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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)).
 
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)).
 
==Closing Cutpoints==
 
==Closing Cutpoints==
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<p style="margin-bottom:1em;">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. </p>
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  +
''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.
  +
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''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).
  +
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''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.
 
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.
   

Revision as of 10:54, 23 December 2014


Cutpoints

To make a cutpoint in the:

  • Original interface - right click a segment and choose Cut from the pop-up wheel
  • Selection interface, select two connected residues and press C

A yellow connector (band) will appear 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 vica 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 special 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)).

Closing Cutpoints

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