Changes between Version 1 and Version 2 of phenix-1-12-23


Ignore:
Timestamp:
Jan 10, 2023, 4:59:59 PM (3 years ago)
Author:
pett
Comment:

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  • phenix-1-12-23

    v1 v2  
    22 * Decided on implementing Randy Read's fit-in-map tool.
    33 * Implemented command version
    4    * It has syntax issues
     4    * Executable name changed, so changed command name (phenix emplaceLocal) to correspond
     5    * Full-map arg now no longer required or accepted
     6      * Unclear how removing pre-fitted density will work
    57
    68**ChimeraX completed**
    7  * Dump sqm.out on antechamber failure
    8  * Fixed Matchmaker not being completely disposed of by "OK"
    9  * Minimal Render By Attribute tool
    10  * Realignment in same window
    11  * Mutation updates sequence window
    12  * !MatchMaker automatically used nucleic matrix if appropriate
     9 * NIAID: Don't do missing-structure calculations when adding atoms to residue during copy
     10 * Coordinate set playback tool speed control
     11 * swapna command
     12 * Ensure !MatchMaker orders /A-F as expected
     13 * NIAID: Dock Prep tool
     14 * Sequence RMSD computation was wrong due to mis-indentation
     15 * Compute coulombic volumes
     16 * Developed charges for 5' phosphorylated nucleic acids
     17 * NIAID: Have Mol2 reader add missing-structure pseudobonds and change residue names like ALAxy to just ALA
     18 * NIAID: SDF with just a '0' in charges section means missing charges
     19 * Sanity check PDB coordinates for !NaN
     20 * NIAID: Add Charges tool