Changes between Initial Version and Version 1 of phenix-4-9-26


Ignore:
Timestamp:
Apr 6, 2026, 5:38:17 PM (35 hours ago)
Author:
Eric Pettersen
Comment:

--

Legend:

Unmodified
Added
Removed
Modified

  • phenix-4-9-26

    v1 v1  
     1= Phenix =
     2
     3=== AlphaFold2 Barbed Wire ===
     4 * Show [https://pubmed.ncbi.nlm.nih.gov/40937679/ Richardson lab categorization] of !AlphaFold structures
     5 * Based on feedback:
     6   - Color atoms as well as ribbons
     7   - Filter out structures with missing structure from command/tool
     8   - Simple results dialog
     9   - Tweaked "uncategorized" color
     10 * Elaine created help pages
     11
     12=== AlphaFold2 Barbed Wire ===
     13 * Due to changes in Phenix's naming of default JSON output files, use explicit output file name
     14
     15Put bundle with all the above on Toolshed
     16
     17= 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
     37 * 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