puzzle picture
1311: Hfq TB puzzle - fixed
Status: Closed

Summary

Name: 1311: Hfq TB puzzle - fixed
Status: Closed
Created: 11/30/2016
Points: 0
Expired: 12/07/2016 - 23:00
Difficulty: Intermediate
Description: Note: Due to a large number of crash reports, this puzzle has been made worth zero points. The puzzle will remain active, and players are encouraged continue playing the puzzle if they can. We will still analyze players solutions for scientific merit!

This TB puzzle is summarized in http://fold.it/portal/node/2003049. It is a hexameric protein responsible for virulance factors in TB. We do have crystals and phase data, but none of our models work! Help us get a model to solve this structure. VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRVGFGVGVDAAAGSAGKVATSG
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Comments

Joined: 01/12/2015
Groups: None
I think it is fixed now. If

I think it is fixed now. If there are more problems, I will investigate. Thanks for pointing out all the errors before!

Susume's picture
User offline. Last seen 4 days 22 hours ago. Offline
Joined: 10/02/2011
More about the protein

The article "LSm" in wikipedia talks about the family of proteins that 1311 belongs to.

https://en.wikipedia.org/wiki/LSm

jeff101's picture
User offline. Last seen 5 days 3 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
More about the protein

The Wikipedia article Susume cites above looks very useful.

I would like to add that a BLASTP search using the 90-segment monomer sequence
run on the pdb database found no significant similarities:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=3ZKGN6R8015

Meanwhile, a BLASTP search run on the Non-redundant protein sequences (nr)
database found many hits:
https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=3ZK5XJY3014

The latter search lists the DUF3107 superfamily with accession pfam11305.

Susume's picture
User offline. Last seen 4 days 22 hours ago. Offline
Joined: 10/02/2011
Sidechains in active site?

The few Hfq proteins that are solved and in the PDB have a different SS sequence than ours - they start with a helix and then have all their sheets. The little piece of RNA they bind to goes in the middle of the hexagon - so there are presumably some sidechains in the "hub" of the hexagon that contact the RNA. I would expect those sidechains to be heavily conserved across homologs to the proteins in the PDB. Even though our solution will be different from the solved ones (because of different SS), I would expect the same or very similar sidechains to fall in the hub of our hexagon. I would expect those sidechains to be heavily conserved across homologs to our protein (a different set of homologs than the proteins in the PDB have, because of different SS). If we knew what positions those conserved sidechains have in homologs to our protein, we would know which residues to put in the hub.

SaraL's picture
User offline. Last seen 1 year 15 weeks ago. Offline
Joined: 09/20/2011
Groups: Gargleblasters
Problems

Finding frequent crashes while hand folding or running recipes. Hard to nail down the cause as the program simply stops working.

Joined: 05/19/2009
Groups: Contenders
Not fixed.

I have halted work on this puzzle until it gets fixed *and tested*. See feedback for crash log.

manu8170's picture
User offline. Last seen 2 days 3 hours ago. Offline
Joined: 09/09/2010
Still many crashes.

Still many crashes. Impossible to work on the puzzle

dcrwheeler's picture
User offline. Last seen 1 day 22 hours ago. Offline
Joined: 09/05/2013
Groups: None
Crash

Crashed on first wiggle.

Debug.txt

version: 1
{
"build_id" : "20161025-b1cee28202-win_x86"
"crash_id" : "682a2256-552c-493b-a0c2-c8948c2302ae"
"current_actions" : ""
"current_tool" : "Pull Mode"
"file" : "core/conformation/Conformation.hh:385"
"machine_id" : "33fdce14-69eb-4b50-9b79-5877cd411c1b"
"macro_id" : "-1"

"message" : "Error in core::conformation::Conformation::residue(): The sequence position requested was greater than the number of residues in the pose."

"player_id" : "513977"
"puzzle_id" : "2003048"
"puzzle_running_time" : "2"
"running_time" : "967992"
"timestamp" : "1478759067"
}
verify: 1250bf8b841c82e70aeac254790ffa3a

Joined: 11/16/2012
crash on initial shake

I opened 1311 (fixed), my first action was to select manual shake, and client crashed within 3 sec

I note, for the developers, that the symmetric design beginner puzzle has the same issue - any shake, manual or within a script, caused an almost immediate crash.

Running on Windows 10

jamiexq's picture
User offline. Last seen 16 hours 58 min ago. Offline
Joined: 07/31/2011
not fixed at all

puzzle crashes immediately upon shake, wiggle, anything really
windows 10 laptop

jeff101's picture
User offline. Last seen 5 days 3 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
Will 1311 solutions load into 1312?

Can we load solutions from puzzle 1311 into 1312?

jeff101's picture
User offline. Last seen 5 days 3 hours ago. Offline
Joined: 04/20/2012
Groups: Go Science
Contact Map for 1311/1312

The site below is calculating a Contact Map for
the 90-segment monomers in Puzzles 1311 & 1312:

http://raptorx2.uchicago.edu/ContactMap/myjobs/60338832_109300/

Joined: 11/16/2012
18 crashes

Last night, I really tried to work on 1311. I had 18 crashes in one hour, I counted. Shake crashes, a wiggle for more than a fraction of a second crashes, standard scripts crash as soon as they try to wiggle or shake. This is beyond frustrating.

Joined: 09/24/2012
Groups: Go Science
Crashes avoided

I have random crashes ONLY when I'm busy on screen.

No crash in the following situation:

(Windows 7)

View not viewing the symmetrics
Graph properties 0 memory and 0 length (susume)

Limiting movements of the mouse on the window (I surround the window) and very slow actions (not doing many thinks quickly one after the other).
Don't move the mouse when an action is ongoing (e.g. shake: only start and stop, nothing else).

Recipes: never crashed on window minimized.

It looks like the problem is linked to video display.

LociOiling's picture
User offline. Last seen 50 min 52 sec ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
See also feedback 2003167

I agree with Bruno that interacting with the window while a foldit action is running seems to cause crashes. But I've also had crashes while running a recipe with the window minimized. I haven't yet tried reducing undo steps and memory usage to zero.

I also noticed that the "show isosurface" view option only shows the isosurface for three of the six chains. See feedback 2003167.

Joined: 09/24/2012
Groups: Go Science
Several Safe recipes for 1311

Several recipes can be used without crash if they don't contain a ShakeSidechainsAll action. Following recipes would be safe for using on 1311 (minimizing the window is much safe):

Quickfix 3.3.2, for fixing after hand work

Quaking Remix 1.4.4, for science valid rebuild

Tvdl enhanced DRW 2.8.1a, here you must absolutely check the option "Do shakes only local".

Rav3n_pl GAB BiS Filter v2.2.3, good for fine tune linking the monomer elements

Acid Tweeker V2.6.1 Filter, for fine tuning at the end

Joined: 09/24/2012
Groups: Go Science
Another option for short term further work

As structure.shakeSidechainsAll() makes most of the bugs (possibly structure.shakeSidechainsSelected as well when all or non residues are selected), a short term solution might be to re-post the puzzle without Shake.

When shake will be called, nothing would happen (and no crash).

Joined: 09/24/2012
Groups: Go Science
Tip for hand shaking without crash

The following recipe does one shake that doesn't crash:

Quick Shake Algorithm

It has been implemented in some of the recipes above, explaining why they less often crash.

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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, Amazon, Microsoft, Adobe, RosettaCommons