Changes between Version 2 and Version 3 of phenix-4-9-26


Ignore:
Timestamp:
Apr 6, 2026, 5:56:52 PM (17 hours ago)
Author:
Eric Pettersen
Comment:

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  • phenix-4-9-26

    v2 v3  
    1616
    1717= ChimeraX completed =
    18  * Find Cavities/kvfinder improvements (Tristan suggestions)
    19    - Specify search box by using a set of atoms (and a pad value) instead of x/y/z/width/height/depth
    20    - Allow non-polymeric atoms to be treated as part of the receptor
    21  * Scene support
    22    - 2D label interpolation
    23    - Ribbon styles
    24    - Better interpolation of pseudobonds and coordinate sets
    25  * Made Gromacs reader use less peak memory
    26  * Made local Modeller execution not mistakenly require specifying a license key
    27  * Profile Grid
    28    - Show changes in prevalence based on chosen cells
    29    - Allow cells corresponding to a particular sequence to be chosen
    30    - Headers containing individual sequences
    31    - Turn off auto-association for very large alignments
    32  * Added 'is_reference' attribute to Sequence class
    33    - For sequences whose numbering should not be changed regardless of structure association (e.g. !UniProt)
    34  * OpenMM
    35    - Doesn't like non-unique names in a residue
    36    - Doesn't like missing backbone atoms
     18 * Have !ViewDock hotkeys honor the *sorted* column order
     19 * Trajectory clustering
     20 * Support dark mode in sequence viewer
     21 * Added underlying atomic support for straight helices
     22 * Option to scroll to newly selected cells in Profile Grid
     23 * "omit" keyword for trajectories
     24 * Added 'dockerize' build target
     25 * Fixed bug with mis-positioned histogram markers when placed outside data range
    3726 * Now that Qt no longer remembers editor custom colors automatically, do it ourselves
    38  * Render By Attribute
    39    - Programmatically configurable
    40    - Show it in more cases: !Clashes/Contacts tools; defattr; measure mapvalues
    41  * Updated docs to use Sphinx [https://pydata-sphinx-theme.readthedocs.io/en/stable/index.html PyData] theme
    42  * !ViewDock shows count of compounds listed in table
     27 * "rmsd" keyword for matchmaker command
     28 * Auto-break "triangle" waters
     29 * Made Clashes/Contacts shorter