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Puzzle 542

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Puzzle 542 Advanced Alignment Cutpoint Puzzle

Same protein as Puzzle 369 CASP9 Puzzle 38

PDB id 2L3B Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron. Ramelot, T.A., Yang, Y., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Kennedy, M.A.,

[01:34:16] <gmn> @boots--did you use threaded temp?

[01:38:36] <gmn> @boots--yeah, i got lucky with a quick evo from RabidNimravid :P

[01:39:21] <BootsMcGraw> @gmn: I was just happy that I was able to untwist that beast into something almost good-looking.

[01:39:31] <gmn> lol

[01:39:42] <gmn> i did it as de novo :P

[01:39:53] <BootsMcGraw> Seriously... When I did the alignment, the score was negative infinity.

[01:40:08] <BootsMcGraw> AFter a shake and a wiggle, it was still -750K.

[01:40:08] <gmn> same here

[01:40:22] <alwen> I thought my -246000 was bad.

[01:40:27] <gmn> wow

[01:40:29] <BootsMcGraw> I did a lot of manual work to het the score over zero.

[01:41:15] <gmn> i just took straight chain and aligned sheets--never liked the threaded temp

[01:41:31] <BootsMcGraw> With six cutpoints? I don't blame you.

[01:41:40] <gmn> lol

[01:41:56] <@MikeCassidyToo> Today mine was -1007942.737 pts

[01:42:20] <TimovdL> No that was your gain

[01:42:38] <@MikeCassidyToo> after getting it to 8900 or something i quit

[01:43:15] <@MikeCassidyToo> I never really had an idea what to do with it

[01:43:15] <TimovdL> It took me about 2 hours to clean up after alignment

[01:43:44] <gmn> this was a tough one for sure to get usuable structures

[01:45:05] <ghost-white> i folded 542 from the unwrapped start too. but mostly because i found the alignment confusing, since it's the first time i've needed to use it. somehow got 23rd with it

[01:45:33] <gmn> nice, ghost-white

[01:53:16] <TimovdL> 542 was an exercize for cutpoints. To clean up after closing I did select the bad parts and wiggle lllloooonnng

[01:53:33] <TimovdL> Has anybody found a better way?

[01:53:48] <gmn> @timo--not me

[01:54:13] <BootsMcGraw> @Timo: You need to manually rebuild the short section on either side of the cutpoint, maybe 5 residues in total.

[01:54:14] <gmn> sounds like boots has a method though

[01:54:30] <BootsMcGraw> Then locla wiggle the section.

[01:54:36] <BootsMcGraw> ....local wiggle...

[01:54:51] <TimovdL> Boots, that did not work for me, tried that a few times

01:55:14] <BootsMcGraw> @Timo; I had to do it several times to make it work.

[01:55:32] <TimovdL> The rebuild did nothing for the backbone score

[01:55:42] <Datacute> What do you do before closing the cutpoints?

[01:55:43] <gmn> nor for me, timo--i must be too impatient :P

[01:55:50] <TimovdL> only wiggle worked

[01:56:00] <TimovdL> but slow

[01:56:01] <BootsMcGraw> I swear, I made mine jump from negative hundred of thousands to negatove thousands.

[01:56:32] <BootsMcGraw> And then, using GAB, it brought the score into the positives.

[01:56:35] <TimovdL> But those neg thousands took forever

[01:57:32] <BootsMcGraw> @Datacute: I manually moved the cut pieces closer together before I joined them.

[01:57:58] <BootsMcGraw> Not by cut and paste, but by rebuilding/stretching them.

[01:58:08] <gmn> i got my threaded version to about 10200--never higher--after a lot of manual and script work :P

[01:58:56] <Datacute> @Boots, I also selected a few either side, and local wiggled before removing the cut pot. I don't know if that makes any difference to the resulting cut removed segment

[01:59:35] <BootsMcGraw> @ Data: I am not sure, since cutpoints are a very new type of puzzle, and I don't have much experience with them.

[01:59:45] <gmn> bbl--and again--nice work folders on 542

[01:59:52] <TimovdL> data was that fast?

[02:00:00] <BootsMcGraw> [tips his stetson to gmn]

[02:00:37] <Datacute> Timo, yes

[02:01:08] <TimovdL> Not too dirty negatives then?

[02:02:06] <Datacute> Still got them, but wiggling before removing them seemed to work better - especially when one of the parts wiggling wasn't constrained by being joined to other non-wiggign segments - i.e. at an end

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