(Sun, 07/11/2021 - 09:58 | 6 comments)
How to detect and fix backbone issues from within a Foldit LUA recipe?
|Opened on:||Sunday, July 11, 2021 - 09:58|
|Last modified:||Monday, July 19, 2021 - 20:30|
Lately I have been forcing my protein designs into unusual conformations, and when I check the "Show backbone issues" box in the View Menu, I see many red circles with white exclamation points in them. When there are so many red circles, I find it hard to count them all so I can tell if the recipes I am running are reducing their number. Because of this, I would like to find a way to automatically count them from within a Foldit LUA Recipe. Are there any LUA commands that tell if a particular segment has a backbone issue? Are there any that list the total # of backbone issues in the protein? A related question is how Foldit decides which segments have backbone issues. Does Foldit use each segment's Backbone and Ideality subscores to decide? If so, what ranges of these subscores should give backbone issues? Finally, if anyone can recommend good recipes for removing backbone issues while preserving the general shape of the protein, please let me know. My sense is that recipes using remix, rebuild, and/or idealize are good at removing backbone issues, but it is tricky to remove them while preserving the overall shape of the protein. Thanks, Jeff