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jeff101's picture
User offline. Last seen 1 hour 56 min ago. Offline
Joined: 04/20/2012
Groups: Go Science

I've been using the Blueprint Tool in recent puzzles,
but I don't think I am using its yellow boxes correctly.
It seems like the yellow boxes enforce constraints for
various ideal loops, so they help at first. Nevertheless,
when I remove the yellow boxes, the structure changes
& the score drops drastically without me doing a single
wiggle shake rebuild etc. What is the best way to use
the yellow boxes? Should they be left on the structure
throughout the puzzle? Should they be removed at some
point, and if so, when is the best time to remove them?
Can they be removed in a way that doesn't cause drastic
(or any) structure & score change? Is there a video or
web page you'd recommend for help?


Susume's picture
User offline. Last seen 12 hours 50 min ago. Offline
Joined: 10/02/2011
Have you deleted any residues?

If the structure is pretty stable (can be wiggled without exploding), removing the yellow boxes should not cause it to deform much on the next wiggle, and the score typically goes up significantly on the first wiggle after they are removed. The top folders I have heard from remove them very early - one removes them immediately after dropping the blueprint on the protein. I typically remove mine after the first 3 or 4 wiggles.

One thing that does sometimes cause significant deformation is adding or deleting residues and then undoing that move. This can cause the constraint (the yellow box) to be lined up with the wrong residues. Removing the yellow boxes (which removes the constraints) should clear this problem up, however.

I have never seen that removing the constraint causes a shape change or score change by itself (without wiggling) - that part is very strange.

Joined: 09/24/2012
Groups: Go Science
Removing with caution

I usually keep the yellow boxes as long as possible. Only when I cannot move anymore, I remove them and score can again rise up.

After removing the boxes, I use red fuse in order to find a new higher score.

In order to remove them without exploding the structure, I carefully click and drag the border of the yellow box, not touching the residues inside and not coming back in the blueprint windows (otherwise, a new structure is added to another part of the protein). I think that exploding the structure might be linked to touching the structure inside of the box (which seems to create another kind of yellow box) or passing on the rest of the structure with the box.


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons