Whenever I rebuild sheets, I have to band the things up, be very patient or just say a prayer that it ends up as a straight zig-zagged structure.
Can rebuilding sheets please by default produce a zig-zag straight structure so we can spend time on doing other things ? As a straight zig-zag structure is what we want with a sheet.
Rebuilding in structure mode is nice…but it rarely works. 99.9% of the trial positions are rejected. I always, always end up just changing it to loops.
It's TRYING to make a zig zag, but it just can't make the ends meet. Need to use cutpoints to make it work.
I think the algorithm to figure out what is important for the structure needs a change. Even with plain-obvious free space, an open end and nothing to obscure a straight path the algorithm very very often comes up with bent sheets. This is a waste of time, because we all know we want that zigzag straight line.
Maybe the segments that have sheet property and are connected should have absolute priority over any loop arrangement connected to it unless the loop is frozen.
Generally it works fine for helices, why not for sheets ?
The tweak tool, unfold the sheet on the same manner on both side beginning with the second segment, it will be better for me if one side unfold from the beginning of the sheet and one side from the end. Which one wich? arbitrary , we will try.
In the meanttime, the quicker way to have a straight sheet is to put a band at each end in the opposite direction and wiggle to stretch
I'm not sure it's really desirable that sheets should come out as a straight zig-zag, geometrically pleasing though this may be. The sheets in real world proteins such as those in the RCSB protein data bank always seem to be bent or twisted in some fashion.
They will end up being twisted or bent eventually through scripting based on better scoring but that is not how I would like them to be when starting my folding. In most cases I have seen, having the straight zig zag is a desireable shape. Maybe make it a switchable property ?
I agree with marie_s' approach, although i just use tweak. all you need to do is cut-point the sheet off and straighten it out. no rebuilding required. Same thing with a helix by the way. rebuild is essentially there to randomize a rebuild, not to necessarily make it better.
"Rebuilding in structure mode is nice…but it rarely works." supports my point.
"The tweak tool, unfold the sheet on the same manner " It unfortunately does not unfold misformed sheet-like structures (zig-zig-zag) into a proper sheet (zag-zig-zag). I have verified this to be true.
"I'm not sure it's really desirable that sheets should come out as a straight zig-zag" I would like to have that as a starting point. I can then decide to bend or misform it.
"all you need to do is cut-point the sheet off and straighten it out. no rebuilding required. Same thing with a helix by the way. rebuild is essentially there to randomize a rebuild, not to necessarily make it better." You'll be amazed what you can learn here.
also I can live without wriggling out cut points - bores me silly
I don't think it would be desirable for rebuild to default to straight sheets when running in a script. I often run a rebuilder with structures on in early game to help keep the general shape of the protein, and those sheets need to be able to twist and curl a reasonable amount while still remaining "sheety." I agree with using the cut tool and tweak, or wiggle or rebuild with bands at both ends, to create a completely straight sheet.