Clashing importance mod

Case number:845813-988236
Topic:Game: Tools
Opened by:Sidran
Opened on:Friday, August 13, 2010 - 21:25
Last modified:Thursday, July 28, 2011 - 00:44

This suggestion is very simple.
Clashing importance slider should be allowed to go beyond one. It would allow "inflating" of protein and possibly better placement after slider is returned to 1.
I might be wrong but I think that would help resort and reshuffle proteins in certain cases.

(Fri, 08/13/2010 - 21:25  |  14 comments)

Joined: 06/17/2010

Clashing importance more than 100%?
How you want to make it happen?
In CL=1 all operations want to avoid clashes. You can decrease it when you want to move backbone easier.
What behavior you expect when is more than 1?

Joined: 12/15/2009
Groups: None

You could have waited for my answer before down-voting :|

My explanation:
Current value of 1 assumes absence of clash. That doesnt mean that molecule distance could not be artificially raised just for the purposes of possible better placement and "reshuffling" of certain parts.
For example: Two bonded sheets could be separated with surgical precision by selecting them and wiggling with clashing importance higher than 1. After they are somewhat separated we could apply bands to directly and easily influence how they will meet after we reduce CI back to 1. this is just one possible application.

Operation is subtle, but I still believe that it would help in many cases of "locks".

Is it clear? What do you think now?

Joined: 10/19/2008
Groups: Oma Gawd

Great idea Sidran. I had the same thought while becoming reacquainted with the new for me) tools.

Joined: 10/19/2008
Groups: Oma Gawd

I had the same thought while becoming reacquainted with the new for me) tools.

Joined: 12/15/2009
Groups: None

Thanks for support xiando.

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

So, a clashing importance value bigger than 1 would have a negative gravity effect, right?

Joined: 12/15/2009
Groups: None

Crashguard303, thanks for interest.

I would not compare CI with a force. CI is essentially distance (at least in my head :D ).
"0" being the least possible distance to keep "some" order. "1" not being final or maximum distance, but proper distance. Proper in a sense that molecules tend to keep such distance in nature. As we are able to decrease that proper distance (artificially) by going toward "0", we could also increase that proper distance by going beyond "1". Going toward "0" shrinks proteins, going beyond "1" would "inflate" them (whole or just parts).
Do you agree? If yes, do you see the potential I am seeing?

Joined: 05/13/2008

Hmz, could work yes.
Might give it a different slider, otherwise CI 1 is more difficult to slide to (now it's at the end of the slide)...and yes that's really being lazy..
It could be interesting for many recipes that use different clashing importances and then wiggle to try to avoid local energy minima.

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

I would stay comparing clashing importance to a force (gravity), because the chemical charge of the atoms is calculated in the ROSETTA engine, as far as I know.
Unequal charges attract each other, equal charges repell each other, so the charge prevents molecules getting too close, but it can also help keeping them together.

Take the relation between earth and the moon:
As the gravity is constant, moon has a stable orbit around the earth, so moon-earth distance stays almost the same.
If gravity would change and be stronger in the next moment, they would crash together (CI<1), if gravity would be weaker (CI>1), they would drift apart.
This is what you do by changing CI.
By changing the CI, you tweak the variables of "physical rules".

If CI is 0, there is no order, it only looks like this, because the game-engine keeps the distance from segment to segment constant, only the sidechain-to sidechain-distance is modified by chaning CI.
The sidechains are as close as they can get, regardless if they are stucked "in" each other, which is physically not possible (only almost in the bose-einstein-condensate at almost zero celvin-degrees)

But, yes, as you say, going toward 0 shrinks the distance, 1 is normal physical behaviour, above 1 will expand it, so I see the potential ;)

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

Maybe Dr Baker can tell us, what exactly CI is.

Joined: 12/15/2009
Groups: None

Your comparison with moon's orbit sounds just right. While reconstructing systems of cosmic bodies we should be allowed to both decrease and increase their orbits until we find satisfying equilibrium.

When I rejected "force" for "distance" it was only for the purpose of simplicity. Also, my approach is purely intuitive.
Thank you for constructive and meaningful discussion.

And yes, any comment from someone "high above" who knows more about "deep below" would be quite helpful.

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

Thanks :)
I always try to keep things constructive.

Joined: 01/19/2011

Clashing importance goes up to 2.00 on the standalone foldit client. This client accepts pdb files instead of the ones provided by the baker lab.

Joined: 05/09/2008
Groups: None

re-assigning, maybe we can implement what is in the standalone as an advanced option (so as to not confuse new players)


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