High wiggle leaves huge ideality score loss

Started by AsDawnBreaks

AsDawnBreaks Lv 1

I had thought that a custom waiting of wiggle would be nice (not affecting the score function itself, just telling wiggle what to look at, like CI).

AsDawnBreaks Lv 1

I used low, medium, and high, and ideality was -500 on a few segs the whole time until I did a lot of local wiggling (different lengths, sometimes 1-3, sometimes te whole chain). My issue is that there's a -500 seg that should somehow be taken care of.

And I don't get how HP would reduce idealization, as the tooltip says it uses high idealization!

jflat06 Staff Lv 1

"High Idealization" is a bit of a misnomer, I agree. Often times we have to come up with short descriptions for complex things, and inevitably something is miscommunicated.

What is meant by High Idealization in this case is that Wiggle is optimizing a higher number of degrees of freedom which are constrained to ideal values. It doesn't mean that it will necessarily increase the ability to resolve the ideality term.

As for your case where you had -500 Ideality on a particular segment - it could be that by allowing that segment to have bad ideality, the rest of the protein was allowed to be much more compact or form a bunch of hydrogen bonds (or something else). It's obviously better if you can find a similar shape that doesn't have that bad ideality term, but if Wiggle cant find that shape, the messed-up-ideality shape is still the second best option.

AsDawnBreaks Lv 1

The issue I'm having is that my score was at ~3000. My score after local wiggles and such was around 7-8000. That's a few THOUSAND lost points wiggle was ignoring. Seems either wiggle is ignoring a huge loss, or the weighting for ideality is a tad off. If the ideality score drops 10,20, even 50 points? Sure. But the only other way to loose 500 points is if the protein was almost on top of itself, in which case my protein would blow apart. A "we'll allow a little freedom" shouldn't result in several completely red segments (which, by the way, are set to turn red at ~-100 points, a fifth of the loss of what I'm seeing).

spmm Lv 1

Yes agree gitwut, apologies, misunderstood your comment being solely related to removal of HPW.

gitwut Lv 1

No apology necessary. I wasn't very specific with my leading comment, so your reply was quite reasonable.

alcor29 Lv 1

My observations so far are neither planned nor methodical or conclusive, but my impression is that sometimes high works best, and sometimes low does. Medium is a mystery and doesn't seem really useful. So I would get rid of medium, and set the default to low.

spmm Lv 1

I think they do three different things and some of the same things, and I don't think we should throw any of them out until we have had a chance to experiment more.

karstenw Lv 1

I only barely understand this discussion, but let me talk in terms of the behavior of the protein. Wiggle gets stuck. I have sections that never had cutpoints, but didn't wiggle out all the way. Often I can just run a very mild bander for about five seconds (tremor with weak bands)and it dislodges the wiggle and i'm back in business. Also, it will finish wiggle when I jerk the behavior slider down low and back up(sometimes). So, I don't know about something being super ideal somewhere else in the protein that's locking in the unideal portion. It feels to me like wiggle is hanging, not- finding an optimal wiggle based on criteria that I'm not familiar with.
In any event, I doubt anyone is keeping the half complete wiggle and preserving the super optimized portion then carefully retweaking the hot spots so as not to disturb the rest of the protein. I suspect we're all just working around the stuttering wiggle.
We'll probably rewrite drw to have stronger fuses (perhaps a couple GAB bands in the fuse) to push past the stutters and make sure we don't miss a good rebuild because wiggle didn't complete its wiggling.
ps. aside from sticky wiggle, I like the way low and high wiggle function a lot.