Enable Cut Bands

Case number:845813-995906
Topic:Game: Tools
Opened by:bertro
Status:Open
Type:Question
Opened on:Wednesday, September 11, 2013 - 00:32
Last modified:Monday, January 28, 2019 - 09:42

Can someone explain what is "Enable Cut Bands" checked and unchecked are supposed to do?

Or what is the usage/purpose in unchecking it?

Thanks

(Wed, 09/11/2013 - 00:32  |  7 comments)


Susume's picture
User offline. Last seen 2 days 22 hours ago. Offline
Joined: 10/02/2011

Sometimes you want to wiggle the protein while there are cutpoints open, and not have the blue bands pull the pieces together. For example, if you have placed a few pieces together and want to wiggle them into place, but there are other pieces waiting at a distance that you haven't placed yet. So you uncheck Enable Cut Bands, and the blue and yellow cutpoint bands don't pull during your wiggle. If you want a little bit of pull at the cutpoints, but not as much as the very strong cutpoint bands provide, put a regular rubber band where the cutpoint is and disable the cut bands before wiggling.

When there are no cutpoints, there are no cut bands, so the checkbox has no effect.

bertro's picture
User offline. Last seen 5 days 18 hours ago. Offline
Joined: 05/02/2011
Groups: Beta Folders

Thanks Susume.

Joined: 04/15/2012
Groups: Beta Folders
Status: Open » Closed

Answered.

Joined: 09/24/2012
Groups: Go Science
Status: Closed » Open

I noticed an effect even when there are no cut. Can anybody explain this?

1) Enabled cut bands

I go to an optimal untill Wiggle gains no point. Same on local wiggle (right click) on an unideal loop that was ever cut before (I notice it is unideal when using the tool "idealize").

2) Disable cut bands, wiggle all (low, medium or high): no effect

3) Disable cut bands, wiggle on an unideal loop (right click) that was ever cut before:
score goes down -190 pts with Low, - 160 pts with Medium, and -185 pts with High.

4) Enable cut bands and local wiggle: score goes up but never returns to previous high score.

jeff101's picture
User offline. Last seen 2 days 1 hour ago. Offline
Joined: 04/20/2012
Groups: Go Science

When the Enable Cut Bands box under Behavior is checked,
what are the strengths and target lengths of yellow and blue cut bands?

Also, when the Enable Cut Bands box is unchecked,
what are the strengths and target lengths of yellow and blue cut bands?

It might be possible to find the answers by adapting DoBandsObeyHookesLaw1
https://fold.it/portal/recipe/46844
to put a normal band into a tug-of-war with a cut band,
but if someone already knows the answers, please let me know.

Thanks,
Jeff

jeff101's picture
User offline. Last seen 2 days 1 hour ago. Offline
Joined: 04/20/2012
Groups: Go Science

A related question is if the present length
of a cut band is simply the distance between
the alpha-carbons (CA's) it seems to connect.
Is it instead the distance between a backbone
N atom and a backbone C atom (the C attached
to O)? Also, do cut bands distinguish between
trans and cis peptide bonds? trans peptide
bonds have CA-CA distances near 3.79 Angstroms
while cis peptide bonds have CA-CA distances
near 2.91 Angstroms. You'd think that cut bands
for trans and cis peptide bonds would have
different target lengths. Does Foldit give all
cut bands the same target length, around 3.79
Angstroms, as if they were all for trans peptide
bonds?

brow42's picture
User offline. Last seen 3 weeks 2 days ago. Offline
Joined: 09/19/2011
Groups: None

I'm pretty sure it's a pair of constraints on the peptide bond: 1.47 A, and 0 or 180 degree dihedral angle. The distance constraint is stronger than a strength 10 band. You should be able to work out the coefficient (in energy units) with your band script.

The cuts are drawn between CA, but that's just for visualization.

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