Allow Delete and Add on design puzzles

Case number:845813-998416
Topic:Game: Tools
Opened by:Susume
Opened on:Monday, September 1, 2014 - 19:15
Last modified:Thursday, August 13, 2015 - 20:55

On ABeta binder and other design puzzles, it would be very helpful to Delete and Add residues (up to the total allowed). There's nothing so frustrating as finding that you need a little more slack between two helices or sheets, and you have residues free elsewhere in the protein, but no easy way to get the extras from point A to point B. If it is important that we all have the same length protein, you could strike through the score when residues are deleted and only give credit when they have all been added back.

(Mon, 09/01/2014 - 19:15  |  9 comments)

wisky's picture
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For the love of god, PLEASE implement this. This is an incredibly frustrating problem.

viosca's picture
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For those of us with older CPUs/hardware, this would let us build up a design in stages. Big design puzzles would be much more playable.

Susume's picture
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Wishing for this again on 1118! So aggravating. I estimate how long the structures and loops need to be before I build, but the chance of getting it just right the first time is approximately nil (unless I am building identical-length helices for the umpty-seventh time) and the cost of starting over from scratch is very high. With all the other challenges inherent in design puzzles, couldn't we please get rid of this one?

See also

spvincent's picture
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I agree: it's very frustrating not to be able to do this.

jeff101's picture
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Adding to or removing from the ends seems simple enough.

If you remove a residue from the middle of the protein,
you could leave the rest of the protein intact but have
its remaining 2 parts be connected by a cut point.

I'm not sure what to do if you want to add a residue
to the middle of the protein. It seems like part of the
protein would have to move to make room for the extra
residue. Would cut points on both sides of the inserted
residue work?

brow42's picture
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I agree with susume, puzzle makers should enable insert/delete on any unlocked and unconstrained residue in a design puzzle, with a boolean constraint on residue count.

I can see that there could be an issue with residues that have a constrained position, like in marburg. If i and i+1 are unlocked, but constrained so as to remain in the interface, then you wouldn't want to allow insertion between the two. Also risk of crashing bugs.

Jeff points out power shift This was was written for exactly this situation. But it is very hard to use.

If tlaloc's hooks into tweak were completed (at least the shift) I could write an automated version. This would be easier to use. Although still very finicky.

jflat06's picture
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There is a technical limitation of Rosetta in that symmetric insertion and deletion aren't supported (or else I would have implemented it like everything else when we added symmetry). There might be some workarounds, but even those have a lot of issues that would be difficult to resolve.

jeff101's picture
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Can you implement insertion and deletion for non-symmetric puzzles at least?

jeff101's picture
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Please try the recipe shiftit0 (
It shifts alpha-carbons along the protein chain from their original
positions to the positions of other alpha-carbons. Perhaps it will
help with design puzzles.


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