1 reply [Last post]
joshmiller's picture
User offline. Last seen 4 hours 53 min ago. Offline
Joined: 09/08/2017
Groups: Foldit Staff

I've been doing some research on the best ways to do things, and the veterans seem conflicted on what CI to shake and wiggle at. I'm curious to collect some more opinions on how you prefer to shake and wiggle.

Argument for Wiggle at higher CI than Shake
Shaking at a low CI will bury the sidechains better into the core, allowing wiggle (at a higher CI) to expand out.

Argument for Shake at higher CI than Wiggle
A higher CI for shake ensures that there's enough room for the backbones. Wiggling at a lower CI then compacts the structure to make use of that room.

robgee's picture
User offline. Last seen 5 hours 43 min ago. Offline
Joined: 07/26/2013
shake and wiggle CI

Hi josh,
I use the same CI for shake and wiggle.

the only time i do this 'Shake at higher CI than Wiggle' is when i've got red HBonds,
high CI shake seems to help them go blue then a lower CI wiggle in the fingers-crossed
hope that the newly aquired precious blue bars don't vanish.

If i was writing a recipe that used something like a banded wiggle
then i'd do this 'Wiggle at higher CI than Shake',
and that's 'cos ...errmm, well its what most other recipes do [emoji].

Sitemap

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, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons