Screenshot - A pair of rubber bands in 3-space

Rubber Bands

Rubber bands are created by using the center mouse scroll button, or shift click or right click and drag in the selection interface.

Select the segment (residue, amino acid) you want as your rubber band base point and click and hold down the middle/scroll button. Drag away from the segment and a purple band is formed. You can either attach the band to another segment by dragging the end of the band to the targetted segment, or you can leave the band with the end point in open space. The band will pull the segment that is its base point toward its end point.

Bands are tools used to pull parts of a protein together with the use of a wiggle. They are more controlled than a pull. A band can be created between two residues/sidechains or between a residue/sidechain and nothing. The wiggle normally just seeks to relax the backbone and increase score but a band affects that by defying the wiggle and moving the protein in a different direction. Increasing the strength of a band increases the priority of the band over the wiggle. The length of a band can be changed to either push two residues apart or limit the amount a band can contract.

Changing strength and length of bandsEdit

A short video :
Right click on a band to see the dialogue box to make changes to the band's strength and length.

Using Rubber Bands With Global Wiggle

I have found that after a global wiggle has stopped, and the score is no longer moving, more points can be garnered by employing rubber bands while the global wiggle is still on. This will not always work, but when it does, the points obtained can be substantial. (This does not work well with a large protein, if at all.)
Your first step is to look at the protein to identify the different pieces of it, and look for any hinge points (where protein movement occurs easily). Second, you can either stop the global wiggle to attach banding (recommended for beginners), or you can do it on the fly with wiggle still engaged. You need to be fast if you do it while the wiggle is still engaged, however, or your protein will start moving about with large swings. Stability is the desired end result of adding these bands.
Now, once you have done your homework and have an idea on where the protein is easily moved, you can start adding rubber bands. Select a hinge point segment and attach 2 rubber bands to it. These bands should be pulling away from each other, so that the protein is stable, and the score should not move very much. Let any movement settle down and watch the score. It will swing lower at first, but will go back up when the protein finds its comfort spot. Keep adding bands to other key points, following the above directions. (I usually can find at least 5 to 10 segments that I want to add bands to.)
After all the bands have been added, the fun can start. (Make sure you save your puzzle after all bands have been added, so that you won't need to do them all over again.) Move a band just enough to move the score. The idea is to have the score start going up. Just play with the bands and move one, two, or three really quickly. The score will swing down, but will normally swing back up after it has moved and is resettling. If everything works right, it will swing up past your high score. Yay.
This can be worked with for quite some time. I have gotten as many as 50 points at one time, in small increments, using this process. Experiment and try different things. Finally, after you get no more points and have hit the wall, turn off wiggle, remove the bands, then global wiggle again. This can sometimes produce another jump in points. Even if the whole process has netted nothing, this may give back some points, so try it.

Band Attributes

Grey rubber bands are disabled (meaning that they don't have any effect). You can disable/enable all bands at once by hitting "D" on your keyboard. You can disable/enable individual bands by right-clicking on them and choosing "Disable/Enable Band" in the context menu.
Each band has attributes:
1. Length: how long a band is. If the band length is bigger than the distance between banded segments, then the band is pushing instead of pulling! Length can be set from 0 to 20.
2. Strength: how much power a band has. In recipes or scripts, this can be set from 0 to 10. Manually, it can be set from 0 to 2.5. 0 is useless (equivalent to a disabled band) but 10 is sometimes needed :)

HaveFun! August 3, 2008‎ by Stormrobberee

I have included a screen shot below of the set up that I used on the Nucleosome Protein.


Rubber Banding With Global Wiggle

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