Hydrogen bond shown only on one side of a Tetramer (and get 1 Buns for free!)

Case number:671071-2011798
Topic:Game: Other
Opened by:HuubR
Opened on:Friday, June 25, 2021 - 20:43
Last modified:Friday, October 8, 2021 - 18:24

In puzzle 2006, I noticed a strange situation: a Hydrogen Bond that is shown from segment 1 on Chain 1 to segment 9 on Chain 0, but not shown as its "mirror image", from segment 1 on Chain 0 to segment 9 on Chain 1.  And, even stranger: it leads directly into a blue Buns.

I found this when a Buns emerged in my solution, and I wanted to fix it by making a Hydrogen Bond.  To my surprise, that bond was already there!   It could be that I am missing something here, but in my mind, a Buried polar that makes a hydrogen bond cannot be UNSatisfied at the same time, so it cannot be a BUNS.

I made two almost identical views of the same situation, looking at two different corners of the Tetramer.  One view, with Chain 0 at the top and Chain 1 (purple) at the right hand side, shows two hydrogen bonds to the backbone of Chain 3 (brown, bottom left), as well as one Buns on the N terminus (segment 1: the yellow one).  That could make sense, although one of the acceptors of the purple segment 9 (in the middle of the picture) seems to be in an ideal position for a hydrogen bond.

Segment 1 showing two H-Bonds to the left
This view DOES show the H-Bond to the right

The second view shows another corner of the Tetramer.  This view has Chain 0 at the right hand side and Chain 1 (purple) at the top.  The two bonds from segment 1 to the left are not shown in this view, because in this corner they go from Chain 1 (purple) to Chain 2 (green).  But the bond to the right, that was not shown in the other view, is now shown, together with the Buns!

Around the time this puzzle closed, I have uploaded a similar solution for scientists (Puzzle 2006, 22155 points), showing the same phenomenon.

I have no idea how often a situation like this occurs.  There are a couple of specific circumstances that might play a role here:

  • It is a hydrogen bond between backbone (donor side) and sidechain (acceptor), which is not very common.
  • The donor side is the N terminus, which means that this Amino group has three Hydrogens (all other residues have only one H in the Amino group).  In my example, all three of them make H-Bonds.  That is probably even less common.

I do not think this bug (if it is one indeed) should get a high priority to be fixed.  But I would like to know whether it is indeed a bug, or I have simply misunderstood something here.

(Fri, 06/25/2021 - 20:43  |  2 comments)

HuubR's picture
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Would somebody be able to answer the question that I asked three months ago: is this indeed a bug, or is it just me, misinterpreting the situation?

I am seeing the same issue again, in Puzzle 2050.

bkoep's picture
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Joined: 11/15/2012
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Yes, this looks like a bug, possibly related to the weird band behavior in D2 symmetry. I’ve reproduced the issue, but it seems to involve some old and somewhat obscure code deep inside Rosetta, so may take some time to figure out.

In the mean time, please let us know if you see similar behavior in other symmetry puzzles—especially if you see it in non-D2 symmetry.


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