Combine: trying to pass pointer of non-numpy object

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202107300307 (2021-07-30 03:07:03 UTC)
Description
tried to use combine command

open 3p5b
open #1 from alphafold search true
combine #2

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

executed startup.cxc  
UCSF ChimeraX version: 1.3.dev202107300307 (2021-07-30)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open https://wpreview.rbvi.ucsf.edu/chimerax/download.html

Opened https://wpreview.rbvi.ucsf.edu/chimerax/download.html  

> open https://preview.rbvi.ucsf.edu/chimerax/download.html

Opened https://preview.rbvi.ucsf.edu/chimerax/download.html  

> open https://preview.rbvi.ucsf.edu/chimerax/download.html

Opened https://preview.rbvi.ucsf.edu/chimerax/download.html  

> open 3p5b format mmcif fromDatabase pdb

3p5b title:  
The structure of the LDLR/PCSK9 complex reveals the receptor in an extended
conformation [more info...]  
  
Chain information for 3p5b #1  
---  
Chain | Description | UniProt  
A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN  
L | Low density lipoprotein receptor variant | Q59FQ1_HUMAN  
P | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN  
  
Non-standard residues in 3p5b #1  
---  
CA — calcium ion  
  

> open #1 fromDatabase alphafold search true

Summary of feedback from opening #1 fetched from alphafold  
---  
notes | Matchmaker 3p5b, chain P (#1) with AlphaFold Q8NBP7, chain P (#),
sequence alignment score = 446  
RMSD between 92 pruned atom pairs is 0.378 angstroms; (across all 92 pairs:
0.378)  
  
Matchmaker 3p5b, chain A (#1) with AlphaFold Q8NBP7, chain A (#), sequence
alignment score = 2594  
RMSD between 454 pruned atom pairs is 0.649 angstroms; (across all 493 pairs:
2.223)  
  
Matchmaker 3p5b, chain L (#1) with AlphaFold P01130, chain L (#), sequence
alignment score = 1907.9  
RMSD between 283 pruned atom pairs is 0.617 angstroms; (across all 394 pairs:
31.521)  
  
Chain information for UniProt Q8NBP7 chain P #2.1  
---  
Chain | Description  
P | Proprotein convertase subtilisin/kexin type 9  
  
Chain information for UniProt Q8NBP7 chain A #2.2  
---  
Chain | Description | UniProt  
A | Proprotein convertase subtilisin/kexin type 9 | PCSK9_HUMAN  
  
Chain information for UniProt P01130 chain L #2.3  
---  
Chain | Description  
L | Low-density lipoprotein receptor  
  
Opened 3 AlphaFold chain models  

> combine #2

Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/cmd.py", line 57, in combine_cmd  
combination.combine(s, chain_id_mapping, structures[0].scene_position)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 127, in combine  
StructureData._combine(self, s, chain_id_mapping, ref_xform)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molobject.py", line 1469, in _combine  
pos_ptr = pointer(ref_xform * s.scene_position.inverse())  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 319, in pointer  
cty = numpy_type_to_ctype[a.dtype.type]  
AttributeError: 'Place' object has no attribute 'dtype'  
  
AttributeError: 'Place' object has no attribute 'dtype'  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/molc.py", line 319, in pointer  
cty = numpy_type_to_ctype[a.dtype.type]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.18
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro11,4
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 2.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 427.140.8.0.0
      SMC Version (system): 2.29f24

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1323)
      Kernel Version: Darwin 19.6.0
      Time since boot: 1:28

Graphics/Displays:

    Intel Iris Pro:

      Chipset Model: Intel Iris Pro
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0d26
      Revision ID: 0x0008
      Metal: Supported, feature set macOS GPUFamily1 v4
      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: (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
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    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: 1.28
    ChimeraX-AtomicLibrary: 4.1
    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
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.3
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    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
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    ChimeraX-ColorKey: 1.3.2
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202107300307
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    ChimeraX-coulombic: 1.3
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    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
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
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    ChimeraX-ListInfo: 1.1.1
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    ChimeraX-MapData: 2.0
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