I can think of a concrete example to answer your query above.
I once proposed the inclusion of the ability to clear bands during the wiggle using a hotkey for the express purposes of allowing snap functionality to the folding process early on in the public release. it was accepted and implemented.
The reason that the R bug was so prominent? Because a whole lot of people rely on this ability for folding.
it's a silly "tool" but it IS a tool. and imo although perhaps an insubstantial tool when compared with a more obvious choice like "Rebuid" or Rotate", a valid example of how a tool changes the way people work. I believe it also meets the implied requirement in your query of being a tool that actually exists and who's use can be measured and proven, rather than a hypothetical situation, as would be the case for any proposed but un-implemented suggestions located in the feedback tracker suggestion bins, as their beneift to the community is unsubstantiated except by hypothesis, promotion, and a boat load of background work to back the first two up.
regards,
To continue the dialogue by making some suggestions to get around the problem I point to in this thread I would like to say:
1) I avoid reading other people's ideas until I have given myself a chance to think through the problem. I do this by training. I have found I am too likely to get locked into other's thinking if I look at their solutions before I come up with my own.
2) I don't know much about proteins or protein folding so I might have to ask more questions than provide answers while thinking this through.
That having been said, please forgive me if my contribution is redundant or just not workable due to the nature of protein folding that I am unaware of. I would love to do more reading on the subject and welcome any suggested reading.
OK. My first suggestion is simply to change the scoring. It might not be as pleasing or fun to play but if the scoring was done differently, it would encourage people to solve differently.
For example, add the rule –"Increases in scores can only be achieved in 100 point increments." Small incremental advances wouldn't count until a player could put together 100 points worth. In this case, people would opt for the major rebuilds and spend several hours trying out different strategies to achieve them rather than wiggle pairs of amino acids. In so doing, people will focus on the types of tools that they would need to better do this sort of folding, e.g. better FREEZE, LOCK and BANDing. (See 2. FREEZE, LOCK improvements)
- FOLD, LOCK, BANDing improvements
In order to do major folding, taking large chucks of protein strands and rearrange them, the user needs the ability to truly lock together a section such as a helix, and treat it as a single entity to be able to place it in a new location, all at once. To do this freeze or lock should be available to lock a section together, BUT allow the section to be moved around in space. AND, bands should allow a user to guide such a large section into a new position.
To improve the ability of folders to rebuild in more profound ways than just a few segments at a time, the tool set should include better ways of handling larger sections. The problems with existing tools are:
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There seems to be some confusion of the functions of these tools. As is, they don't match the intuitive understanding a player would assign to each. FREEZE, intuitively, should freeze the amino acid in every way. It should freeze its position in space. It should freeze its relationship to its immediate neighbors. LOCK, intuitively, is a different name for the same function and should do the same. Sometimes they perform as expected, sometimes they don't.
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Banding doesn't work well. It's confusing. Is it allowing the user to tie the amino acid to a fixed point in space, OR, tie it to a fixed point in relative relationship to the protein, e.g. a fixed distance from the backbone. I'm not sure what Banding is supposed to be doing. I understand when tying together two amino acids with a band and there is a pull between them that has been created. But I don't understand what's going on when banding an amino acid to a point in space. Sometimes the pull is pulling the acid to a point in space. Sometimes that point in space seems to remain fixed, causing the entire protein to twist and turn. To combat that effect, I have tried to put the amino acid between two equal bands. I'm guessing, that because I did not setup that pair of bands exactly equal, the amino acid is pulled toward one and away from the other. But in either case, the entire protein is pulled out of wack with little control by the user. I also don't understand why banding cannot be used to pull on two neighbors.
SOLUTION
I would like to see FREEZE divided into two functions: freeze the relationship of an amino acid with its local neighbor, and, freeze the amino acid in space. The user should be able to do both or each function separately. I would suggest using two words to equal two functions: FREEZE = fixed in space. LOCK = fixes relationship with neighbors. In this way a section could be LOCKED and moved around as a block.
I would like to see BANDing improved by also being divided into two functions. Banding should allow user to tie an animo acid to a point in space. OR, banding should allow user to tie an amino acid to a fixed point in relation to the backbone. If we give the backbone a direction, e.g. start to finish. And give backbone an angle reference 0-360 degrees a band could be described with two angles, e.g. 0-360 around backbone and +90 to -90 from start to finish. This would allow banding to be used to straighten a group, for example.
Hi Xiando. Thanks for your comments. I believe I do understand INTERIM BEST. It will prove to be a useful tool, albeit a little more difficult to use than VERY BEST. It is a step in the right direction, however, it won't help solve the problem I'm referring to. Here's why:
Let's say to do a major rebuild of a section and loose 1000 points before you start shaking out the new tensions created during the rebuild. You do a good job and recover 700 points THAT YOU PREVIOUSLY DIDN'T HAVE. By that I mean those were just not recovered points but new found points!.
Unless you are able to move the overall score over the old high score you will not be allowed to keep these points unless you never use VERY BEST again. And you and I both know that using VERY BEST is a oft used function we could hardly do without.
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Suggestions need to be sent to the feedback tracker, not posted here. The development team does not really pay attention to this forum regarding suggestions to improvement, as it is not the forum in which that type of discourse is meant to be posted, and the content cannot be assigned or tracked when players submit ideas in the wrong location.
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re: Very best and recent best.
I don't think you quite get it yet. You have no idea that you "found new points", you just found 700 points. Prior to that you reduced the stability of the protein and lost 1000 points, therefore you have simply regained 700 of the 1000. These are not a provably "new" source, as you have not exceeded your losses and you would have a score 700 points above your original.
back to the perplexing issue…
Very Best calls back the very highest score. nothing else. That is it's purpose…to track and store the very best score. it values is updated by a comparison with the current score, and it is otherwise static, ie, it cannot be reset by the user without playing tricks that were unintended by the developers
Recent best call back the best score achieved following application of a user-specific setpoint. That's it's purpose…to track and store the best score achieved following a reset (Set recent best) event.
Both behave identically from a mathematical standpoint, except that Recent Best tracks the score from a user-specified starting point by setting that start point using the "set recent best" command.
I simply don't see that the situation you're describing is overlooked here. In fact, that situation is WHY recent best was originated. Please read the wiki entry on this feature, as the situation you was specifically addressed in that entry.
I'm not sure why you're not getting it, but I'd suggest that you talk to others in the chat to resolve any further confusion on your part as to what is possible and what isn't using very best and recent best. Perhaps I'm missing some fundamental point you're making, but I really don't see the issue.
This actually sounds like a good idea to me, so long as it was added as a separate stage in the folding. Have both, first release the protein requiring 100 point gains then release it with standard parameters. This would of course be accompanied by a separate ranking system.
I suggest you post it in the feedback tracker, or if you don't want to do you mind if I do?
Ty ZZZ. Xiando has been encouraging me to move these suggestions over to the feedback tracker so I will.
Using Bands to Compress the Protein
A good technique, early in a protein puzzle is using bands to compress the protein, making it more compact. To do this, randomly click an amino acid segment while holding the shift key and drag the newly formed band to another segment. Let go when the cursor is over another segment and a band is formed between the two. Try three or four bands stretching from one side of the protein to the other. Next, hit "W" to do a global wiggle. Experiment with how long you allow this to continue before stopping the global wiggle by hitting SPACE BAR. Hit "R" to remove bands and hit "W" to global wiggle again. Watch scoring. If it slows and stops without hitting a new high, hit "A" to restore best. If it reaches new high, VOILA! You've successfully used bands to compress the protein. You might want to try it again.
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