The spheres make the backbone very hard to see, but if I turn them off I can't find the matching piece of guide. It would be helpful to have "show stubs" available as a compromise - so we could see backbone and some generic version of the sidechains simultaneously.
The blobs (they look like ticks, ugh) obscure the structure, but if they are turned off, there is no way to see where they are on the guide.
With this large of a puzzle, when I zoom out so I can see the guide & protein at once, the guide is so far away from the protein that by the time I move my mouse over to adjust a band, the guide blobs have turned back off already. I don't want them to persist forever, but they need to show long enough to be useful.
Thank you both for your suggestions.
We know there are going to be a lot of things that need to be changed for centroid mode, and we'll try to address them as quickly as we can.
Please make sure you have read tamirh's blogpost about centroid puzzles (if you haven't already):
http://fold.it/portal/node/995050
We tried to address the feedbacks we got for the centroid puzzle in devprev (thank you to everyone who reported bugs with that one) but we realize a lot more people will be trying it out now, so we thank you in advance for your patience.
If you execute a GUI script in centroid mode that uses the "shake sidechains" function, the script executes that function for a long time (indefinitely?), doing nothing, until you hit the space bar to stop the function and allow the script to continue. All GUI and LUA functions such as shake sidechains, mutate, etc. should return immediately if executed in centroid mode.
With the lack of sidechains, the wiggle functions has very little effect on this puzzle. This means that the only way to change a section of the puzzle and gain points is to rebuild, which on a QTTN is counter productive, as you end up diverging from the original shape.
Without an effective wiggle function I can't see that it would be possible to get anywhere near a native structure on a de-novo puzzle using this format.
Agree with the above posts that the bubbles are way too big.
Also would like to add that this puzzle is not that much fun to play either - too few tools to use on it, and no natural feel to the puzzle's movement (if you are lucky enough to get it to move at all).
Bug ?
If you isolate a section of segments by freezing either side of them, and then wiggle these segments, the rest of the protein also moves. Is this a bug, or a feature of the centroid system ?
I've played with this a little this morning.
I knew local wiggle and wiggle did different things, but this was pretty drastic.
I've saved and uploaded for myself two solutions, CutRebuildBeforeWiggle and CutRebuildAfterWiggle (local wiggle).
Before:
After local wiggle:
Local wiggle destroyed the helix.
from alwen's comment above:
"I don't want them (guide blobs) to persist forever, but they need to show long enough to be useful."
Suggestion: I would like to add that a way to adjust the ON and OFF timer lengths for showing/hiding the "guide blobs" would be appreciated. Sometimes, I like it short and at other times longer.
Thanks
Once you add a band to a blob, that blob never disappears even when show sidechains is off - this is standard behavior. Unfortunately, once the band length becomes zero, you can never see the band to click it because the blob covers it up. Even in line view the blobs stay fat and blobby and in the way. One solution might be to make the blobs semi-transparent (or let us turn them into stubs as mentioned earlier).
I'll add a comment to Susume - yes, if you band from the individual segment centroid, the centroid will persist on-screen, so that when you waft a mouse over it, you'll see the corresponding guide shadow, which is helpful.
But, when banding, you're aiming for the middle of the guide segment. The centroids are off-set to the edge of a segment when you 'shift a' in the displaying of them, so that needs to be fixed
CFC
Thanks for all of the comments about centroid mode. We know it's very different and we appreciate you guys playing with it and finding issues with it. I'll try and address all of your comments as best I can:
Stub mode: I think having the spheres show up differently in stub mode is a good idea. Perhaps they will just be smaller, or we might think of a different way of visualizing them. We will do something about this.
Sidechains on guide: It would be good to have this time in options.txt or as a GUI editable value. We might add something like this.
AA Coloring: This is kind of separate from centroid mode, but it may help. There was a request to be able to color the backbone based on AA. That change has been implemented and should go out in the next version.
Shake in scripts: We've fixed this issue. It hasn't made it to the released version yet. It will be in the next update.
We're looking into if we can add more scoring terms that are compatible with the approximated sidechains to get wiggle to behave closer to what you guys have gotten used to in normal puzzles. Centroid puzzles are inherently different though, so wiggle (and other tools) will always be different.
We will look into some way of dealing with 0 length bands.
The amino acid spheres are intentionally offset to the position where the sidechain approximation origin is.