Serious issues rebuilding helices

Started by auntdeen

auntdeen Lv 1

In working on the GUI script only puzzle in devprev, I've encountered a problem that I'd seen before recently.

Hand rebuilding of helices (at least) has serious issues. No matter the CI used (I've used both .05 & 1.0) and whether or not BB constraints are checked, helices can be either extremely slow in finding a reasonable pose, or will not do it at all - in many, but not all cases.

I've noticed this (and have been hearings grumblings about in both team and global) since the CASP roll puzzles started. It may date to the IE filter, or be a by-product of the BB constraints exacerbated by the IE filter.

I went back to the Platypus puzzle, where I recall was the last time rebuild worked normally to form a helix. I reset the puzzle, and tested with checked/unchecked, .05CI and 1.0 CI. I used the helix on the free end - and added some of the loop to it. Within a normal rebuild timeframe, it worked in all cases (see pix below).

I then moved on to 646, used what loaded, and tried to make a helix out of one end. Worked well.

On to 643. From the denovo chain, made a helix on an end no problem. Then on that puzzle, did an alignment, clicked on a yellow cutpoint, and tried rebuild. Fail (look at the distortion in the center of the helix in the second pix of that puzzle).

Came back to the GUI Scripting only puzzle, and tried all CI with BB checked and unchecked. The helix at segs 63 - 76 simply will not rebuild properly. I've tried doing it under all circumstances - the entire helix, just that one nasty end - no matter what, it will not form properly at any pose.

In the pix below I have the Undo graph open - you can see how fast you can get a helix shaped where it works, and how long you can let it go on when it is not working with bad results.

I am hoping that others who have encountered this problem will post, so that it can be nailed down.

One other note to help diagnose: apparently, scripts are not encountering this problem. I know that seems bizarre, but it is what it is.

Platypus pix:

Puzzle 646:

Puzzle 643:

GUI No Script Puzzle:

phallicies Lv 1

Interesting enough while trying to rebuild by hand in normal client, I've had issues on 645. i had a piece of loop as well, but only the loop part was being rebuilt. It stopped me completely from exploring one of my tracks.

jflat06 Staff Lv 1

The residueIE filter only affects the code in the design puzzles where we've enabled it, so I do not think that is the culprit. There's the potential that it is related to the backbone constraint checkbox (but if this is the case, it should be a problem on all puzzles). There's also the possibility that is somehow inherent in the starting structure or sequences of these recent puzzles, as this has caused similar issues in the past.

auntdeen Lv 1

Some of my team members have reported this, that a helix will bend in the middle. I can say for myself that no matter what I did, my attempts to incorporate the entire length of movable loop (presented as sheet) by turning it into helix, refused to utilize the last 2 segments next to the frozen seg - they remained misshapen.

auntdeen Lv 1

Yes - it could be co-incidence, but how then does rebuild work well in a puzzle if used on the denovo chain - but not work on a free strip if that chain is aligned? See the pix for puzzle 643 above.

utaca Lv 1

I want to add a very crazy helix. I saved it on my computer but forgot to upload it. Now I can't upload it because the puzzle is closed. Here is a screenshot:

brow42 Lv 1

I have to agree that long helices won't rebuild, even if cut points leave the ends free. Literally, some segments don't ever change, and segments that have already been rebuilt keep changing. I see this in CASP and other prediction puzzles. The only way I can get the entire helix to rebuild is to freeze the part that has been rebuilt already, and rebuild the shorter segment.

Sometimes I wonder if its related to how rebuild seems to hold one end fixed, and freezing a middle segment moves the boundary point.

Possibly unrelated, I'm attaching a screenshot of a helix with a band. The band is practically zero length, it should be trivial to displace the backbone atom a tiny bit, and then continue the rebuild. In this picture, a denovo sheet is being rebuilt into a helix, with a tiny band on the middle atom (only there to keep it from wandering from the symmetry point during rebuild). As you can see, half the segment is completely untouched. I don't remember which end was the N terminal. This is from way back in July.

spmm Lv 1

yes I have noticed that you have to manually pull helixes into roughly the right shape or they will just blether about and be quite unable to rebuild themselves even on CI=1, even rebuilds of loops etc on CI=1 will just happily bury themselves into the body of the protein in much the same way you expect from a rebuild on CI+0