I usually do the same as silverberg but in this case with the protein mostly so far from the guide, I aligned the guide to one helix and then by mostly pushing and pulling at CI0 and freezing and rebuilding bits with a few bands I ended up with something close to the guide. I then created the rest of the bands and wiggled the result in whole and part till it reached a stable state.
What I really REALLY wanted was the ability to create zero length bands - which you can't do in GUI
I think everyone should collectively completely ignore these new puzzles. Impossible to work with.
wiggle doesn't work
behavior has no effect
backbone wiggle (Y) doesn't work
of course, no shakes work
can't use Rebuild in GUI recipes, so that's out
can't pull, then wiggle back, just sits there looking stupid
and probably a lot of other issues I can't remember because I'm too pissed off about it.
This centroid puzzle is an entirely new thing.
For us to help science, we should try to handle bigger proteins at the current technology available.
Foldit should not be confined to small proteins.
We should try to evolve our techniques and scripts to make this possible.
I think this will improve with more feed back and with more time.
We should give it a chance.
A suggestion :
I can see why centroid puzzles are going to be useful, to manipulate large proteins, and I am sure you will get them working well over time, but for now why don't you release smaller puzzles (normal foldit size with max 200 blobs) in centroid format whilst you are ironing out the problems.
Thank you all for your feedback.
Centroid mode is a tool from Rosetta that has been empirically shown to be useful in certain situations. With that in mind, we are interested in adapting it for use in Foldit. Doing so isn't trivial - there will be issues both with the code and with player strategies while using the tool.
Running this puzzle has given us insight into a lot of issues that did not present themselves in the developer preview release of centroid mode. We will be working on resolving these issues for the next release.
How about working on adding scoring conditions? This would help the wiggle issue, which is huge. Shake sidechains usually does inprove wiggle, though.
I mentioned this in the other feedback about Puzzle 705: http://fold.it/portal/node/995054#comment-22960
but I really want to apologize about this puzzle, since clearly it was not ready for primetime.
We really thought that we had addressed the main concerns from the feedback we got when we posted it in devprev:
http://fold.it/portal/node/994916
but clearly there was a lot more to address than just the bugs in the above thread (or why the clashing importance acts differently, which we tried to explain in the blogpost: http://fold.it/portal/node/995050)
Just to let you know that we will NOT be posting round 2 of 705 anytime soon, as we work to address your centroid suggestions.
I also think it's important that in the future we somehow transition more smoothly between a very novel puzzle posted in devprev and when that puzzle finally makes its debut in main.
Maybe it should be worth fewer points and not have any categories so that more players will try it (compared to devprev), but nobody will feel like "I have to play this horrendous puzzle or my ranking will go down".
As steveB suggested above, perhaps we should post a smaller centroid puzzle at first (once we address the many issues that have come up, of course).
This was actually the motivation for posting this first centroid puzzle as a Hand-Folding Puzzle. To be able to catch and address the basic bugs before uncovering the Lua bugs (that will certainly arise). It wasn't to make this puzzle even harder than it already was!
We thank you again for your patience with this puzzle and your understanding, and do apologize for how this went down.
(Hope this helps) My experience on 705.
Wiggle almost never worked, however sometimes it did.Using cut to position parts of the protein failed, because later joining the cut proved to be not working. Wiggle of just the cut parts (when open) moved big parts of the protein.
Rebuilding a joined part did not work well because of the big negative backbone.
Bands. Either it did nothing or it moved the protein violently. Quake made just a pile of the protein. Bands to space worked oke with wiggle if there were enough bands.
Rebuilding with bands worked normally (just about the only thing that did).
The score function had weird effects. Because bonds have no scoring effect strange positions were scoring well. See what I did to the big helixes: http://fold.it/portal/files/chatimg/irc_308854_1368093615.png
Also that clashing is not counted while the drawing makes clashes visible is strange.
Finally: negative backbone scores came in pairs. Selecting the segments and wiggle had no effect. Making a cut and wiggle repaired the negative backbone scores. Making cuts anywhere and wiggle the 2 segments also gained sometimes, while closed wiggle did nothing.
For this size of puzzles either the tools must be specially designed, or maybe it is possible to just locally recompute the score if local changes are made (with an special function to recompute the real total) might make these big ones playable with the normal sidechains.
Bump: still very much want stubs available instead of spheres - the spheres get in the way of seeing through the protein, seeing the center of the residue, seeing short rubber bands, seeing whether you have banded the backbone or the sidechain - but we need them turned on to find landmarks on the guide. The spheres have a place on the backbone and a direction, which should be enough to describe a stub. Please give us stubs as an option.
so far as I can see the blobs are only occlusive and of no benefit to play whatsoever