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[DEVPREV] Symmetric Dimer: Buried Hydrogen Bond Networks
Status: Closed

Summary

Name: [DEVPREV] Symmetric Dimer: Buried Hydrogen Bond Networks
Status: Closed
Created: 04/27/2017
Points: 0
Expired: 05/04/2017 - 23:00
Difficulty: Intermediate
Description: This puzzle previews the updated HBond Network filter. H-bond networks are most effective when the hydrogen bonds are shielded from solvent, in the core of the protein complex. In this puzzle, an H-bond must involve at least one core residue in order to contribute to an H-bond network. Use the "Core Existence: Complex" filter to see which residues are considered to be in the core (check the Show checkbox in the Conditions panel). See this blog post for more info about the HBond Network filter.
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Comments

markm457's picture
User offline. Last seen 4 weeks 3 days ago. Offline
Joined: 11/16/2012
Unresolved Symmetric Design Crash Bug

The previously reported crash bug with all symmetric design puzzles is still unresolved. This bug makes all symmetric design puzzles unplayable for some foldit users like myself.

In the case of this specific puzzle, I opened the puzzle with devprev, selected manual shake and had a crash in under 2 seconds.

On the previous symmetric design puzzle, 1311 Hfq TB puzzle - fixed (http://fold.it/portal/node/2003148), I had 12 crashes in under one hour and most of that hour was spent saving/reloading to recover from crashes -> unplayable. This bug makes almost any script crash in less than a minute. For manual operations, a crash happens immediately on manual shakes and in under a minute for extended manual wiggles.

This symmetric design crash problem has been reported by more than one foldit user but does not seem to affect everyone. I experience these immediate crashes on both a Win 10 desktop and a Win 8 laptop, both with respectably fast cpus and lots of memory. I have had this problem on every symmetric design puzzle since returning to foldit in Oct. 2016.

In the 1311 crash bug feedback (http://fold.it/portal/node/2003127), Susume did some testing on previously issued symmetric design puzzles and showed that this bug has been present in symmetric design puzzles since at least Feb. 2016 including the beginner symmetric design puzzles.

I do not experience any issues with other puzzle types. This is definitely an issue with every, but only, symmetric design puzzles.

Susume's picture
User offline. Last seen 44 min 21 sec ago. Offline
Joined: 10/02/2011
clarifying

To clarify, the Feb 2016 symmetry puzzle did not receive any feedback about crashes when it was open, so I assume the puzzle itself was fine. The fact that it was crashing in Dec 2016 shows that the symmetry bug appeared in the software (not an individual puzzle) sometime between Feb 2016 (when it was fine) and Oct 2016 (when markm457 crashed on the beginner symmetry puzzle).

bkoep's picture
User offline. Last seen 1 hour 58 min ago. Offline
Joined: 11/15/2012
Groups: None
Thanks for the clarification!

That should be helpful!

bkoep's picture
User offline. Last seen 1 hour 58 min ago. Offline
Joined: 11/15/2012
Groups: None
Re-opened client?

Have you restarted the devprev client since the crash?

If any exceptions were raised in the crash, then your client should send us a crash report the next time it starts up. We haven't received any crash reports from this puzzle, which leads me to believe that no exceptions were raised in your crash (or, alternatively, you just haven't restarted the client).

We're aware of one extremely elusive symmetry-related bug, but it has been incredibly difficult to track down (it typically arises during long scripts, and can only be reproduced irregularly). While we haven't pinpointed the cause of that bug, we can recognize a symptom of it and trigger an "canary" exception. With the canary exception, we've been able to track crash reports from that bug, and it seemed to have gotten better in the last symmetry puzzles.

Your crash seems to be something different—it sounds like the same crash from Puzzle 1311 (which I thought we had figured out, but I'll have to revisit...). Hopefully we can find a way to reproduce your crash on a machine here and track it down. Thank you for the thorough report!

markm457's picture
User offline. Last seen 4 weeks 3 days ago. Offline
Joined: 11/16/2012
Re-opened client

I had not restarted the devprev client at the time of my initial post.

I just restarted the devprev client a few minutes ago (4/28/2017 ~ 6:40 am PST). It downloaded an update before restarting. Hopefully, you'll get the crash report.

jeff101's picture
User offline. Last seen 1 day 1 hour ago. Offline
Joined: 04/20/2012
Groups: Go Science
Does Random Idealize 1.8 still crash on symmetry puzzles?

Please see https://fold.it/portal/node/2000404
about symmetry puzzle crashes from a few years
ago when using Random Idealize 1.8.

Joined: 09/24/2012
Groups: Go Science
yes

I had a crash during local idealize (NOT on a shake) on a pose that had no crash on shake all (but well a crash on local shake)

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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, Microsoft, Adobe, RosettaCommons