Move selected model moving other models

[cchen@…]

The following bug report has been submitted:
Platform:        macOS-13.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
Openned two pdb files (each containing one chain). Selected one and chose "move picked models". Turned out that the other unselected model is also moving.

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/cchen/Downloads/AF-A0A1A8U1T9-F1-model_v4.pdb

Summary of feedback from opening
/Users/cchen/Downloads/AF-A0A1A8U1T9-F1-model_v4.pdb  
---  
warning | Ignored bad PDB record found on line 38  
DBREF XXXX A 1 495 UNP A0A1A8U1T9 A0A1A8U1T9_NOTFU 1 495  
  
AF-A0A1A8U1T9-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for rieske domain-containing protein
(A0A1A8U1T9) [more info...]  
  
Chain information for AF-A0A1A8U1T9-F1-model_v4.pdb #1  
---  
Chain | Description  
A | rieske domain-containing protein  
  

> open /Users/cchen/Downloads/AF-P9WJ93-F1-model_v4.pdb

AF-P9WJ93-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for 3-ketosteroid-9-α- monooxygenase,
ferredoxin reductase component (P9WJ93) [more info...]  
  
Chain information for AF-P9WJ93-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | 3-ketosteroid-9-α-monooxygenase, ferredoxin reductase component |
KSHB_MYCTU  
  

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-A0A1A8U1T9-F1-model_v4.pdb, chain A (#1) with
AF-P9WJ93-F1-model_v4.pdb, chain A (#2), sequence alignment score = 97.9  
RMSD between 8 pruned atom pairs is 1.379 angstroms; (across all 277 pairs:
28.043)  
  

> hide #2 models

> show #2 models

> select add #1

3762 atoms, 3825 bonds, 495 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select add #1

3762 atoms, 3825 bonds, 495 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right translate

> ui mousemode right "translate selected atoms"

> ui mousemode right "translate selected models"

> select add #2

6447 atoms, 6563 bonds, 853 residues, 2 models selected  

> select subtract #2

3762 atoms, 3825 bonds, 495 residues, 1 model selected  

> help help:user

No help found for 'help:user model'  

> help help:quickstart

> help help:user

> ui tool show Matchmaker

> matchmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker AF-A0A1A8U1T9-F1-model_v4.pdb, chain A (#1) with
AF-P9WJ93-F1-model_v4.pdb, chain A (#2), sequence alignment score = 97.9  
RMSD between 8 pruned atom pairs is 1.379 angstroms; (across all 277 pairs:
28.043)  
  

> view matrix models #1,1,0,0,-5.9931,0,1,0,6.2975,0,0,1,3.4875

> ui mousemode right "rotate selected models"

> ui mousemode right select

> select #1/A:107

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #1/A:107

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select up

41 atoms, 40 bonds, 5 residues, 1 model selected  

> select up

3762 atoms, 3825 bonds, 495 residues, 1 model selected  

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right "translate selected models"

> ui mousemode right "move picked models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right translate




OpenGL version: 4.1 Metal - 83
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro17,1
      Model Number: Z11C000HRD/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.60.44
      OS Loader Version: 8419.60.44

Software:

    System Software Overview:

      System Version: macOS 13.1 (22C65)
      Kernel Version: Darwin 22.2.0
      Time since boot: 12 days, 22 hours, 43 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
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    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
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    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-SDF: 2.0
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    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
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    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
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    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
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    ipython-genutils: 0.2.0
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    Jinja2: 3.1.2
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    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
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    zipp: 3.11.0

[Eric Pettersen]

Reported by Chu Chen

[Tom Goddard]

The mouse mode called "Drag model" in the toolbar (command 'ui right "move picked models"') moves the model under the mouse, not the selected model. If you hover the mouse over the "Drag model" icon it explains this, and the documentation also explains it ​https://www.cgl.ucsf.edu/chimerax/docs/user/tools/mousemodes.html. Drag model will move all models if you click on empty space and drag.