Rebuild ruLeZ

Case number:671071-786041
Topic:Game: Other
Opened by:xiando
Status:Closed
Type:Suggestion
Opened on:Tuesday, December 30, 2008 - 22:52
Last modified:Monday, July 23, 2012 - 23:07

Ok, let' face it. rebuild is unquestionably very useful but imo not quite as useful as it might be, in part because of a lack of user control over its behavior.

Suppose for a minute, that a user could apply rules to rebuild aside from the guidance that a rubber band applies to the affected sections.

1. allow players to determine point thresholds for determination of saved output of the rebuild. I would rather walk away *and allow foldit to crunch than to attempt to view the backbone thru the purple shadow to see if the position subsequent to a rebuild iteration is worthy of consideration or just another dead-end position, (which more often than not it is). It is difficult to see the progress as is, and imo, since rebuild already uses some sort of rules to determine "valid" output and has currently no user input aside from "go!" and "Stop!", it would not be contrary to the paradigm. In fact it would further that aim.

2. Allow players to check a box that causes rebuild to discard any "solution" causing hydrophilic residues in the selection to perform translations resulting in inward facing orientation. Again, user-selectable so that those players desiring the transitions could use them those that do not could choose not to allow them...

3. Allow players to check a box that causes rebuild to discard any "solution" causing hydrophobic residues in the selection to perform translations resulting in inward facing orientation. Again, user-selectable so that those players desiring the transitions could use them those that do not could choose not to allow them...

4. Allow the player to select a minimum/maximum allowable negative score transitions as a final constraint to "saved" "solutions" to allow either fine tuning or gross movement to the output

Regarding work involved: I think aside from GUI inclusion of a "Rebuild config" menu tab to the main configuration menu, that the mainstay of this suggestion can be implemented with code already contained within foldit's subroutines and variable list (the original iteration of rebuild used a ?score-better-than-present-score? threshold function to determine whether a new position was valid, ie stored as a file and added to the undo "buffer"), although it would require some additional work adding code associated with the hydrophobic and hydrophilic orientation test. Prescanning the rotamer lookup table and flagging "illegal states" (per philic/phobic rules selected) could also speed up generation of valid, progressive solutions.

Note that #3 and #4 could be used whether for an aqueous or lipid-based protein so for future use it would likely still have value...

thanks for listening .... again

(Tue, 12/30/2008 - 22:52  |  7 comments)


axcho's picture
User offline. Last seen 8 years 30 weeks ago. Offline
Joined: 12/18/2007
Groups: None

I see what you are saying. I'm thinking that the inventory system I'm planning to implement should make it easier for the dev team to add advanced options/tools like the one you mention, at least in terms of integrating it into the game interface. I'm hoping to get the inventory system in by the end of January. After that, advanced tools requests should be addressed more quickly, I imagine.

xiando's picture
User offline. Last seen 5 years 43 weeks ago. Offline
Joined: 10/19/2008
Groups: Oma Gawd

Correction, the word inwards in #3 above should be "outwards", not "inwards"

Joined: 09/18/2009
Groups: SETI.Germany

By lua scriping, many issues mentioned above are possible.
But there is one question left to me:

Why do you clip the scores to zero in the GUI?
I mean, as far as I understand the puzzle score calculation, a sum of each segment property of the puzzle is calculated, giving the overall score.
But if you start from scratch (freeestyle), you can´t notice a positive change when the scores are clipped.

Joined: 04/19/2008
Groups: None

I also think that the rebuild tool could be one of the most valueable tools in FoldIt if it would see a bit of improvement. For instance, I don't really like that rebuilt structures are saved in undo history. Undo should keep my own actions and movements so that I can revert any changes I made, but should not be used as a storage tool for rebuild. Also, this prevents easy access to structures that rebuild generates from scripts (the number of generated structures is unknown to scripts, undo/redo commands don't exist (yet?)).
Another improvement that could be very helpful would be a rebuild where the player can draw a path in the 3D space (perhaps by setting multiple way points) and rebuild tries to build a loop that matches more or less the path. Often I know exactly where a loop should go but am unable to tell FoldIt to rebuild it that way. And in this case rubber bands aren't very helpful either.

Joined: 09/18/2009
Groups: SETI.Germany

I like the storing of the rebuilding steps. It gives me some new intial points for a complete puzzle change, but turning the storing off would be helpful sometimes and save undo memory.
If the rubber bands had another snapping behaviour and could be pulled in all 3 axes at the same time, they would be a better help for rebuild.
Anyway, I´m using them for rebuild.

Joined: 06/17/2010
Status: Open » Closed

We can use undo graph in manual rebuild (up to 100 positions) and have 100 save slots to use in scripts.
Done.

xiando's picture
User offline. Last seen 5 years 43 weeks ago. Offline
Joined: 10/19/2008
Groups: Oma Gawd

Done? lol...You didn't do anything. You're simply saying that one can use the undo tool to crawl back in time. That's not conditional by a long shot and has been in game for quite a while. I think, like so many others I've seen float by my inbox as "done", you mean "Officially ignored".

Sitemap

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