Changes between Version 1 and Version 2 of phenix-3-16-23


Ignore:
Timestamp:
Mar 15, 2023, 1:31:58 PM (3 years ago)
Author:
Eric Pettersen
Comment:

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  • phenix-3-16-23

    v1 v2  
    11**Phenix**
    2  * Decided on implementing Randy Read's fit-in-map tool.
    3  * Implemented command version
    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
    7   * Implemented most of tool GUI
    8     * Needs place-marker mouse-mode control
     2 * Fixed bug in "phenix location" (wasn't setting location)
     3 * Further work Randy Read's fit-in-map tool, emplace_local:
     4    * Interactive adjustment of search center, and size of marker indicates search size
     5    * Move structure to fitted position rather than open a copy
     6    * Use emplace_local JSON output
     7    * For center-of-view search center:
     8      * Use pivot point or fixed center of rotation (if any), otherwise...
     9      * Use displayed map (if only one) instead of half map
     10      * Improved initial Z-depth estimate (bounding box face intercepts rather then bounding-plane intercepts)
     11    * Elaine created documentation
     12    * Emplace_local now can estimate resolution, change command and tool to make resolution optional
     13    * Awaiting emplace_local outputting transformation matrix
    914
    1015**ChimeraX completed**
    11  * NIAID: Don't do missing-structure calculations when adding atoms to residue during copy
    12  * Coordinate set playback tool speed control
    13  * swapna command
    14  * Ensure !MatchMaker orders /A-F as expected
    15  * NIAID: Dock Prep tool
    16  * Sequence RMSD computation was wrong due to mis-indentation
    17  * Compute coulombic volumes
    18  * Developed charges for 5' phosphorylated nucleic acids
    19  * NIAID: Have Mol2 reader add missing-structure pseudobonds and change residue names like ALAxy to just ALA
    20  * NIAID: SDF with just a '0' in charges section means missing charges
    21  * Sanity check PDB coordinates for NaN
    22  * NIAID: Add Charges tool
    23  * Support 8-character PDB IDs
     16 * SwissDock format
     17 * Build Structure "Invert" tab (invert chiral center) and command
     18 * Palette and color-key support in Render By Attribute