Changes between Initial Version and Version 1 of phenix-9-11-25


Ignore:
Timestamp:
Sep 8, 2025, 1:38:21 PM (3 months ago)
Author:
Eric Pettersen
Comment:

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  • phenix-9-11-25

    v1 v1  
     1= Phenix =
     2
     3=== General ===
     4 * Reduce length of author list ("et al.") in citation widget
     5 * Need to add '.bat' to Windows executables' names
     6
     7=== Local EM Fitting ===
     8 * Open sharpened maps in main thread
     9 * Handle JSON output regardless of Phenix version
     10 * Note that pre-fitted structures option only available in Phenix 2.0+
     11
     12=== Fit Ligand ===
     13 * "Show clashes" option
     14 * Got feedback from Tom T. as to why map cropping is needed if there's a search center
     15 * Worked on placing a ligand for specifying search center and bounds
     16
     17= ChimeraX completed =
     18 * Find Cavities: show search box
     19 * Thermal Ellipsoids
     20 * Updating mutated sequence was slow (call for C++ residues once per character)
     21 * Alternate parser
     22 * Minimization command (95%)
     23 * !ViewDock
     24   - Made H-bonds/clashes buttons add columns
     25   - Refined set of options presented to user for H-bonds/clashes
     26   - Save Mol2 button
     27   - Close-compounds button
     28   - Preserve table state in sessions
     29   - Separate rating area
     30   - Register toolbar button itself
     31   - Allow user to reorder columns
     32   - Make description area selectable/copyable
     33 * MD plotting
     34   - Surface areas
     35   - RMSDs
     36   - Save to CSV/TSV files
     37   - H-bonds
     38   - Save plot as image
     39   - Optional plotting types
     40   - Scalar plotting support