@jflat06> i really want to get centroid mode in the game...

[02:16:59] <tokens> centroid mode?

[02:18:22] <@jflat06> centroid mode makes things a lot faster at the cost of precision

[02:18:34] <@jflat06> makes early-game much more managable

[02:18:50] <tokens> sounds nice :)

[02:19:06] <infjamc> I might have considered submitting that as a request before...

[02:19:07] <tokens> just what we need

[02:19:18] <infjamc> ...but didn't because I thought that this would be too much insider information

[02:19:41] <@jflat06> the new alignment panel uses it

[02:19:43] <@jflat06> in dev-prev

[02:19:56] <@jflat06> the 'score' in the title bar calculates using centroid mode

[02:20:22] <@jflat06> which basically means it treats sidechains as a single large 'atom' in a single position

[02:20:28] <Brow42IRC> jflat, centroid mode won't have the hiding contribution will it?

[02:20:28] <@MikeCassidyToo> new dev to dl??

[02:20:49] <@jflat06> as of yesterday, yeah mike

[02:20:49] <infjamc> Brow42: I doubt it

[02:20:50] <Brow42IRC> oh, it will? I knows sidechain orienation?

[02:21:01] <@MikeCassidyToo> I got that one

[02:21:10] <@jflat06> there was another new one today

[02:21:14] <@jflat06> that resolves some autosave issues

[02:21:20] <infjamc> After all, what centroid mode does is simplifying the side chain to one giant sphere

[02:21:27] <@jflat06> yeah

[02:21:27] <infjamc> So an entirely different score function has to be used

[02:21:28] <@jflat06> basically

[02:21:49] <Brow42IRC> well, I just want it to know if I have the oranges and blues on the right side of the sheet

[02:22:00] <infjamc> The side chain terms would have to be replaed with a lumped term that captures van der waals interactions, I think

[02:22:02] <@jflat06> it approximates each AA sidechain by a single large atom

[02:22:05] <@jflat06> so you never have to shake

[02:22:14] <tokens> that explains why it is call centroid mode

[02:22:19] <@jflat06> yep

[02:22:19] <@jflat06> lol

[02:22:29] <@jflat06> but yeah, you have to use a different score function

[02:22:31] <Brow42IRC> I thought it replaced SEGMENTS with a large atom

[02:22:32] <infjamc> Obviously that's a huge loss of information for long side chains

[02:22:34] <@jflat06> or the game will crash...

[02:22:35] <infjamc> E.g. Lysine

[02:22:47] <@jflat06> not segments

[02:22:51] <@jflat06> the backbone atoms are all there

[02:22:54] <@jflat06> just the sidechain atoms

[02:23:11] <Brow42IRC> cool, this sounds like a good improvement for early game as you said

[02:23:28] <tokens> yeah, or arginine

[02:24:11] <@jflat06> generally when someone uses rosetta on an extended chain, they'll use centroid mode, and then refine it later in fullatom mode

[02:24:18] <tokens> well, it will be interesting to see if centroid mode works in practice

[02:24:27] <@jflat06> it works for the baker lab

[02:24:28] <@jflat06> lol

[02:24:57] <@jflat06> and i believe local minimize and the pull tool actually convert portions of the protein to centroid

[02:25:03] <@jflat06> err local wiggle

[02:25:20] <infjamc> How does that work?

[02:26:12] <@jflat06> it just changes the residues in the copy of the protein it's working on temporarily while it's working, then copies the backbone atoms back when its done

[02:26:14] <@jflat06> i think

[02:26:41] <@jflat06> but yeah, it's pretty cool with the alignment tool

[02:26:49] <@jflat06> you can immediately see the feedback of say, flipping a sheet

[02:27:06] <@jflat06> if you shift by one, it gets horrible, and shifting another time will bump it right back up

[02:32:36] <tokens> jflat: I always like to try a new feature, so please let us try this new mode out, and we can give feedback on how it works

[02:32:56] <@jflat06> if it was that simple, i would have done it long ago

[02:33:06] <@jflat06> there's quite a bit of work that needs to be done to get it working in foldit

[02:33:32] <@jflat06> the entire game assumes you have a full-atom pose everywhere

[02:33:43] <@jflat06> it wouldn't take kindly to plugging a centroid pose in instead

[02:33:44] <@jflat06> lol

[02:34:35] <tokens> How does centroid mode handle clashing/steric hindrance?

[02:35:31] <@jflat06> clashing is all the same, dont know about the hindrance.

[02:36:45] <Brow42IRC> sounds like it's just one big ball

[02:36:55] <@jflat06> yeah

[02:37:03] <@jflat06> from my understanding

[02:37:08] <@jflat06> seems dead useful though

[02:37:09] <Brow42IRC> so it won't pack right

[02:37:24] <Brow42IRC> *correctly

[02:37:25] <@jflat06> well, it will pack 'approximately'

[02:37:32] <@jflat06> but running repack on it will do nothing

[02:37:33] <@jflat06> lol

[02:37:37] <@jflat06> (aka shake)

[02:37:49] <@jflat06> which is the reason why shaking does nothing to the score in the alignment panel

[02:38:14] <tokens> so the size of the ball depends on the size of the sidechain? That would sort of explain how it would avoid clashes.

[02:38:16] <infjamc> Is the centroid score calculated the same way as well?

[02:38:30] <infjamc> Namely, Foldit score = 8000 - (Energy score) * 10?

[02:39:01] <@jflat06> @tokens, yeah. but you still get clashes if the atoms are too close

[02:39:12] <@jflat06> and yes, it's the same function

[02:39:22] <@jflat06> though with different score terms in the underlying energy function

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