Next Science Chat March 28

Hi everybody! A quick announcement today- our next Science Chat is March 28. Be sure your questions get posted here (this thread, right here) so I can send them to the team in advance of the chat. As long time chat fans are aware, the more questions we have prepared ahead of time the more questions we can likely get in. Keep in mind there were a lot of questions for our last chat (which we appreciated so much) and if we don't get to your question during the chat (it is unlikely we will be able to address development related questions during this hour, although you're free to ask them and we will endeavor to get an answer later), it's entirely possible you may see it in a future blog.

The Date: Tuesday, 28 March 2017
The location: #veteran, IRC
The Time: 2100-2200 (or so, but the official chat ends after an hour) GMT (aka 1400-1500 PT)
The Time Zone Converter: Right this way!

We look forward to discussing science with you!

(Mon, 03/13/2017 - 17:00  |  15 comments)
bertro's picture
User offline. Last seen 4 hours 25 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
From last chat questions
inkycatz's picture
User offline. Last seen 9 hours 53 min ago. Offline
Joined: 04/24/2014
Groups: None
You don't have to wait! (dev qs)

http://fold.it/portal/node/2003481 should have what you're looking for :)

bertro's picture
User offline. Last seen 4 hours 25 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Still pending:
bertro's picture
User offline. Last seen 4 hours 25 min ago. Offline
Joined: 05/02/2011
Groups: Beta Folders
Thanks for answer to
tokens's picture
User offline. Last seen 8 hours 27 min ago. Offline
Joined: 11/28/2011
Difference in rosetta score between design and prediction puzzle

Ignoring the filter score in design puzzles what are the differences in the scoring function between design puzzles and prediction puzzles? It seems that the backbone score is significantly lower for segments lying outside their rama areas in design puzzles versus prediction puzzles. Also I've noticed that the top score for "unsolved denovo freestyle puzzles" (1) based on a foldit design in generally higher that the same score for the original foldit design (2) (substracting the filter bonus), and that the dots in the rama map for (1) is more spread out than they were in (2).

Susume's picture
User offline. Last seen 3 hours 14 min ago. Offline
Joined: 10/02/2011
Try other sidechains on foldit design?

Do you ever take an interesting backbone from a foldit design and use Rosetta to find better sidechains for it?

saksoft2's picture
User offline. Last seen 2 days 2 hours ago. Offline
Joined: 08/06/2010
Groups: Contenders
Improving ideality in all puzzles

Why can't the Blueprint tool be enabled on all puzzles?

One of the big themes to a recent share from the developers is that they really want to help us design good loops (close to ideality). Applying the BP tool to a loop helps to constrain its shape while you do other things to the tertiary structure.

The Rama Map is hard to use because it represents everything in stick mode. I can't tell where the SS's end and the loop begins. But it does offer some interesting ways to build your tertiary structure.

Shawn

saksoft2's picture
User offline. Last seen 2 days 2 hours ago. Offline
Joined: 08/06/2010
Groups: Contenders
Progressive puzzle feedback.

Why aren't you giving the prediction scores for the SS any longer? The recent sequence of 1344, 1347, 1350 didn't list the confidences for the SS predictions.

Having those prediction confidences, along with the Alignment tool (for 1347 and 1350) may have helped us get closer to a real solution to this protein. For 1347 and 1350, selecting slightly randomized (detuned) versions of the top 5 best scoring general shapes would have benefited everyone. This is how the you in the lab can collaborate with us (the explorers) to drive towards a native solution more quickly. You could call this the "scientist filter". That way, if you don't have a team to evo from or you didn't play the earlier puzzle, you still get some starting points.

saksoft2's picture
User offline. Last seen 2 days 2 hours ago. Offline
Joined: 08/06/2010
Groups: Contenders
Symmetry crashes (dev q)

Have you made any progress with improving the stability of the client in symmetry puzzles?

alcor29's picture
User offline. Last seen 5 hours 43 min ago. Offline
Joined: 11/16/2012
Submission to scientists

Is it really worthwhile to submit to scientists a fold which is only r50? Bearing in mind that r50 might only be 200 energy points from r1 in some cases and in other cases 2000 points lower than r1. Also some r50s may be just rough folds with no refinement while others may just represent an unstable fold?

Joined: 06/06/2013
Groups: Gargleblasters
Feedback regarding surfing hotdogs

If it doesn't violate patent concerns or other such things, can we get some more feedback about what does and doesn't make a "good" surfing hotdog fold.I'd like to know about what makes the wet lab folds work and not work, rather than the score. So far, we mostly have either horseshoe helices (from one end), helices from each end, or a "seatbelt" fold which is similar to the Koga & Koga designs. The "seatbelt" keeps the helices pretty close, so they can't have many aromatics. The others, or "ankle strap" ones have more room and can have things like a pi sandwich in the middle.
I would be nice to be able to focus our folds on things that would be useful, even if our machines are too small to get top scores

Susume's picture
User offline. Last seen 3 hours 14 min ago. Offline
Joined: 10/02/2011
Cutoff for sending to Rosetta?

In the recent blog comments, bkoep mentions that the box plots about improvement in "top scoring solutions" are based on the top 10 solo and evo solutions per puzzle. Was 10 the cutoff just for those graphs, or is that a cutoff you use for sending things to Rosetta as well? I'm wondering, if my best solution finishes at rank 11-30, will you for sure look at it, or do I need to share that best one with scientists as well as my lower-scoring tracks?

Joined: 06/06/2013
Groups: Gargleblasters
what can we do to contribute and help

As we US citizens know, funding is getting tougher and tougher. What can we do to help -- time, energy, tech support, whatever
We'd like to know. Really

Joined: 09/24/2012
Groups: Go Science
Filters in Rosetta ?

Do you use filters when you send some "ideal" design to Rosetta?

Joined: 09/24/2012
Groups: Go Science
Loops versus disordered

I dont' understand the difference between loops and disordered sections.

In ED, some "disordered" portions are outside of the cloud, which I understand they don't have fixed specific shape (do they move position into water depending on temperature etc ?). In your latest co-players-authored paper, you had to get these disordered regions out in order to demonstrate we found a good solution.

Some loops are inside of the cloud: their exact position seems important to get points.

What is the difference ? are there disordered loops and ordered loops?

Get Started: Download
  Windows    OSX    Linux  
Windows
(Vista/7/8)
OSX
(10.7 or later)
Linux
(64-bit)

Are you new to Foldit? Click here.

Are you a student? Click here.

Are you an educator? Click here.
Search
Only search fold.it
Recommend Foldit
User login
Soloists
Evolvers
Groups
Topics
Top New Users
Sitemap

Supported by: UW Center for Game Science, UW Department of Computer Science and Engineering, UW Baker Lab, VU Meiler Lab,
DARPA, NSF, NIH, HHMI, Microsoft, Adobe, RosettaCommons