[NewChapter] rebuild is very slow and sometimes not finding anything

Started by Timo van der Laan

Seth Cooper Staff Lv 1

There will be an update to newchapter shortly that should allow rebuild to find more potential solutions. Let us know if this helps out with this issue.

Susume Lv 1

Attached is some data from newchapter rebuild after the update - it is finding more solutions now, as many as devprev was, but at CI 1.0 they are still only high-scoring solutions. Solutions with bad sidechain clashes that could be cleared by shake are still excluded (at CI 1.0).

Newchapter found more good rebuilds (ones with net increase in score after shake and wiggle) than devprev on TR663, and fewer on the ED puzzle. On both puzzles, the overall gain from rebuilds was much less for newchapter than devprev, because the gain from each good rebuild was less.

Susume Lv 1

Note: If you are having trouble with rebuild, be sure to shake first, rebuild a while, then shake again and rebuild some more. Rebuild will reject poses with bad sidechain clashes that it used to accept, so it needs help from shake.

If there is a cut where you are rebuilding, disable cut bands before rebuild. They will pull like superstrong rubber bands if you don't.

Also, try different CI levels. Rebuild at zero CI will put the backbone through itself repeatedly and makes horrible helices.

spvincent Lv 1

I certainly think we need to go back to the previous rebuild. I thought after the last scientist chat that this was going to happen but this doesn't seem to be the case.

NickyCGS Lv 1

Thanks for all the feedback and wanted to give an update. Reproduced/verified this yesterday and we brought it up during the meeting and it is being looked at now.

Susume Lv 1

Got the update of Feb 3 to devprev, which was expected to fix some of the rebuild issues. It is not better.

Rebuild has gone back to being extremely slow to find poses. On segs 54-58 of the ED puzzle (beginner), in 2 minutes of rebuild it found only 4 poses.

It is putting the backbone through itself even at CI 1.0. This is a bug. In my experience, rebuild should pay attention to backbone clashes according to clashing importance, putting the backbone through itself only at CI 0. It should ignore sidechain clashes, since those can often be resolved by shake.

It is completely deforming an already well-formed helix, mashing it into a jumble, again crossing the backbone despite CI 1.0.

BootsMcGraw Lv 1

I suggest all players refuse the most recent update until this issue is resolved, and also to always keep a backup directory with the last working version of the game in it, in case an update turns out to be a huge flop. We're offered no options to "downgrade" back to a former version of the game.

auntdeen Lv 1

I accepted the Feb 3 devprev update and opened 841 for the first time.

I tried using rebuild for the little helix at the end, and it did rebuild - although it ended up embedded in the sheet next to it (I changed no Behavior from default). But a local shake and local wiggle brought it out of the sheet and it looked normal.

Then I tried to rebuild the large helix. First I cut both ends, unchecked Enable Cut Bands, and selected Rebuild from the wheel. One end immediately homed in on the sheet next to it, and rebuild did nothing - just small differences, nothing visually curling.

I moved the helix far away from the rest of the protein… The helix still tried to home in on that sheet, and again, nothing much happening.

Then I tried the new NC method of rebuilding a helix - tweaked it until it finally curled up. Did a local shake and wiggle… Completely red and distorted.

Finally I tried the old school way of banding both ends to create some slack for the helix, and did rebuild. Ten minutes later, it's still a distorted mess.

Susume Lv 1

To reproduce the problems, just put all settings to default values, reset the ED beginner puzzle, right click the long helix and hit rebuild.