Cutpoints also affect the operation of some tools, such as wiggle, although the exact reasons for this are not clear.
When cutpoints are open, the protein's score is not valid. All cutpoints must be closed for the player's solution to be counted.
If the ends of a cutpoint are too far apart, the cutpoint can't be closed. Cutpoints which can be closed are shown in yellow. Cutpoints which can't be closed are shown in blue. Clicking on a yellow cutpoint closes it.
Cutpoints act as a band, if the "Enable Cut Bands" option is selected in Behavior Options. This means that the wiggle tool tends to turn cutpoints from blue to yellow. Unlike regular bands, there is no way to adjust the strength or goal length of a cut band.
The method for creating a cutpoint varies depending on the version of the user interface:
- Original interface - right click a segment and choose Cut from the pop-up wheel
- Selection interface, select two adjacent residues and click on the scissors icon or use the lowercase "c" keyboard shortcut
A yellow connector (band) appears where the cut is made, the cutpoint appears between the segment highlighted and the next higher (numbered) segment, and a red line will appear through your score.
Score effect: Your score may increase or decrease and you can continue to work with open cutpoints but you must close them for any higher score to be registered. You may have a higher score with a cut point open, use 'Restore Credit Best' from the Undo menu to return to your best credit score.
Enable cut bands checkbox: If you move a cut section too far away from the join position the connector will turn blue, uncheck Enable cut bands so that when you wiggle the cut ends are not dragged together until you are ready. You can use a normal rubber band to hold the cut ends together until then.
When a cutpoint is made, the amino acid is literally being temporarily shortened and a gap is left. the cutpoints separates the two amino acids that are next to each other. This is why there is a score gain/loss.
Why Foldit has cutpoints
Cutpoints let you work on sections of a protein in particular rebuild and change from helix to sheet or vice-versa. You can also move cut sections using the move tool. By using cut points you are not adversely affecting parts of the protein by dragging them into position. Use undo or restore credit best to recover if you don't like the results.
Ever since computers have had the ability to protein fold, they have run into some problems. Computers find it very difficult to deal with cutpoints. Yet, since people are good at spatial recognition, the Foldit team suspected that people would be much better closing cutpoints than computers.
Shortcuts and speed
Cutpoints offer more precision and flexibily compared to other tools. Tools like tweak, straighten, rotate, and in some cases rebuild, are slow. if you are using rotate, it is faster to make a cutpoint and rotate. Stabilize the protein before closing the cutpoints.
As for the straighten tool; simply make cutpoints at each end of a structure and straighten or rebuild. Do not close cutpoint. Stabilize the protein, then close it. You may like to freeze the structure after straightening or rebuilding, then make bands, shake and wiggle (maybe at low (CI)).
If the cutpoints are blue, it means that either the endpoints are too far apart or that they are not ideally positioned (angled) to each other.
Position. Position the endpoints closely together (leaving roughly one segment of space between them). If the cutpoint is still blue, use pull mode to vary the angle between the endpoints until it turns yellow. As you vary the angle remember to keep the one segment distance between endpoints--if the endpoints are too far apart they will never turn yellow.
Stabilize. Make sure that "Enable Backbone Constraints" is checked on the Behavior menu, and run a stabilizing recipe (occasionally, just wiggling will do the job).
Join. Left click the yellow cutpoint to join the endpoints. If closing the cutpoint causes the score to go down (it almost always does), stabilize again. Many people like to close all the cutpoints once they have turned yellow (when they can be closed). Through experimentation, i have found that it is best to close 1 – 5 residues at a time. why? If more than five cutpoints are closed, points will be lost that you can’t get back. I like to run random squeeze then hydro puller, (recipes) then close cutpoints.
See videos here by Drumpeter and Madde