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Sat, 03/29/2014 - 09:39
#2
Wiggle power
Best with Low Wiggle power to Medium wiggle power
Sun, 03/30/2014 - 14:53
#3
Ebola Rebuild options (new labels)
Default: Select zones of Segments min length 3 to Segments max length 6. If the loss then is less than GAB Filter (default: 20), launch GAB or Do not launch GAB. Before all of this, you may Transform protein to loop or keep secondary structure (like on early game in order to optimize your design). Main menu
Mon, 03/31/2014 - 11:02
#4
The picture of first dialog box:
Mon, 03/31/2014 - 11:09
#5
oops duplicate
sorry
Sun, 03/30/2014 - 19:39
#6
Advanced options
When pushing on "more" button, you get this: ----------Rebuild filter-------------- ----------Subscore management-------------- ----------Force zone-------------- ----------Launch automatically GAB-------------- ----------Others--------------
Mon, 03/31/2014 - 10:59
#7
Thank You
Bruno
Mon, 03/31/2014 - 11:11
#8
thks Porky
It encourages me to continue with 3th pannel ...
Mon, 03/31/2014 - 17:10
#9
and the GAB options
When pushing on "GAB", you'll see something like this (some options might change depending on the type of puzzle, e.g. ligands see bellow): The Ebola GAB strategy: GAB is started if rebuild gave a sufficient score (see first panel), either immediately after a very good rebuild, either on the best solutions found after a number of rebuild on a focused zone. For each GAB generation, there are a number herds and for each herd, a number of critters to be tested (see bellow). GAB was invented before I came to Fold, by rav3pnl I think. We simple copy-past it to Ebola, like we copy-pasted tvdl's eDRW (+simplifying and harmonizing them). In Ebola, bands are added from and to accepted segments, from worst segments of the zone in consideration (see first panel) to other random segments, including Use Ligand or not or randomly: "Use Ligand options : 0-Never, 1-Random, 2-Allways when relevant. Personally, I find great this ability to focus Precise bands on selected area ! It's also useful for Hotspot puzzles. I don't know exactly the complexity of GAB, but I understand it tries bands one after the other within a group of bands called herds. For each herd, it calculates the score change by each band, keeps only the bands scoring Loss max/crit and go to next critter if under Give up threshold. The default options (embedded in the recipe - you can edit it) are: Very important: do you want to Keep conditions (filters etc) before the recipe decides to keep or reject critters? Fuse threshold determines when to try a Fuze (on, each herd/critter) before to calculate the total GAB generation gain. Remember that here, the Fuze is global (on all protein), thus very slow !!! don't let it to start fuze too often on big proteins ! And use Low Wiggle Power because DRW and GAB need flexibility of the protein. Don't ask me what all of this represents exactly. I don't know. But it works ! What YOU have to know for Ebola options: full random bands ? or Precise bands centered on the "worst" zones in action? and/or to ligands? Many or few bands (critters) to try? High or low perturbation (critter-accepted loss, GAB accepted loss)? GAB max loss determines the total loss of GAB that will be accepted before to try a new GAB generation. This is what I change often (big loss takes much more time but it should be advisable on begin or mid game). This can be endless. that's why we decide to stop GAB after a Max generations without any gain (it's time to try another "worst" zone !). However, if gaining above a certain level, GAB will continue until no gain. When 5-6 "gained another" occur, it's great to see it in the log. If you selected the Precise bands default in the "advanced" panel, it's quite interesting to change strategy after some time and go to a "normal" GAB with Start full random after the given number of generation without gain. And to force Stop if no result after these 2 strategies in order to be able to try other worst zones. Remember that the Start full random works on the all protein like a normal GAB, so be patient and use preferably many Precise bands, stopping immediately after one or 2 additional Start full random. --------------GAB Options------------- --------------Generations------------- Max generations without gain for : --------------Critters---------------- --------------Other-------------------
Mon, 03/31/2014 - 17:16
#10
Don't worry
I'll try to update Ebola with the "best known today" options whenever possible. I'm working on a version that would give you the best default options out of context. But the first priority is stability and best yield in the New Chapter environment.
Tue, 04/08/2014 - 13:51
#11
Recipe outlines
For the worst scoring zones of several segments:
Sat, 11/08/2014 - 17:15
#12
1.12.5
Changed shake selected by QuickShake
Wed, 11/11/2015 - 23:46
#13
longest rebuild first
As for as I know, you cant do longest rebuild first. if that function isnt there, can you please add it? thanks
Mon, 11/30/2015 - 16:50
#14
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This recipe combines the power of the rebuilds from DRW with the ability of GAB to increase the score by banding some segments.
Moreover, we made some improvements :
Whole prot : The possibility to rebuild and GAB one by one each segments of the protein, from segment 1 to segment max.
ScoreFilter : Select the minimum score required to launch GAB. Tick "Do not launch GAB" if you only want to rebuild and fuse.
Allow loss : Ebola will not restore the highscore if the score is included in this Loss threshold
FastFuse : Use 1 fuse instead of 5
Saving module : If you tick the "Start again since the last stop" box, Ebola will restart at the same segment as before stopping the last Ebola run. The data from the last run is stored in a note on segment 1
Language : The structure of the script permits to translate very easily the dialogs in many languages.
"More" options :
Rebuild Filter : Skip wiggle after the rebuild if the score is not included between these 2 values compared to the highscore (highscore-Minfilter Subscore management : Consider only one of these subscores to define the worse segments
ForceZone : Rebuild only a selected part of the protein. It is possible to enter many zones. Tick "Walk in the Forcezone" to rebuild from the first to the last segment each zones.
Launch automatically GAB : Launch automatically GAB if the threshold is exceeded
Precise band : Bands from GAB always start from next to the rebuild segments.
Display more information : Display more information in the output of the recipe
"GAB" options :
Number of critters, generations and allowed loss
Nevertheless, it takes a lot of time for each cycle. Excellent recipe for an overnight folding!
ver 1.12.4: Fixed bugs and NC optimized
Note: for sepsis and hotspots, only "whole protein" will work.
Sorry for that. Contextual options will only be implemented later on.