Changes between Version 3 and Version 4 of phenix-9-11-25

Timestamp:

Sep 8, 2025, 2:18:19 PM (3 months ago)

Author:

Eric Pettersen

Comment:

--

phenix-9-11-25

@@ -11 +11 @@
 
 = ChimeraX completed =
- * Find Cavities: show search box
- * Thermal Ellipsoids
- * Updating mutated sequence was slow (call for C++ residues once per character)
- * Alternate parser
- * Minimization command (95%)
+ * Chirality command
+ * Made opening coordinates by default replace if 1 coordinates set, otherwise append
+ * Profile Grid
+   - Show column number mouse is in
+   - Report number of sequences matching chosen cells
  * !ViewDock
-   - Made H-bonds/clashes buttons add columns
-   - Refined set of options presented to user for H-bonds/clashes
-   - Save Mol2 button
-   - Close-compounds button
-   - Preserve table state in sessions
-   - Separate rating area
-   - Register toolbar button itself
-   - Allow user to reorder columns
-   - Make description area selectable/copyable
- * MD plotting
-   - Surface areas
-   - RMSDs
-   - Save to CSV/TSV files
-   - H-bonds
-   - Save plot as image
-   - Optional plotting types
-   - Scalar plotting support
+   - Rearrange columns by dragging column headers (all tables)
+   - Description text selectable and copiable
+   - Got Maestro to work with new !ViewDock
+   - Improved column-control check box layout in extreme cases
+   - 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 scene data (rather than Atoms, Residues, etc.)
+   - Have Scenes tool handle scene names with spaces
+   - 2D labels