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Helix Straightening

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How to form and straighten a helix

Manually by hand:Edit

This one is good to get familiar with. Learn how to manually manipulate proteins in foldit with bands and pulling, however this can be extremely tedious.

Using only scripts:Edit

There are a number of Helix scripts amoung them being Tlaloc helixer and Helix curler and many others. Search for helix on the script page in foldit, then try running the different scripts and see what they do.

Manually with scripts:Edit

A combination of scripts and manual tecniques can some times bring the best results

[I personally like to use both. I will show my method and from scratch with the basic tools.] [Also keep in mind that the method spoken of underneath is for a denovo puzzle. I will also speak about fixing skewed helices.] [I may also be able to provide clear picture of each step as I had done it in the past with a relatively small puzzle for ease of view. I will look into it] Great!

From a denatured puzzle:Edit

Coiling Freeze everything but the helices and 3 segments at both ends. [picture] Run helixer until the helices are more compact and stop it. (Doesn't matter if they don't have a consistent shape) Turn Cl to 0 Press D (disable bands) One by one, right-click a helix and click rebuild Let it cycle through shapes until a specific one looks good (a near perfect, right-handed coil), and stop it.

Settling Run wiggle all with Cl @ 0.9 until the loops are untangled. Settle with shake at low @ 0.3 and wiggle side-chains @ 0.8 a few times. Run wiggle all @ 0.8.

Cleaning One by one, right-click each helix and click tweak Now press and hold either of 2 purple, floating balls, which is the SS straightener. Wait until your helix is as straight as possible and stop the tweak tool. Now after each straightened helix, shift+double click the helix to preserve it. Do it with every helix and then you'll have everything but the helices bare-bone that are frozen. Repeat the steps in the "Settling" section.

You should now have near-perfect helices; so long as you keep them frozen during scripts like QuakeR, they will not bend around.

Fixing skewed helicesEdit

Tweeking streight and the use of bands and rebuilding can help with skewed helices.

More Techniques at > The Foldit Labs

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