GUI script functions

Case number:699969-994823
Topic:General
Opened by:auntdeen
Status:Open
Type:Suggestion
Opened on:Monday, March 25, 2013 - 18:39
Last modified:Monday, June 1, 2015 - 17:02

If we are continuing to have handbuild only puzzles, there are a few functions that would be good to have added to the GUI script capabilities.

In particular, mutate would be a good candidate for adding.

Have some others you would like? Add below!

(Mon, 03/25/2013 - 18:39  |  29 comments)


Joined: 02/08/2012
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I like your idea. Rebuilt would also be helpful.

Joined: 05/19/2009
Groups: Contenders

Looping is also an absolute necessity.

I cannot spare the luxury in this day and age where people fear for their paid jobs to sit at my pc and restart a banding script over and over again by pushing a button.

The whole notion of being forced to continuously handfold is odd given that, within a limited timeframe, scripts yield better scores to begin with. If handfolding yields better scores for those for whom handfolding works, they will use handfolding even when scripts are available. I use handfolding usually only in the beginning to position things and then let the pc do the tedious work while I earn the money to pay the bills.

Joined: 03/18/2012
Groups: Gargleblasters

So is there anything you consider not to be an absolute necessity?

Scripts yield better scores, but I gather from feedback elsewhere that they do not yield better solutions. So I understand the desire to alter something (as much as I loathe how it's being done).

In any case, whether you do the tedious work by pushing a button over and over again, or by running a long lasting script, it is really a waste of your time. If the virtue of foldit is handfolding, we should submit our handfolded positions to some server that would do the tedious work for us (for instance, by sending it back to our CPU, distributed computing in folding@home style).

Joined: 09/21/2011
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Better yet, just disable wiggle and shake for the Lua scripts, so tooling scripts can be used. (Making bands, getting information ....)

Joined: 05/19/2009
Groups: Contenders

I disagree with Timo here, wiggle and shake are needed to stabilize the protein after many actions including banding, rebuilding or mutating.

Joined: 09/21/2011
Groups: Void Crushers

But without wiggle and shake in LUA you can still get the benefits of a whole class of usefull scripts without having to do stupid work like making lots of equidistant bands by hand. But complicated control sequences will have no purpose (except maybe in the case of mutate and rebuild to pick the best).

Joined: 03/18/2012
Groups: Gargleblasters

Disabling wiggle and shake would make some sense to me, but only if it is also disabled in GUI recipes. If blue fuze is considered handfolding, it doesn't matter how it's programmed. Perhaps a limit on the number of wiggly iterations is in order. Other ideas in http://fold.it/portal/node/994243

Other exampless: after tweaking and pulling, QuickFix irons out the backbone without really changing anything (at least before it starts rebuilding); so that is not handfolding? A handfolding tool like mutate is a complex, magical algorithm (or maybe I'm just naive and it just wastes a lot of time, just like wiggling does when everything is frozen); but QuickMutate, which automates the simple, understandable job of trying to substitute one sidechain at a time, is forbidden. Setting the strength of the latest band added higher than 1.5 is possible using a GUI recipe, but extremely clumsly compared to a LUAv2 one liner.

It all seems quite insane to me. Maybe there is an explanation, but it seems us lab rats are not supposed to know why these things are decided.

tamirh's picture
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truestone, what part seems insane to you?

The idea behind hand-folding only puzzles is to see if we can get more diversity in solutions by delaying when scripts are used. We sometimes see that many different folders will arrive at very similar solutions because the scripts they use are similar and they converge on basically the same result.

"hand-folding" is a kind of wishy-washy term with no absolute definition. We allowed GUI scripts because they don't have all of the power of branching, loops, etc. The GUI scripts were never designed to be synonymous with "hand-folding", but they did seem to line up with the term fairly nicely. There are definitely some oddities about it, but in general we think GUI scripts complement "hand-folding" fairly nicely.

As we release more and more hand-folding rounds, the scientists are evaluating to see if these are useful compared to previous puzzles where there was no such thing as hand-folding only. If you want to know more, you could ask in the next scientist chat about it.

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The new people here don't have the benefit of having played the game when there was no recipes, or with just the GUI recipes. The original GUIs pretty much only automated the end-stage process of manually walking the backbone doing local wiggles. I saved many of those, and they are pretty crude compared to what the LUA recipes do.

It sounds like the project wants to get back to those days of real hand folding, so trying to get GUI recipes to have all or most of the features of the LUA recipes is counter to the purpose.

tamirh's picture
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I've added mutate all, mutate to specific residue, and rebuild to the list of available actions in GUI scripts. These should go out in the next release.

As for what Angus said, that is basically true. We don't want GUI and LUA scripts to have the same power with just a different interface. This is one of the reasons we won't be adding control flow (like condition statements or loops) any time soon for GUI scripts.

Joined: 03/18/2012
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@tamirh Thank you for posting. What baffles me is that the label "hand folding" bans familiar tools that are only there to help you apply your creativity to the solution (to add to those mentioned before: zero length bands, brow's manual rebuild, simply reporting how many cysteines are around, dialogues to work around the horrific builtin sliders http://fold.it/portal/node/994443). Tools unable to get your score up on their own. If there is no better definition of hand folding, I choose to call these tools hand folding tools. "Hand folding" puzzles make hand folding more difficult. If I understand what the reasons are, it's like completely rejecting technical innovation, without any discussion, instead of working to make it better.

@Angus I don't quite agree there. Everyone starts off learning the concepts and basic tools, without having a clue what that cookbook sidebar is for. It takes a while before you start using or writing recipes. It takes a while before you realize how powerful some of these many recipes are. It took me a long while to realize and accept that you can't get a high score without almost mindlessly running such recipes (on a lucky or perhaps somewhat insightful starting position). If only we had a kind of puzzle actually promoting hand work...

utaca's picture
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Rebuild should be added.

And there should be always one hand-folding puzzle online and add a new categorie for ranking.
And the recipes should be sorted by "GUI" and "Lua". Would be easier for newbies to find the gui ones.
And sharing should be allowed, maybe without loading as a guide. And...ok thats enough for this time.

utaca's picture
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Upps, will be fine if all wishes come true before saying them. ;-)))

marie_s's picture
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In my opinion, gui scripts are not useful in hand folding.

You can fold a protein without loops of random actions and complex set of bands.

For me, if you allow random rebuild in loop, you destroy all the meaning of hand folding puzzles.

Rebuild by hand, banding only the part you want is a way to learn how to fold protein. Hand folding is a part of the set of competences useful to Foldit, players who are good in this activities should have a reward by hand folding puzzles.

Players who don't like to hand fold, have the choice to skip these puzzles and wait to the next step, they will have other rewards.

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I agree with marie_s on this. I don't think rebuild belongs in GUI recipes, this is something that should be done by hand. I've gotten lazy with the LUA recipes, rarely doing any good hand folding, and letting the scripts do the work. I rather enjoyed making a decent solution on one of the new hand fold puzzles last night, the old skills came back after a bit of practice and I made something better than an automated de novo recipe might have done.

Banding, pulling, rebuilding selected segments by hand are what makes it hand folding. Automating that last point or two with walking recipes is not going to make a great solution, it only slightly improves what you have created without spending all night manually doing local wiggles between frozen segments. I've done that, it's boring and tedious.

The great solution is going to come from the hand work.

Joined: 09/21/2011
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The last sentence would be true if handfolding was a totally seperate category. I hate handfolding but am forced to play it in order to keep my category scores up.

beta_helix's picture
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There is now a Handfolding Category:
http://fold.it/portal/node/994890

but you mean that Hand-Folding puzzles should only count for that category and nothing else?

Joined: 09/21/2011
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If it would I would never play handfolding again.

Joined: 09/21/2011
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Just to elaborate: I think handfolding is now just a time waister. Just preventind sharing or using another ones solution as a guide (make it an evo immediately), maybe with the exception of a evo of a solo from yourself would be enough to get more diversity. And the real problem is recognizing the best solution like CASP has shown. That will not be solved by the current way of handfolding imho.
If you really want to show there is more diversity you should make a frequency diagram of the distances between the top 100 solutions with on the other axes the rosetta score, together with the same distances to the native. If that really shows that we can get closer to the native I might be convinced that handfolding helps.

marie_s's picture
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How do you know what is a waste of time or not and for whom?
You may consider that hand folding is a waste of time for you. I don't know how you have learn how the best solution is without working by hand but it is how I have learned.
As we doesn't have good results in the same puzzles, I think the experience of hand folding at least for some players give diversity.
At least, hand folding puzzles is less a waste of time wasting than banding a QTTN to the guide.

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I understand the points above - they are objective in my view whether from Truestone or Marie. Pro hand folding or pro script are but two sides of the same coin. But I wonder if the question now is not somewhat deeper. Timo touches on this I think.

It seems that puzzles now have a far broader spectrum than they once did - no prob there. But make me a newbie and give me 690 etc and the fun element really is not high. Overall, 'Foldit' appears to be less of a game today.

Perhaps it is time to separate these facets.

No fun could mean fewer newbies becoming regulars. But once a newbie becomes a regular they might like to try the slower (perhaps more cerebral) stuff. The current scoring would have to be changed - and we have two systems working already.

Just a thought.

marie_s's picture
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Can we wait a little more before spoiling the hand folding puzzles with automatic rebuilds and mutate?

I am afraid that the players than don't like them will not play them anyway and the players who like them will lack a real fun.

The purpose of hand folding is to choose your actions not to let choose the luck.

tamirh's picture
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Thanks marie_s, we'll be meeting on this and discussing exactly what GUI scripts should support.

tamirh's picture
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We will NOT be adding rebuild to GUI scripts
We will be adding mutate to GUI scripts

These changes should go out in the next devprev

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I am coming late to this thread so apologies - one thing that really annoys me is that I cannot rebuild two segments manually, and this makes cut point nasties (backbone -540000000 ones) hard to remove. The first rebuild on a 2 seg script cleans it up.

Can we try 2 seg manual rebuilds? Thanks

marie_s's picture
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In fact, you can rebuild one or 2 segment in old interface freezing the segment outside the part but not in selection.
I have never understand this restrictions and all the very annoying restrictions on local wiggle or rebuild with some frozen segments.

Joined: 04/15/2012
Groups: Beta Folders

Also, change band length. Made a case a little while AGO.

http://fold.it/portal/node/995038

Would make large numbers of bands so much easier to handle.

Joined: 09/24/2012
Groups: Go Science

Adding cut and uncut all in GUI would be fine ! Here we loose a lot of time just stabilizing or idealizing a nice hand folded structure.
Thus:

Cut (By Stride - User pick)

Uncut (All)

Enzyme's picture
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I would like to see our LUA analyzers in GUI puzzles. Almost all of the Get functions including SetSecondaryStructure. Only enough functionality for analyzers and the ability to script the SS, nothing which can create movement.

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