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brbfold's picture
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Hi,
Are there updated instructions for working with a user-defined sequence?
From what I can find here, the standalone Foldit seems to be no longer supported. As far as creating a new contest with a new sequence, I cannot figure out how to import the sequence or pdb file into the contest.
Any help appreciate. Thanks!

Joined: 09/24/2012
Groups: Go Science
I think it's not foreseen, by purpose

I suppose there are many reasons for this, one of them being not multiplying the number of puzzles in competition for limited amount of players, avoiding cheating (exchanging pdb between other players)etc.

For contest, did you try the following: use a free design puzzle (200 or 500 length), assigning your own sequence and deleting the extra segments, then work with this one without mutating ?

brbfold's picture
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Hi, Yes I was able to do that

Hi,
Yes I was able to do that and add my own sequence using the AA Copy Paste compare cookbook. However, it just adds it all in a linear structure. Is there anyway to import the native structure? Also is there any way to add a ligand?
Thanks!

Joined: 09/24/2012
Groups: Go Science
For standalone, ask the researchers

The Wiki explains thinks here:
http://foldit.wikia.com/wiki/Contest

If standalone does not work, consider say it in Feedback.

Importing the native structure would't be allowed in Foldit game in order to avoid cheating, since I think it's possible to export the structure of a game solution (e.g. for CASP competitions). The re-importing by another soloist player would facilitate cheating (players have been banned for that).

So I believe importing a structure is disabled for normal players.

Joined: 04/24/2014
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Standalone

Also if you are interested in working with the standalone version, or have issues with it, please email cgs-info@cs.washington.edu

Thanks!

Joined: 09/24/2012
Groups: Go Science
Testing it

I created a contest with a published "de novo" protein of length 20 here:
http://fold.it/portal/node/2003492

Can anybody try the concept?

The idea is:

1) first mutate the all protein to the published sequence:
NLYIQWLKDG GPSSGRPPPS

2) then try to get the best score never mutating.

Suggestions for Foldit dev:
-allow to paste the structure (and fixing it) when creating the contest
-in this case, make it a "non mutating" puzzle

Afterwards, the top player might always show pictures of their result in the Wiki, it's better than nothing isnt' it ?

Joined: 09/24/2012
Groups: Go Science
another one is here (48 residues): 3V1A protein

http://fold.it/portal/node/2003737

(provided by scopper in a test contest)

Joined: 09/24/2012
Groups: Go Science
Click here if you want to join
Joined: 09/24/2012
Groups: Go Science
Miniprotein contest

It worked !

I opened the contest again.

It's a way to ask for contests on you own sequence (in this case, never mutate then)

http://fold.it/portal/node/2003492

It's then possible to share pictures, to share to group members. But you'll have to ask the owner of the gaining solution to share anything (also pdb file) if you want to see the result. The winner (and Foldit team) still sill be the "owners" of the achievement. It's also a way to use Foldit as "stand alone" for yourselve. May be also an incentive for own citizen research.

Joined: 09/24/2012
Groups: Go Science
The only problem

is that it's difficult not to mutate by mistake (using recipes). If it happens, you can ask the author of the contest to delete you, but once you are deleted, if you come back, you start with your former (mutated) points;

Joined: 09/24/2012
Groups: Go Science
tvdl enhanced DRW mutates

warning: tvdl enhanced DRW mutates even if you disallow it => don't use it !

Joined: 09/24/2012
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A new eDRW with no mutate

I adapted eDRW so that it never mutates here:
http://fold.it/portal/recipe/102335

Joined: 09/24/2012
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The only problem

is that it's difficult not to mutate by mistake (using recipes). If it happens, you can ask the author of the contest to delete you, but once you are deleted, if you come back, you start with your former (mutated) points;

LociOiling's picture
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Joined: 12/27/2012
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contests wiki page updated

The contests page on the wiki has been updated since this thread started. For custom sequences, it basically repeats the advice Bruno has given here.

The link for the standalone version of Foldit had changed, and has been updated. It looks like the standalone version is still supported. It's considered an optional component of Rosetta, an "add-on". You must apply for a license from the University of Washington. It's not clear if licenses are granted to unaffiliated individuals. I didn't try applying for a license.

I did notice there's a Rosetta™ Academic License for .com emails, but it still asks for "organization" and "organization type". The .com page is lacking the legal verbiage found on the .edu link, but there's still a button that says "execute license", which seems to imply some sort of automatic process.

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Yes I was able to do that and

Yes I was able to do that and add my own sequence using the AA Copy Paste compare cookbook. However, it just adds it all in a linear structure. Is there anyway to import the native structure? Also is there any way to add a ligand?
Thanks!.
joe root.

Joined: 09/24/2012
Groups: Go Science
Not in normal Foldit

I don't know for Stand alone Foldit, but I suppose it's possible there.

In contests or in Foldit in general, there is no way for us players to import a native structure. The tools are disabled in order to avoid cheating (copy paste of another player's design).

Importing a ligand is curently impossible. With the coming drug design tools, we may add Foldit team to add a contest type puzzle that would allow the inclusion of user ligand.

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