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Recipe: clean 1.0
Created by LociOiling 2 1
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Name: clean 1.0
ID: 103719
Created on: Sun, 07/19/2020 - 13:11
Updated on: Sun, 07/19/2020 - 20:11

Cleans up the pose after a recipe or a crash, by recentering, unfreezing, deleting band, and applying automatic secondary structures. Doesn't attempt to restore the best score.

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LociOiling's picture
User offline. Last seen 5 hours 29 min ago. Offline
Joined: 12/27/2012
light housekeeping

Recipes can leave frozen segments or hard-to-see bands that get in the way of further progress. Some recipes set all segments to loop and then leave them that way. And it's common for players to move the protein off the screen while a recipe is running in an attempt to speed things up a little.

"clean 1.0" attempts to recenter the protein in the Foldit window, then unfreezes everything and removes all bands. It also applies automatic secondary structures.

"clean 1.0" doesn't attempt to find the best score. Especially after a Foldit crash, players may need to select the correct track, then attempt to restore the best score. A recipe can't change the current track.

There are some limitations to the cleaning.

Re-centering the protein actually means centering the "camera" or "viewport" on the protein. The effect is similar to the 'q' hotkey. It centers and resets some of the visibility options, notably far cutoff, near cutoff, and fog. It doesn't reset the zoom level, so the protein may be almost invisible in the distance, or zoomed in too close for comfort.

Also this q-type recenter doesn't change the orientation of the protein. So if you dragged the protein off the screen, you'll still be looking at the same side when it's re-centered.

The Home key on Windows is similar, but resets the zoom level and the camera position. You may end up looking at a different side of the protein. Recipes can't do this type of re-centering.

Automatic secondary structures also has a slight glitch. Some puzzles, especially binder or docking puzzles, have segments with locked backbone, but moveable sidechains. It's possible to change the secondary structure assignment of these segments, either manually or using a recipe. The automatic secondary structures function won't change these segments, however. So a locked segment with a moveable sidechain may get changed from sheet or helix to loop by a recipe, but "clean 1.0" won't change it back. The same limitation applies to using the "Auto Structures" tool manually.

LociOiling's picture
User offline. Last seen 5 hours 29 min ago. Offline
Joined: 12/27/2012
more on re-centering...

The various methods for re-centering the protein and other puzzle parts have a common limitation. If a puzzle has multiple pieces -- multiple protein chains or a mix of proteins and other molecules -- the pieces may be far apart.

The hotkeys 'q' and 'Home' and the script function ui.CenterViewport all have some center point. We can't see the x, y, and z coordinates in Foldit, so it's not clear if the center point is 0, 0, 0 or some other point determined by the current pose.

In the extreme case of separate chains or other pieces being far apart, none of the centering options guarantees you'll be able to see anything. You may need to rotate the camera around by dragging on the background, and zoom out by shift-dragging upward on the background to see where things are.

Joined: 10/10/2015
Groups: Team China
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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, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons