I have 3 contiguous residues with ideality -8.3, -13.7, -6.3. I select them in selection interface and hit Idealize peptide bonds. That whole end of the protein moves, and then their idealities are -5.6, -10.4, -5.6. Why doesn't the idealize tool fix the bonds so the ideality is zero? How can I improve their ideality, if not with the tool that is made for that purpose?
In the Selection Interface, there are 2 buttons for Idealize:
Button 5, a paintbrush labeled "Idealize the secondary structure!",
appears when 1 or more segments are selected.
Button 2, a wrench & screwdriver labeled "Idealize peptide bonds!",
appears when 2 or more segments are selected.
What is each of these buttons supposed to do?
Do both buttons affect the ideality scores?
Do they work best for a certain number of selected segments?
Perhaps using Random Idealize 1.8 or 2.1.1 would give better results.
http://fold.it/portal/recipe/100243
http://fold.it/portal/recipe/100786
I think "Idealize Peptide bonds" is the same thing as "Fix backbone issues" in regular interface https://fold.it/portal/node/995580 .
My understanding is that the backbone and ideality terms depend on bond lengths, bond and torsion angles, and perhaps other things too. I doubt if it's always possible to optimize a sequence so that everything's ideal because of the constraints imposed by the fixed ends. A bit like trying to fit a carpet into an area that's slightly too small for it.
If the end points were fixed that would make sense, but the idealize tool swings half the protein out of place, so it seems to be moving one of the end points - why not move it to a place that makes the bond lengths and angles work?
This has been the case for a while I shared a minus 14 idealise score on one seg with the scientists - amonth or so ago - even if I cut the section out and idealised it it didn't change, even tried on different wiggle factors. Rebuild on different CIs and frag gizmo did nothing either. it was in a fairly loose loop so nothing clever about the pose.
Imho segs get stuck in some cases - bad luck if they get stuck with a bad score.
Same for remix. Moreover, with remix, there seems to be no link with the fragment score.
Remix does something but fragment score is going down (and the score too).
It's confusing.
I'm having trouble reproducing this behavior here.
Susume, in which puzzle did you encounter this? Could you share that solution (or another that behaves similarly) with scientists?
On 1091, shared solution "1091 Idealize does not set ideality to zero" with scientists.
In selection interface, select segs 16-18. Click Idealize peptide bonds. Ideality on those segs changes but does not go to zero. Same thing happens with segs 35-37.
Sorry for the delayed response, everyone.
This issue has to do with proline residues, which are handled uniquely by Rosetta. Because proline has to maintained its closed ring, "idealizing" this residue does not result in bond lengths, angles, and torsions that are considered "ideal" by the Rosetta score function. As a result, players should not expect to see an Ideality score of 0 for proline residues.
Additionally, because a residue's torsion angles depend on atoms of both the previous residue and the next residue (four consecutive atoms define a torsion angle), this also affects the Ideality score of those residues on either side of the proline.
In puzzle 1091, there are prolines at positions 17 and 36, which is why you are observing this discrepancy for segments 16-18 and 35-37. I expect you will see similar results around other prolines in the puzzle.
I understand that this seems nonsensical (i.e., the Idealize tool yields an imperfect Ideality score), but this is expected behavior, and is unlikely to change.