I think it is fixed now. If there are more problems, I will investigate. Thanks for pointing out all the errors before!
The article "LSm" in wikipedia talks about the family of proteins that 1311 belongs to.
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:
Meanwhile, a BLASTP search run on the Non-redundant protein sequences (nr)
database found many hits:
The latter search lists the DUF3107 superfamily with accession pfam11305.
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.
Finding frequent crashes while hand folding or running recipes. Hard to nail down the cause as the program simply stops working.
I have halted work on this puzzle until it gets fixed *and tested*. See feedback for crash log.
Still many crashes. Impossible to work on the puzzle
Crashed on first wiggle.
"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"
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
puzzle crashes immediately upon shake, wiggle, anything really
windows 10 laptop
Can we load solutions from puzzle 1311 into 1312?
The site below is calculating a Contact Map for
the 90-segment monomers in Puzzles 1311 & 1312:
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.
I have random crashes ONLY when I'm busy on screen.
No crash in the following situation:
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.
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.
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
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).
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.