Changes between Initial Version and Version 1 of phenix-11-20-25


Ignore:
Timestamp:
Nov 19, 2025, 2:03:27 PM (24 hours ago)
Author:
Eric Pettersen
Comment:

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  • phenix-11-20-25

    v1 v1  
     1= Phenix =
     2
     3=== Fit Loops ===
     4 * If structure lacks sequence information, tell user how to supply it
     5
     6=== Fit Ligand ===
     7 * Added instructions for blob picking
     8
     9= ChimeraX completed =
     10 * Model-panel interface for grouping models
     11 * Profile Grid
     12   - Show number of chains associated with cell mouse is in (in addition to number of sequences)
     13 * Minimization
     14   - Improved finding the OpenMM atom type for single-atom ions
     15   - Temporary kludge to fix charges in non-standard residues
     16   - If GPU fails, fall back to CPU
     17   - Don't protonate sulfurs coordinating metals
     18   - 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   - Interpolation of coordinate sets
     30   - Catch error restoring scene with deleted structure elements, warn user, and restore what we can
     31   - Remember more structure attributes in scenes, and interpolate simple numeric ones
     32   - Tool:
     33     - Drag and drop to reorder scenes
     34     - When adding scene, ignore conflicting name if it was automatically generated