Actual shifting is done with the tweak tool.



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brow42's picture
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Joined: 09/19/2011
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Threading in non-alignment puzzles

The Sheet Tweak tool works almost exactly like the alignment tool. In fact, I'm sure they use the same code. You can use the tweak tool to shift your protein along its current shape exactly, even if your protein isn't a simple sheet. Normally the tweak tool has to arrange the loops that you didn't tweak after the shift, which can make the tweak fail. If you also use the cut tool, then this isn't necessary.

This is more like a wizard than a script; it can't be fully automated. You can do the shift by hand by converting everything you want to shift to sheet, making cuts, tweaking, closing cuts, and then reapplying the original secondary structure (to the shape, not to the segments). This script handles all the structure changes; you still have to do the cutpoints and tweak yourself. You run the script once to set up the tweak, and then you run it again to clean up the structure.

How to run:
First, tell the script what you want to tweak but selecting or freezing your region of interest. Double-click freezing can be handy here. There must be one single continuous frozen/selected region. Alternatively, you can freeze exactly 2 segments and it will include all the segments between. If the script is confused, you get a dialog and an option to clear all freezes and selections (which could exist invisibly to original interface users). Just clear, reselect/refreeze and run it again.

The script will set your region to sheet, set the required buffer region to loop, record the original structure in the notes, and make a pair of bands at the ends. Your region will be re-selected for you.

Make cutpoints outside the buffer region (optional). Use the tweak tool on the sheet to shift the sheet. Be careful about which arrow you click (see bottom of post)! Quicksave before and after tweak would be a good idea.

Run the script again. It will attempt to autodetect how far you shifted; you can also set this number yourself. If you shift segments to occupy the space of lower numbered segments, that is a negative shift. You can cancel out and make no changes, or click finish.

Finish will re-apply all the saved structure, but to the original positions in space instead of the original segments. It will then remove the added notes and added bands (the original notes will remain).

If you want to start a new shift, but it goes to the finalize part instead, you can click abort, and it will clean up the notes and turn everything into loop.

Limitations:

  • Your shift region needs to overlap so that the auto shift detection will work. If you shift beyond that, you'll have to enter the shift by hand.
  • Autodetection looks at atomic-band distances, so don't wiggle, tweak rotate, or anything else that changes the backbone positions.
  • Cutting is optional, but the tweak will eventually fail when you run out of slack space (a large buffer will help). Also, not using cutpoints will increase the distortion and hurt autodetection since the protein is becoming distorted.
  • Not really tested: really long shifts, shifts near protein ends, shifts containing cutpoints, shifts involving ligands, shifting back and forth, selection interface. Be warned.

Things I discovered about tweak sheets:

  • The atom positions are not exactly the same!
  • You need at least 2 loops on each end outside the tweak region or the tweak will fail (wiki says 3).
  • The cutpoints must be at least three away or it will not thread properly.
  • The tweak tool will be located in the center of the tweak region, but the direction arrows relate to something else, perhaps the average orientation. This can be confusion in something like a zigzagging sheet, where the arrows could point in the OPPOSITE direction of the shift of the segment directly below the tool.
  • Using the rotate function rotates the entire group about its center, like the move tool. It doesn't rotate segments.
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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