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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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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:
Things I discovered about tweak sheets: