ISOLDE: All atoms for zone mask must be from a single model

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/kurumizaka-lab/Desktop/Fukushima/211124_KpNCP_16.pdb

Chain information for 211124_KpNCP_16.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D H | No description available  
E | No description available  
F | No description available  
G | No description available  
I | No description available  
J | No description available  
  

> open "/Users/kurumizaka-lab/Desktop/211019_fukushima
> 2/211117_postprocess_masked.mrc"

Opened 211117_postprocess_masked.mrc as #2, grid size 180,180,180, pixel 1.06,
shown at level 0.0346, step 1, values float32  

> isolde start

> set selectionWidth 4

Chain information for 211124_KpNCP_16.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D 1.2/H | No description available  
1.2/E | No description available  
1.2/F | No description available  
1.2/G | No description available  
1.2/I | No description available  
1.2/J | No description available  
  
Done loading forcefield  
Opened 211117_postprocess_masked.mrc as #1.1.1.1, grid size 180,180,180, pixel
1.06, shown at step 1, values float32  

> select / F:20

Nothing selected  
Traceback (most recent call last):  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2599, in _xtal_mask_to_selection  
self._xtal_mask_to_atoms(sel, focus)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/isolde.py", line 2607, in _xtal_mask_to_atoms  
sh.isolate_and_cover_selection(  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/symmetry.py", line 987, in
isolate_and_cover_selection  
self.map_mgr.cover_atoms(atoms, transforms=transforms,
transform_indices=indices,  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/kurumizaka-lab/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon HD - FirePro D700 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: Mac Pro
      Model Identifier: MacPro6,1
      Processor Name: 12-Core Intel Xeon E5
      Processor Speed: 2.7 GHz
      Number of Processors: 1
      Total Number of Cores: 12
      L2 Cache (per Core): 256 KB
      L3 Cache: 30 MB
      Hyper-Threading Technology: Enabled
      Memory: 64 GB
      System Firmware Version: 428.140.7.0.0
      SMC Version (system): 2.20f18
      Panel Illumination Version: 1.4a6

Software:

    System Software Overview:

      System Version: macOS 11.6 (20G165)
      Kernel Version: Darwin 20.6.0
      Time since boot: 25 days 16:27

Graphics/Displays:

    AMD FirePro D700:

      Chipset Model: AMD FirePro D700
      Type: GPU
      Bus: PCIe
      Slot: Slot-1
      PCIe Lane Width: x16
      VRAM (Total): 6 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6798
      Revision ID: 0x0000
      ROM Revision: 113-C3861J-687
      VBIOS Version: 113-C3861XA-028
      EFI Driver Version: 01.0D.687
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.11 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Connection Type: No Display Connected

    AMD FirePro D700:

      Chipset Model: AMD FirePro D700
      Type: GPU
      Bus: PCIe
      Slot: Slot-2
      PCIe Lane Width: x16
      VRAM (Total): 6 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6798
      Revision ID: 0x0000
      ROM Revision: 113-C3861J-687
      VBIOS Version: 113-C3861XB-028
      EFI Driver Version: 01.0D.687
      Automatic Graphics Switching: Supported
      gMux Version: 4.0.11 [3.2.8]
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        Thunderbolt Display:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: C02N864QF2GC
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort

Locale: (None, '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
    biopython: 1.79
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
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    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
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    ChimeraX-CageBuilder: 1.0
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    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
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    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
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    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
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    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
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    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
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[Tristan Croll]

This was happening in situations where Clipper was asked to mask the map to an empty selection. Will be fixed in the new release.