Changes between Version 2 and Version 3 of phenix-10-15-25

Timestamp:

Oct 15, 2025, 11:54:38 AM (7 weeks ago)

Author:

Eric Pettersen

Comment:

--

phenix-10-15-25

@@ -6 +6 @@
 
 = ChimeraX completed =
- * Chirality command
- * Made opening coordinates by default replace if 1 coordinates set, otherwise append
+ * Model-panel interface for grouping models
  * Profile Grid
-   - Show column number mouse is in
-   - Report number of sequences matching chosen cells
+   - Show number of chains associated with cell mouse is in (in addition to number of sequences)
+ * Minimization
+   - Improved finding the OpenMM atom type for single-atom ions
+   - Temporary kludge to fix charges in non-standard residues
+   - If GPU fails, fall back to CPU
+   - Don't protonate sulfurs coordinating metals
+   - Tool
  * !ViewDock
-   - Got Maestro to work with new !ViewDock
-   - Improved column-control check box layout in extreme cases
+   - Buttons to hide rating categories
+   - Adding later columns that start hidden produced traceback
    - Long description values in one column instead of two
-   - Scrollable description area
-   - More readable column titles
- * Minimize handles NAD, etc. now
- * Fixed session-combine bug with global pseudobond manager (don't clear groups)
- * Scenes
-   - Don't try to call restore_scene on intermediate-derived classes
-   - Get pseudobonds to save/restore
-   - Don't restore Model.overall_color
-   - Make Structure responsible for all atomic scene data (rather than Atoms, Residues, etc.)
-   - Have Scenes tool handle scene names with spaces
-   - 2D labels
+   - Hotkeys
+   - Hiding many rows was slow
+ * Simplify/improve Scenes tool UI as per Elaine's suggestions
+   - Single click restores scene
+   - Put scene names above the thumbnails
+   - Remove disclosure area/triangle
+   - Scene names are just integers