Changes between Version 2 and Version 3 of phenix-12-14-23

Timestamp:

Dec 13, 2023, 5:17:38 PM (2 years ago)

Author:

Eric Pettersen

Comment:

--

phenix-12-14-23

@@ -1 +1 @@
 = Phenix =
-=== Fit Loops Work ===
- * Use JSON output
- * Reworked command to use atom spec instead of chain ID and start/end residue numbers
-   - Warn if spec selects nothing
- * Reported (additional) fit-loops bugs:
-   - JSON option not working
-   - JSON output includes null results
-   - Chain ID w/o start/end res numbers does whole structure
-   - Python !IndexError into solution list
-   - Phenix's Python 3.10 build basically doesn't work
-     - Same problem as ChimeraX had: automatic type conversion to C/C++ disabled
- * Preliminary results-viewer tool
+ * Incorporated Billy's changes for finding/using Phenix on Windows
+ * Improved feedback when installation not found
 
-=== Emplace Local Work ===
+=== Fit Loops ===
+ * Need to determine if phenix.fit_loops can "handle" //just// gaps
+
+=== Emplace Local ===
+ * Randy Read paper
+   * Wrote section on tool (why ChimeraX; how plugins work; plugin details)
+   * Mocked up control for placing symmetry copies
 
 = ChimeraX completed =
- * Region Browser
- * Combine sessions
- * Actions→View → Actions→Focus
- * Fixed bug with proportional spacing of vertical colors in Color Key
- * Automatically open ViewDockX tool for appropriate formats (`showTool` keyword)
- * Fixed problem where Help Viewer was starting with zero height
+ * Made tables more compact
+ * Don't send blank residue names to Antechamber
+ * idatm_failed boolean for SPICE processing
+ * File→Fetch by ID
+ * Glycosylation support in Change Chain IDs and command
+ * Specify model number in 'open'
+ * Size atoms by attribute value
+ * Don't output SEQRES for manually joined chains
+ * pbond command
+ * Modified sequence-header code to work in library distribution
+ * 'measure rotation' can now make true axis objects
+ * Don't send truncated HIS to Antechamber
+ * Modeller: handle target deletion relative to template