20201223-e20c1e0f15-win_x86 bad loop shows ONE residu in a helix

Case number:671071-2011112
Topic:Game: Other
Opened by:Bletchley Park
Opened on:Sunday, January 24, 2021 - 09:34
Last modified:Monday, March 15, 2021 - 05:53

20201223-e20c1e0f15-win_x86 solution shared with scientists: 'faulty_filter'

When checking for bad loops, ONE residu in the middle of a longer helix is highlighted.
Working on the helix segment can get rid of the 'bad loop' designation but it seems odd to me that a helix section is identified as a loop.


(Sun, 01/24/2021 - 09:34  |  7 comments)

Joined: 12/06/2008
Groups: Contenders

I have the same issue on puzzle 1951. One of the four residues in my loop (203-206) is marked as a bad loop, while the rest of the loop shows to be okay. Engaging the "Auto Structures" function changes 203-205 to an extension of helix 186-202.

How can one residue residing between two helices be marked a non-ideal loop?

My structure: https://ibb.co/nbHryJs
Auto Structure: https://ibb.co/bm8NPzC

Joined: 12/06/2008
Groups: Contenders

Uploaded to scientists as "1-residue-bad-loop".

Joined: 12/06/2008
Groups: Contenders

I am still seeing this in design puzzles. I have found there is no way to remove this penalty, no matter how many hundred times I remix/rebuild that section of my protein.

Joined: 12/06/2008
Groups: Contenders

Here is the latest 1-residue bad loop, this time at the very end residue of 1960:


I'll upload this solution to the scientists, if y'all want it.

Joined: 12/06/2008
Groups: Contenders

And yet another one.


Uploading to the scientists as "1-residue-bad-loop-4", since this is the fourth time I have recently encountered this.

bkoep's picture
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Thanks for the reports, Bletchley Park and BootsMcGraw! There does seem to be a bug here, and we are looking into it.

Note that it is possible to have a bad loop that is only one residue long, for example if that residue is between two helices and has an unrealistic backbone. However, the Ideal Loops Objective should never flag a single residue at the end of the protein chain.

jeff101's picture
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Joined: 04/20/2012
Groups: Go Science
Come to think of it, I may have encountered this bug too in Design Puzzles
where, say, segment 89 is the end of the fixed and non-mutable part of 
the protein (like the target) and segment 90 is the start of the mobile 
and mutable part that we can design (like the binder). Segments 89 and 90 
are not connected to each other, and I think this is what causes a 
non-ideal loop at residue 90. It also makes strange spots on the Rama Map 
for segments 89 and 90.

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