puzzle picture
1027b: 80 Residue Symmetric Tetramer Design
Status: Closed


Name: 1027b: 80 Residue Symmetric Tetramer Design
Status: Closed
Created: 12/19/2014
Points: 100
Expired: 01/05/2015 - 23:00
Difficulty: Intermediate
Description: This puzzle again uses separate "Core Existence" filters for the monomer unit and the symmetric complex. Click the "Show" checkbox beneath the Core Existence filter to see which residues have been identified as Core (orange), Boundary (green), or Surface (blue). There are several other filters in effect; see the puzzle comments for details. The Baker Lab will run folding predictions on your solutions for this puzzle, and those that perform well will be synthesized in the lab. Remember, you can use the Upload for Scientists button for up to 5 designs that you want us to look at, even if they are not the best-scoring solutions!

This puzzle will be online for two and half weeks, so take the opportunity to try several different designs!
Categories: Design, Overall, Symmetry

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bkoep's picture
User offline. Last seen 1 hour 31 min ago. Offline
Joined: 11/15/2012
Groups: None

Residue IE Score: Monitors that all PHE, TYR, and TRP residues are scoring well.

Core Existence: Monomer: Ensures that at least 30% of the residues are buried in the core of the monomer unit.

Core Existence: Complex: Ensures that at least 38% of the residues are buried in the core of the entire complex (including the interface between monomer units).

Fragment Score: Scans for parts of your design that are unlikely to fold up naturally. Use Rebuild and Remix tools to fix these regions of your design!

Secondary Structure Design: Penalizes GLY, ALA, and PRO residues in helices and sheets.

Joined: 06/06/2013
Groups: Gargleblasters
my machine has a headache thinking about this

no way this will run with so many filters....

Joined: 09/24/2012
Groups: Go Science
using "filtrer disabled" recipes

With the button disable slow filter, you gain a lot of time.

Porky just released many recipes dealing with this, in the public recipes. Great for this kind of puzzle.

Joined: 09/24/2012
Groups: Go Science
Thanks for the long deadline

This puzzle being very slow, it's great that we got a lot of time to finish it. It even ask us less manual work: a recipe lasting one night now last 1 day or more. This gives us opportunity not to care about our results during a full day.

Thanks that you also provided a short quick puzzle so that we can still satisfy our day to day addiction :)

Joined: 09/19/2011
Groups: None

This puzzle makes my computer sad. :(

Norrjane's picture
User offline. Last seen 3 hours 22 min ago. Offline
Joined: 09/27/2014
Groups: Gargleblasters
;-( too

I think I may be too new for this. Thanks for the people who have tried to help and maybe I should just let it go for now. But if anyone could give hints on how to get started on something like this I'm sure a lot of us may appreciate it. What is the VERY FIRST thing you do......then what.....*

*And how did you learn it? I've been thru the tuts 3 times and and have done a few puzzles but I need to learn much more extensive skills.

spmm's picture
User offline. Last seen 13 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
First thing is

Put a cross in the 'disable slow filters box' it will still be very very very slow but you can get some shapes started, then turn the filters back on and do a small move, shake or wiggle, check your score. Turn filters off rinse and repeat.
Working out exactly what you want to do first with filters off is probably the way to go.

Joined: 06/06/2013
Groups: Gargleblasters
Norjane response

There is no one answer to this. I suggest get a shape of helix bundles and play with them. Try 3 or 4 or 5. put a loop of 3-5 segments between each helix and idealize the helix. freeze them and rubber band them to a symmetric shape. turn the clash index to 0 at first and position them close to each other. the core is the color one you can work on. the other three gray ones will mime your color one, and you want your color one close to those shadow ones as well. Use lots of rubber bands.
then mutate. there are some programs, like mutate no wiggle, that allow you to specify that you want to exclude gly, ala and pro. run that next. then reset clash index to one and run blue fuse. just play with it from there using something like tvdl drw 2.6.2 or moving the colored part by hand
These are very hard, and the puzzle moves very slowly because of all the filters. So I would work in cartoon mode for view, then turn view to hydro, line and no stubs with nothing else on except the pulse gui button. Walk away and do something and come back later to check
Hope this helps you at least get a start.

Norrjane's picture
User offline. Last seen 3 hours 22 min ago. Offline
Joined: 09/27/2014
Groups: Gargleblasters
Skippysk8s help

Thank you so much. I'm sure you have helped many of us who want to try to make a difference.

spmm's picture
User offline. Last seen 13 weeks 1 day ago. Offline
Joined: 08/05/2010
Groups: Void Crushers
Finding your own way is really important

The main reason that people who have been playing for a while don't give new players precise instructions especially in design puzzles is because that is not really what the game is about, it is far more important to find your own way, make your own discoveries and keep trying.

It takes a while to get the hang of it, but suddenly 'getting it' or a small part of 'it' can be very rewarding. Especially when you know its your own design.

There is a great new video about design puzzles
http://fold.it/portal/node/1998900 Also a new page on the wiki about design structures. And lots of screen shots of previous winning solutions on the wiki as well.

Norrjane's picture
User offline. Last seen 3 hours 22 min ago. Offline
Joined: 09/27/2014
Groups: Gargleblasters
Finding our own way

I can certain appreciate that. And I hope you don't think I was looking for 'the answer'. It's easy as a beginner to get frustrated and feel that some how you missed out on a second group of tutorials, or instruction booklet or something, when you work for several days and can't get up to 0!
Or to feel that you just 'don't have it' and should give up.
Thank you for the video and I very much look forward to the learning process!
Take care,

Joined: 06/06/2013
Groups: Gargleblasters
technical problem

this program keeps crashing each time I restart and try to get the track name lined up....Any way this can be simplified at the basic level (e.g. not allowing banned AAs) so we can play the game instead of rebooting all the time? I am having to use puzzle names to designate track. very annoying on top of the extremely slow speed. should have never opened....
Please fix these. they are interesting and would be fun if us ordinary computer owners could work them
Happy Holidays

Joined: 06/06/2013
Groups: Gargleblasters
Developer note problem with log files

This puzzle jams up the log file, which slows it down even more. Is there a way to fix this? My group has found we have to shut the client down and restart regularly to limit the problem, but since programs can take 12-15 hours to run on our ordinary computers this can be hard.
This fix might make me willing to do one of these again. I feel like I am losing due to machine speed.... kind of a bummer

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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, Microsoft, Adobe, RosettaCommons