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Puzzle 657 Blind Electron Density 3 same protein as Puzzle 602







[00:02:02] <MooMooMan> Ad's top ones seem to map fairly well.

[00:02:21] <Brow42IRC> my backbone matches but my side chains don't

[00:02:30] <BletchleyParkirc> mine *seemed*  too :)

[00:02:52] <MooMooMan> yeah - i've seen that as well. many of the long chains do not have density around them.

[00:03:44] <Brow42IRC> one of the neat things about ED is you can see the flat circles for phen and tryp

[00:04:04] <Brow42IRC> I can see those flat circles in the ED in this puzzle, and the nearest phen is like 6 segments away

[00:04:05] <BletchleyPark> indeed. I had this one at some point

[00:04:24] <BletchleyPark> IMAGE: http://fold.it/portal/files/chatimg/irc_108474_1354662265.png

[00:04:45] <MooMooMan> This is Galaxie's share.

[00:04:59] <Brow42IRC> I turned off the density at the end, too, and just tried to fold that

[00:05:01] <MooMooMan> IMAGE: http://fold.it/portal/files/chatimg/irc_184172_1354662302.png

[00:05:44] <BletchleyParkirc> wow

[00:05:46] <Brow42IRC> there's lots of density there in the upper right in galaxie's picture....I could't fill it either

[00:05:50] <TimovanderLaan> Evo, main contributer Steve

[00:05:59] <pauldunn> IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662360.png

[00:06:02] <BletchleyParkirc> done by hand ?

[00:06:03] <MooMooMan> IMAGE: http://fold.it/portal/files/chatimg/irc_184172_1354662364.png

[00:06:25] <pauldunn> IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662386.png

[00:06:41] <Brow42IRC> my approach to ED currently is lots of tvdl rebuild, then hand fold loops back into the density and back to rebuild

[00:06:50] <MooMooMan> @bp dont know i would think it was positioned mostly by hand at the start.

[00:07:04] <BletchleyParkirc> i'm impressed

[00:07:55] <steveB> IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662476.png

[00:07:58] <MooMooMan> i see paul's also has that bunch of density with no occupancy.

[00:08:15] <Brow42IRC> I reset once...the first time I tried to position the helices, then the sheets, but couldn't fit the sheets.

[00:08:19] <steveB> IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662500.png

[00:08:32] <Brow42IRC> 2nd try I started with sheets, particularly with the obvious hairpins, and placed the helices last

[00:08:40] <Brow42IRC> almost no cutpoint use

[00:08:58] <BletchleyParkirc> I used the prediction

[00:08:58] <steveB> IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662540.png

[00:09:17] <BletchleyParkirc> then mapped it by counting helix winds, zigzags and used cutpoints

[00:09:26] <MooMooMan> looks like VC and AD got almost exactly the same solution - only 6 points in it.

[00:09:27] <BletchleyParkirc> and did not work out that well

[00:09:31] <pauldunn> IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662573.png

[00:09:35] <steveB> IMAGE: http://fold.it/portal/files/chatimg/irc_86905_1354662576.png

[00:09:44] <pauldunn> IMAGE: http://fold.it/portal/files/chatimg/irc_215720_1354662586.png

[00:10:05] <BletchleyParkirc> I am fairly shocked that you had the sidechains line up so well.

[00:10:06] <MooMooMan> you could almost see the helices if you played with the threshold.

[00:10:20] <TimovanderLaan> IMAGE: http://fold.it/portal/files/chatimg/irc_308854_1354662622.png

[00:10:23] <BletchleyParkirc> oh, I did see the helices and the sheets too

[00:10:43] <TimovdL> finally it worked Evo of Steves

[00:10:55] <pauldunnirc> MooMooMan, the sidechains fill in most of the density not filled in by the backbone.

[00:11:19] <brow42> IMAGE: http://fold.it/portal/files/chatimg/irc_269484_1354662681.png

[00:11:56] <MooMooMan> there is still a bit at one point that seems unoccupied, right near the terminus of the protein that JPRED said was a helix but became a sheet..

[00:12:06] <brow42> IMAGE: http://fold.it/portal/files/chatimg/irc_269484_1354662727.png

[00:12:10] <BletchleyParkirc> Steve, how on earth did you get the sidechains so well lined up ?

[00:12:11] <TimovanderLaan> IMAGE: http://fold.it/portal/files/chatimg/irc_308854_1354662732.png

[00:12:24] <MooMooMan> IMAGE: http://fold.it/portal/files/chatimg/irc_184172_1354662745.png

[00:12:42] <MooMooMan> right at the top of the image i just posted.

[00:14:22] <Brow42IRC> I seemed to have EXTRA loops everywhere, and was missing loops nowhere

[00:14:32] <Brow42IRC> so I didn't know where to shift them

[00:15:06] <steveB> BP - using the ED mesh in wireframe mode. I then uploaded to group and we evo'd about 10 of them between us

[00:15:16] <pauldunnirc> I think there are extra ED regions that didn't get trimmed out when they tried to create an ED cloud for just one copy of the protein.

[00:15:21] <TimovdL> This ED data was far from perfect I think

[00:15:41] <@Madde> IMAGE: http://fold.it/portal/files/chatimg/irc_42629_1354662943.png

[00:15:45] <MooMooMan> they did take it from a repeating unit - thats probably the origin of the unmapped stuff.

[00:15:47] <Brow42IRC> I will try wireframe next time

[00:15:49] <alwen> I think they said that at one point

[00:15:52] <BletchleyParkirc> i'm really impressed

[00:15:54] <alwen> That it had extra

[00:16:03] <steveB> BP - I also use a repacking technique which is my secret weapon and speeds things up enormously

[00:16:32] <BletchleyParkirc> seems to work wonders

[00:16:32] <Brow42IRC> yes you got a high score very early on

[00:17:02] <TimovdL> The highest other score (ED match) was just above zero!

[00:17:26] <steveB> Yes Brow, I was about 3000 pts up and then the pack started to chase. It was a close run puzzle

[00:17:33] <Brow42IRC> hey, timo, could you real quick give the sum of Other subscore for your solution?

[00:17:57] <TimovdL> -1409.2537.......

[00:18:19] <BletchleyParkirc> what is Other subscore Brow ?

[00:18:34] <TimovdL> Best score on seg 107 0.022

[00:18:38] <drjr> cat's out of the bag now

[00:18:42] <brow42> mine is -2526.54 :(

[00:18:50] <MooMooMan> look at the scores box as you move the protein BP...

[00:18:59] <brow42> other is the bonus/penalty for filling/unfilled ED

[00:19:00] <pauldunnirc> I think that is the subscore that Foldit uses to penalize or reward you for matching the ED cloud

[00:19:14] <TimovdL> I am sure of that

[00:19:35] <pauldunnirc> I'd like to know Steve's other score for the previous puzzle.

[00:19:55] <BletchleyPark> i'm puzzled with that 107 score

[00:20:02] <steveB> I'll go get pual if you wait a second

[00:20:08] <steveB> *paul

[00:20:20] <Brow42IRC> I'm pretty sure I had a +10 other score somewhere during folding

[00:20:54] <@Madde> IMAGE: http://fold.it/portal/files/chatimg/irc_42629_1354663255.png

[00:21:15] <TimovdL> Me too Brow, but to prevent big negatives proved more fruitful

[00:21:36] <BletchleyPark> M3, which score should I look for on 107 ?

[00:21:42] <pauldunnirc> I was -1501

[00:22:19] <MooMooMan> we think the match to the ED is in the Other score, but i am sure on one puzzle, i saw other parameters changing as i translated the protein.

[00:22:31] <BletchleyPark> -32

[00:22:57] <brow42> my best is 75 -1.6

[00:23:20] <steveB> How do I get the 'other' score from my puzzle folks ?

[00:23:24] <MooMooMan> the problem is that they don't exactly excel at documentation of what they are doing...

[00:23:40] <BletchleyPark> -30 if I move it entirely out of the cloud

[00:23:51] <Brow42IRC> current.GetEnergySubscore(i,"other")

[00:23:52] <BletchleyPark> steve, use the TAB key to display details

[00:24:18] <Susume2> aww, I missed the party

[00:25:09] <steveB> yep the TAB key gives me an individual residue OK, but how do I get the whole puzzle, other than writing an iterative script

[00:25:22] <BletchleyPark> I do not know

[00:25:40] <Brow42IRC> MooMooMan, I don't think translation is perfect for some reason. I can sometimes unstick wiggle by using the move tool

[00:25:47] <pauldunnirc> I think you have to write the recipe unless someone has shared one.

[00:26:00] <BletchleyPark> ah, so that is the name of that recipe

[00:26:07] <Brow42IRC> there are ceratinly recipes that give the sum of all subscores

[00:26:18] <TimovdL> Note that the Total score counts the other score twice 

[00:26:29] <Brow42IRC> hey, maybe now would be a good time to plug my reciple :)

[00:26:30] <BletchleyPark>  'OtherSubscore '

[00:26:51] <Brow42IRC> if i could remember the name

[00:27:10] <TimovdL> Real score=total segment score+total other score

[00:27:23] <Brow42IRC> http://fold.it/portal/recipe/38634

[00:27:26] <TimovdL> and other score is also counted in the segment score

[00:27:43] <TimovdL> +8000 of course

[00:27:59] <BletchleyPark> thank you Timo

[00:28:36] <Brow42IRC> timo, I've never noticed other score is counted twice, you're positive?

[00:28:37] <Susume> IMAGE: http://fold.it/portal/files/chatimg/irc_341210_1354663718.png

[00:28:58] <Susume> IMAGE: http://fold.it/portal/files/chatimg/irc_341210_1354663740.png

[00:29:03] <pauldunnirc> nice job, Susume

[00:29:28] <Brow42IRC> here's the output of my script for just the other score:

[00:29:30] <Susume2> ty

[00:29:33] <TimovdL> Because it is included in the segment score it is

[00:29:34] <steveB> Thanks Brow42 On blind ED 2 it's giving me +359.7

[00:29:40] <Susume2> congrats to steveB, i just couldn't catch you

[00:29:45] <Brow42IRC> 001111111000100012112211011 00000000000111123322211 212222222222110101112 333333321223334443322 1111112223222112122233 

[00:30:08] <steveB> Thanks Susume - good old scrap - I enjoyed it

[00:30:11] <Brow42IRC> 4 = best, 0 = worst

[00:30:31] <Brow42IRC> I didn't think to use this script during the puzzle though :(

[00:30:56] <steveB> Brow42 - how did you copy the data from the script window ?

[00:31:22] <Brow42IRC> I maintain a shortcut on my desktop to the default.scriptlog file

[00:31:40] <steveB> neat trick

[00:32:44] <steveB> On ED puzzle 2 I have ____444444444444444_444444________444444_____4444444444444______________4444444_______444____00

[00:33:03] <Brow42IRC> that's really impressive

[00:33:21] <Brow42IRC> in deafult script settings, all the 4's are the top 20% scoring

[00:33:42] <Brow42IRC> I had 3 4's :(

[00:33:44] <steveB> Nice script brow42

[00:34:03] <Susume2> these are per-segment "other" scores?

[00:34:19] <Brow42IRC> default = sliding average 3 segments

[00:34:23] <Susume2> my tottal other was -1420

[00:35:37] <Susume2> what script, brow?

[00:35:37] <steveB> On ED3 I was -1407

[00:35:46] <Brow42IRC> wait no, default is 7 segment window

[00:35:51] <Brow42IRC> Region Scorer

[00:36:06] <steveB> They definately reduced the ED data quantity when they re-issued the puzzle

[00:37:04] <TimovdL> Shared some simple scripts for other scores

[00:37:09] <Susume2> default settings on region scorer?

[00:38:09] <Susume2> I only have five 4's

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