Update News

[beta_helix]

• General
• The "Enable Backbone Constraints" checkbox in the behavior tab has been renamed to "Enable Cut Bands". This checkbox now should modify only the behavior of the cut bands, and NOT the rest of the backbone. This should fix some of the issues with wiggle.
• A new tool has been added - Idealize. Idealize works on a segment of backbone and sets the inter-residue bonds to their 'ideal' angles.
  This tool should be very helpful for closing cuts, and resolving backbone quality issues. This tool is available anywhere where local wiggle is available. Additionally, there is a script hook called "IdealizeSelected".

• A Delete button has been added to the track dialog. Pressing the button will delete your track (with a confirmation prompt) and return you to the default track.

• Electron Density
• There is a button in the Electron Density Panel to focus rotation on the density. You can use the HOME or Q keys to refocus on the protein.
• The density score of a residue may now be viewed in the tab menu

Be sure to check out the blog post on the new Idealize Tool here: http://fold.it/portal/node/995357

[jflat06]

• Notes
• Notes can be added to the electron density if present. To add one, press TAB with the mouse over the density while the density panel is open. Use the recycle button in the note panel to erase one. (Note: saving and sharing these notes is a feature that should be in the next release).

EDIT: Here is a video where Seth Cooper explains how to add/delete/view Electron Density Notes:

• Cutpoints
• Adjusted criteria for determining if a cutpoint can be closed. In particular, cuts must not be at too wide or narrow an angle to close.

[Seth Cooper]

• General
• Added visualizations for unideal/cis peptide bonds (Backbone Issues). Clicking these will 'fix' the problem, but modify the global structure.

• Added behavior option to use older wiggle parameters; some behavior options only show up in the advanced gui.

• Electron Density

• A 'trim' feature has been added to the electron density panel. Clicking trim will pop up a dialog that allows you to
  only show density within the specified distance from the current backbone.

• Bug Fixes
• A 'sticky' wiggle bug in symmetric proteins has been fixed.

[RicGray]

• Bug Fixes
• Fix an issue introduced on 06-26-2013 where automatic solution uploads for analysis were not being uploaded as often as they should have been.

[jflat06]

• Beginner Puzzles
• Beginner puzzles now have a wiki link in the top score panel to a help page specific to that puzzle

• Veteran players can now still play the <150 puzzles, but will not get credit

• Selection Interface
• The move tool no longer pops up automatically while selecting a single residue. This should make it easier to double click residues. There is now a button + hotkey (3) to bring up the move tool in the Selection Interface.
• 'Remove band' hotkey changed from z to r to be consistent with the original interface, and to avoid an existing collision with the 'undo' hotkey.

• For consistency's sake, you may now rebuild 1-2 segments in the selection interface (although, like the original interface, no actual rebuild will take place. The game simply makes a cut behind the scenes and then executes a closure algorithm).

• Contact Map Puzzles - A new type of puzzle has been added. These puzzles are extremely similar to Exploration Puzzles, but instead of trying to move away from the starting structure, you will be trying to MATCH the predicted contacts of the native.

• Electron Density
• Density notes can now change colors. Right click on a density note to change its color.
• Denisty notes are now saved.
• The hotkey Shift+E can be used to open the Electron Density panel. The hotkey for Show Ligand Constraints is now Ctrl+Shift+E.

• 'Align' has been renamed to 'Center'

• Filters

• Bonuses gained text changed to just state the number of points gained from filters

• Centroid
• Fixed a crash when inserting cutpoints involving a proline
• Fixed a crash when using the 'show expected residue burial' option

• Fixed 'sticky wiggle' in centroid

• Chat
• There is now a "Veteran" chat tab. This will show up for those who have > 150 global soloist points.

• The puzzle chat tab has been removed.

• LuaV2

• A lua function has been added which will return a table of subscore names (puzzle.GetPuzzleSubscoreNames())

• Visualizations

• Backbone Issues is now turned off by default

• General
• Many buttons that bring up dialog panels (such as the density panel) will now close the panel if it is open.

• Memory usage should be significantly reduced.

• Bug Fixes
• The electron density panel will no longer hide when you change tracks
• Switching puzzles will no longer kick you out of the selection interface
• The backbone issues visualization will no longer show up in tutorial puzzles
• Precise wiggle and slow filter check boxes are now disabled during tool running, since this is not safe and was causing crashes

[jflat06]

• Move Tool

• Modified the move tool to have additional functionality in the selection interface. The move tool is now a toggle-button. When on, you may now move all selected parts of the protein as one piece, as long as they are capable of moving. If you have nothing selected, it will try to move everything. If you attempt to move a piece of the protein which cannot move, it will highlight the immovable residues in dark red.

• Notifications Panel

• Removed buddy-related notifications.

• Bug Fixes
• Make note bubbles visible on dark background by default. To pick up the new color, existing players will need to delete the "gui/color/label_panel" setting from theme.txt
• Let note bubbles move with the protein.
• Don't move windows on restore when "update when minimized" is set.
• Fix mode hot keys restoring the original interface when in selection interface
• Don't pulse for eye catch if the pulse when working is not set.
• Fix issue where tutorial bubbles were getting stuck.
• Make windows remember their locations, size, and visibility over puzzle changes, track changes, and sessions.
• A bug in saving solutions with disulfides that prevented them from loading has been fixed.
• A bug that would sometimes cause regions of the protein to move or spin even though they weren't being edited has been fixed.
• Attempting to address GetHeat with 1,1 will no longer crash the program.
• Electron Density puzzles should no longer score oddly during certain runs of the program.
• The Electron Density intro puzzle should now have the move tool available.
• GetSegmentEnergySubscore is now case-insensitive on the score part string.

[jflat06]

• General
• Added a checkbox to hide Beginner Puzzles from the Puzzle select menu.

• Show elapsed time as well as iterations on stop button in advanced GUI.

• Selection Interface

• "Align Guide" hotkey has been changed from A to G in selection interface to match original interface.

• Centroid

• Sidechain stub mode should now show stubs in centroid mode.

• Filters
• ResidueIE wording on the bonus clarified. Visualizations should now be displayed correctly.

• NEW FILTER - Fragment Filter: This filter compares the shape of your backbone to shapes found in the PDB, and will penalize you if there aren't any close matches. This filter will be used for design.

• New tool - Remix

• This tool is designed to work with the new Fragment Filter to help you 'fix' bad backbone shapes. Running Remix on the bad regions highlighted by the filter will fix them, but you'll have to resolve the issues that come up as a result of the fix. This tool will be available on a puzzle-by-puzzle basis for now.

• Bug Fixes
• The game should no longer lock up when you remove bands while dragging the move tool in the selection interface.
• Lua function is_contact will now return 0 on non-contact puzzles instead of crashing.
• Fixed a crash during wiggle with locks and bands in centroid puzzles.

[jflat06]

• General
• Wiggle should experience less slowdown in puzzles with constraints
• An automatic crash reporting mechanism has been added
• The ResidueIE formatting has been cleaned up

• The Track list will now refresh on track change

• Bug Fixes
• The size of the isosurface has been limited so that it will not crash on extended chains.
• The continue button should no longer continue into an old version of the desired puzzle.

[jflat06]

• Wiggle

• Iterations have been modified to represent a machine-independent 'work' unit.

• Behavior

• Wiggle Power added - Wiggle Power allows you to balance speed and points. In particular, low Wiggle Power wont try to idealize the protein as it runs, while medium will try the basics, and high will try to optimize everything.

• Scoring
• Scoring has received a major overhaul to be more scientifically accurate. Please see the related blog post for more details.

• Added an 'Idealization' score part.

• Lua

• Added undo.SetUndo(boolean) that enables or disables pushes onto the undo stack.

• Bug Fixes
• Rebuild should now pay attention to cutpoint bands unless you have them disabled.
• Bands between symmetric copies of the protein should now be applied correctly.

[jflat06]

• Lua
• Added structure.InsertCut(index) and structure.DeleteCut(index).

• Added structure.RemixSelected().

• Bug Fixes
• Fixed a crash on setting language pack.
• Fixed a crash on exit from login menu.
• Rebuild and Pull should now respect the cut bands checkbox.
• Rebuild should again return more useful results.
• Fixed a bug with inserting/deleting cutpoint residues.
• Fixed an issue where some panels were displaying improperly.
• Tweak should now only run when the mouse is held down in the Selection Interface.
• Tweak shouldn't push undos if a register shift failed.
• Reduced Rosetta logfile reporting verbosity.
• Disulfide scores should show up in the score parts again.