Back to Recipes Homepage
recipe picture
Recipe: Lig Detector 1.0
Created by LociOiling 1 1
5
Your rating: None Average: 5 (3 votes)

Profile

Name: Lig Detector 1.0
ID: 101024
Created on: Tue, 05/19/2015 - 19:21
Updated on: Tue, 05/19/2015 - 19:21
Description:

Detects ligands and flags suspicious ligands. In puzzles such as 1088, the last segment sometimes incorrectly appears to be a ligand. The segment's non-zero score may be one clue that this is a bug, not the intended design.



Best For


Comments

LociOiling's picture
User offline. Last seen 2 hours 48 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
Sanity check for ligands

On puzzle 1088, and previously on puzzle 1073, some clients show the last segment as a ligand...but some clients don't. This is apparently a bug. In puzzle 1088, one clue is that the "ligand" segment has a non-zero score.

Lig Detector identifies all possible ligands in a puzzle. The convention has been that a ligand appears as the last segment or segments of a puzzle, and has a structure code "M". Lig Detector finds all sections with structure code "M", and reports them in a dialog box and the scriptlog. Multiple ligands, ligands not at the end of the protein, and ligands with non-zero scores are noted as being suspect.

See http://fold.it/portal/node/2000613

LociOiling's picture
User offline. Last seen 2 hours 48 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
quick method

Another way to find a ligand to use the "EnzDes" coloring under view options. Segments marked as a ligand will show in white.

When you select the "ligand", you find that you won't be able to change its secondary structure, for example to helix. In a design puzzle, however, you'll probably be able to mutate the "ligand".

LociOiling's picture
User offline. Last seen 2 hours 48 min ago. Offline
Joined: 12/27/2012
Groups: Beta Folders
"auto structures" may cause ligand

Just observed a new wrinkle on puzzle 1091. Initially, the puzzle showed no ligands with "EnzDes" coloring. Then after "select all" and "auto structures", segment 139 turned white, and the Lig Detector recipe shows it as a ligand.

In this case, "undo" was enough to un-ligandize segment 139.

Want to try?
Add to Cookbook!
To download recipes to your cookbook, you need to have the game client running.
Parent

none

Children
Authors
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, Microsoft, Adobe, RosettaCommons