Changes between Version 2 and Version 3 of phenix-1-29-26


Ignore:
Timestamp:
Jan 23, 2026, 5:57:53 PM (3 days ago)
Author:
Eric Pettersen
Comment:

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  • phenix-1-29-26

    v2 v3  
    1313
    1414= ChimeraX completed =
    15  * !ViewDock
    16    - Don't forget about hidden ligands when saving session
    17  * Fixed bug where deleting atoms of a model and its submodels would cause a crash
    18  * Moved Log settings from main ChimeraX preferences to the Log tool
    19  * Speeded up opening large ligand files by 2x
    20    - Bottleneck was chain-reporting code for NMR ensembles
    21  * Altloc Explorer
    22    - Button to show/hide all existing altlocs
    23    - Report occupancy in tooltip (also in main 3D window)
    24  * !ProfileGrid
    25    - Reporting column info on the fly too slow for very large alignment; for those only report on hover
    26  * Added ability to time out / continue long-running blocking jobs
    27  * Alert users to use ASCII paths for Gromacs trajectories
    28  * Scenes
    29    - Skip models that don't save in sessions (e.g. individual 2D labels)
    30    - Interpolation of coordinate sets
    31    - Catch error restoring scene with deleted structure elements, warn user, and restore what we can
    32    - Remember more structure attributes in scenes, and interpolate simple numeric ones
    33    - Tool:
    34      - Save→Add and separate !Add/Update buttons
    35      - Drag and drop to reorder scenes
    36      - When adding scene, ignore conflicting name if it was automatically generated
     15 * Find Cavities/kvfinder improvements (Tristan suggestions)
     16   - Specify search box by using a set of atoms (and a pad value) instead of x/y/x/width/height/depth
     17   - Allow non-polymeric atoms to be treated as part of the receptor
     18 * Add support for scene interpolation to 2D labels
     19 * Made Gromacs reader use less peak memory
     20 * Made local Modeller execution not mistakenly require specifying a license key
     21 * Profile Grid
     22   - Show changes in prevalence based on chosen cells
     23   - Allow cells corresponding to a particular sequence to be chosen
     24 * Added 'is_reference' attribute to Sequence class
     25   - For sequences whose numbering should not be changed regardless of structure association (e.g. UniProt)
     26 * OpenMM doesn't like non-unique names in a residue
     27 * Now that Qt no longer remembers editor custom colors automatically, do it ourselves
     28 * Render By Attribute
     29   - Programmatically configurable
     30   - Show it in more cases: !Clashes/Contacts tools; defattr; measure mapvalues