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Recipe: tlaloc Bands for Native 4.05
Created by Tlaloc 69 1797
Your rating: None Average: 4.4 (11 votes)


Name: tlaloc Bands for Native 4.05
ID: 40836
Created on: Fri, 04/20/2012 - 13:55
Updated on: Wed, 04/25/2012 - 20:22

Creates bands from first "knuckle" of the sidechain for each segment for Quest for the Native puzzles. You will still need to position each of the bands, but at least you don't have to create them.

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Tlaloc's picture
User offline. Last seen 8 weeks 6 days ago. Offline
Joined: 08/04/2008
Groups: Mojo Risin'
Details on how to use it

This is only for Quest to the Native (QTTN) puzzles, where you have a guide that you are trying to match.

Recommended settings for QTTN puzzles: View the options, turn on "Show Outline," set the background color to white, and view stubs on the sidechains, view the guide, and set color relative to guide. Turn all the other view options off.

Run it once, set the band to the native equivalent sidechain (hover over the sidechain on the protein to find the equivalent sidechain). You will need to rotate the protein by 90 degrees several times to get the sidechain positioned in 3D since you are working in 2D. Make sure the ball of the band is over the first "knuckle" of the sidechain.

Then run the recipe again. It will remember what the last segment you were working on with a note with the text "Current". The next segment will be selected in the dialog by default. Normally, you can just click the "Start" button.

If you lose which segment you are supposed to be setting, select Modes Note Mode to have the Note show you the segment.

Do not hit Align Guide after starting this process, or you will need to do it all over again.

If you select the "Reband" checkbox, it will remove all the current bands and set all the first knuckles of the sidechains to have zero length bands for all segments that have numbers less than the "current" segment.

Tlaloc's picture
User offline. Last seen 8 weeks 6 days ago. Offline
Joined: 08/04/2008
Groups: Mojo Risin'
More notes

After setting the band, wiggle all, shake, and perform other operations to make the protein fit the band.

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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, Boehringer Ingelheim, RosettaCommons