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Recipe: Rav3n_pl GAB v3.7.1 fc binding
Created by Formula350 21 47
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Name: Rav3n_pl GAB v3.7.1 fc binding
ID: 103434
Created on: Sun, 04/19/2020 - 19:13
Updated on: Mon, 04/20/2020 - 02:13
Description:

GAB for Ligand HBonding by banding to 1st atom of sidechain. Now with filter management to gain time, and with cuts in fuze.



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Joined: 09/29/2016
Groups: Gargleblasters
PRIVATE WHILE IN DEVELOPMENT

This is from Bruno, for debug-testing by Gargleblasters only. When it's determined to be good-to-go, it'll be released for the entire public :)

Not sure exactly how to uses it or I'd provide details.

PLEASE POST BUGS OR WEIRD THINGS HERE IF YOU RUN THIS RECIPE
We're the guinea pigs so Bruno needs to know what may need fixing.


Issue 1:
It runs a massive amount of "DeleteCut" commands... for only one cut segment, and takes forever to finally reach that segment. Sometimes there's not even a cut, but it still runs all the commands anyways.

Issue 2:
No Dialog box shows up, just immediately starts doing what it does. (intentional?)

Issue 3:
Does not disable Filters. Related to Issue 2, where it expected user-input whether to disable them?

Issue 4:
Does not obey Clash Importance that was set prior to running. Related to Issue 2?

Observation:
-Runs a ton of _gses, but that may be by design and needed.
-Does not commit changes to the Undo Graph, likely intentional to keep memory footprint down.

Joined: 06/06/2013
Groups: Gargleblasters
keeping inside group

re issue 1 -- I am ready to go to micro center and send you a machine that can stay up

re issue 2 -- intentional I think

GAB creates a bunch of "random" critters by setting some bands, tugging, mutating and then settle and go back to best case. So if a critter is an improvement, it takes that improved score. If not, it keeps what was there before

What is unique here is that Bruno is using a different mutate protocol to foster H bonds between the "ligand" or frozen part and the part we can design. So far it does seem to be doing that. You are correct there is little visible

I'll look for the filter issue. I don't usually watch that setting in GAB. so I need to run a gab without this version, and one with it. It may be that GAB doesn't allow us to reduce the clash index and sets it's own when it tries to settle the new "critter"

Joined: 06/06/2013
Groups: Gargleblasters
keeping inside group

re issue 1 -- I am ready to go to micro center and send you a machine that can stay up

re issue 2 -- intentional I think

GAB creates a bunch of "random" critters by setting some bands, tugging, mutating and then settle and go back to best case. So if a critter is an improvement, it takes that improved score. If not, it keeps what was there before

What is unique here is that Bruno is using a different mutate protocol to foster H bonds between the "ligand" or frozen part and the part we can design. So far it does seem to be doing that. You are correct there is little visible

I'll look for the filter issue. I don't usually watch that setting in GAB. so I need to run a gab without this version, and one with it. It may be that GAB doesn't allow us to reduce the clash index and sets it's own when it tries to settle the new "critter"

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Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, RosettaCommons