fitmap: AttributeError: 'Volume' object has no attribute 'set_place'

[goddard@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202107231826 (2021-07-23 18:26:57 UTC)
Description
Fitmap search with resolution option gives error.

Log:
UCSF ChimeraX version: 1.3.dev202107231826 (2021-07-23)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1080 format ccp4 fromDatabase emdb

Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32  

> open 1a0m format mmcif fromDatabase pdb

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #2  
---  
Chain | Description | UniProt  
A B | α-conotoxin [TYR15]-epi | CXA1_CONEP  
  
Non-standard residues in 1a0m #2  
---  
NH2 — amino group  
  

> fitmap #2 inMap #1 search 20 resolution 7

Opened 1a0m map 7 as #3, grid size 30,30,28, pixel 2.33, shown at level
0.0401, step 1, values float32  
Found 20 unique fits from 20 random placements having fraction of points
inside contour >= 0.100 (20 of 20).  
  
Correlations and times found:  
0.8752 (1), 0.8656 (1), 0.864 (1), 0.8639 (1), 0.8597 (1), 0.8587 (1), 0.8586
(1), 0.8585 (1), 0.8545 (1), 0.854 (1), 0.854 (1), 0.8527 (1), 0.8523 (1),
0.8505 (1), 0.8497 (1), 0.8484 (1), 0.8475 (1), 0.847 (1), 0.8443 (1), 0.835
(1)  
  
Best fit found:  
Fit map 1a0m map 7 in map emdb 1080 using 656 points  
correlation = 0.8752, correlation about mean = 0.5271, overlap = 238.3  
steps = 108, shift = 17.3, angle = 85.1 degrees  
Position of 1a0m map 7 (#3) relative to emdb 1080 (#1) coordinates:  
Matrix rotation and translation  
-0.59692501 -0.70607655 -0.38096771 40.24451779  
-0.69718395 0.69148053 -0.18918050 -35.70769944  
0.39700769 0.15267798 -0.90502730 12.31407501  
Axis 0.40227219 -0.91546031 0.01046411  
Axis point 10.83941283 0.00000000 8.45373155  
Rotation angle (degrees) 154.85507075  
Shift along axis 49.00708799  
  
Found 20 fits.  
Traceback (most recent call last):  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/search.py", line 315, in mstep  
return move_step(mt, session)  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/search.py", line 337, in move_step  
m.set_place(tf)  
AttributeError: 'Volume' object has no attribute 'set_place'  
  
Error processing trigger "new frame":  
AttributeError: 'Volume' object has no attribute 'set_place'  
  
File
"/Users/goddard/ucsf/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_fit/search.py", line 337, in move_step  
m.set_place(tf)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.19
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,3
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1554.100.64.0.0 (iBridge: 18.16.14556.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1030)
      Kernel Version: Darwin 19.6.0
      Time since boot: 66 days 18:40

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    Radeon Pro Vega 20:

      Chipset Model: Radeon Pro Vega 20
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x69af
      Revision ID: 0x00c0
      ROM Revision: 113-D2060I-087
      VBIOS Version: 113-D20601MA0T-016
      Option ROM Version: 113-D20601MA0T-016
      EFI Driver Version: 01.01.087
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2880 x 1800 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.0
    chardet: 4.0.0
    charset-normalizer: 2.0.3
    ChimeraX-AddCharge: 1.1.4
    ChimeraX-AddH: 2.1.10
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.27.1
    ChimeraX-AtomicLibrary: 4.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1.1
    ChimeraX-BondRot: 2.0
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    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202107231826
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.4
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
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    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.4
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.2
    ChimeraX-ModelPanel: 1.1
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    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.6.2
    ChimeraX-PDB: 2.4.4
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
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    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
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    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
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    ChimeraX-RotamerLibsRichardson: 2.0
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    ChimeraX-ShowAttr: 1.0
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    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
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    ChimeraX-StdCommands: 1.6
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
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    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
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    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.10.1
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    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
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    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
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    grako: 3.16.5
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    ihm: 0.20
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    ipykernel: 5.5.5
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[Tom Goddard]

Fixed.

Placing the fit atomic model and undisplayed simulated map gave an error because the undisplayed map had no bounds and a different code path was used that had some old unported code.