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Recipe: Glycine Flipper 1.0
Created by brow42 76 351
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Name: Glycine Flipper 1.0
ID: 42766
Created on: Tue, 06/26/2012 - 04:42
Updated on: Tue, 06/26/2012 - 11:48
Description:

Tries to rebuild a glycine until it flips over. Experiment with the options. Select the glycine either in selection interface or freezing it. Cancel when Ca is big if it won't flip.



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brow42's picture
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Joined: 09/19/2011
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Rebuilds glycines until the atoms shift

This script rebuilds a glycine until its C-alpha atom moves at least 1.7 A....This is taken to mean that the glycine has flipped over. You can cancel at any time, and the most recent rebuild and your initial state will be placed in the undo buffer.

Unfortunately, rebuild requires some flexibility, so you will actually have to do a 2-segment rebuild. You can pick whether to include the segments before or after the glycine in the rebuild.

3-segment rebuilds are likely to just move all the segments rather than flipping the glycine. You can ask that the c-alpha atoms of the neighbors be pinned. This often breaks the rebuild however, producing no new conformations.

You can ask the script to band the C-a to encourage it to move. This may also break the rebuild. The helper band may also point in the wrong direction. Remember you can disable it during the script with the 'd' key. Don't try to re-enable it though, bands are being used as rulers.

The script does not delete pre-existing bands so you can add your own helper band.

Wait awhile, getting a flip can take time. If rebuild is producing different conformations but it's not stopping, you can hit cancel. You should cancel when the 2nd column in the output window is the largest value. A future update will probably do this for you. This is the largest shift it got, if not a full flip, maybe a 90 degree rotation. There may be reasons why it can't flip. You can always hit undo once to get back your initial state and try again with different options.

If you freeze exactly 1 glycine, or select exactly 1 glycine, the script will run with default options (2 seg rebuild) without showing the dialog.

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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