"rename" bug

[caillancm@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202010080457 (2020-10-08 04:57:57 UTC)
Description
In this example, grouping models with 'rename #1-2 id #3' creates a new model that seems to contain both old models in the top-level model #3 (named 'group'). The two sub-models, #3.1 and #3.2, contain only a part of the original models. Trying to close the session results in a the bug dialogue popping up, but the session doesn't actually close.

If I understand the docs correctly, I'd expect the rename command to change models #1 and #2 to #3.1 and #3.2, respectively.

The commands in the log are a minimal example, but I have found similar behaviour in my own more complex sessions, and also when using version 1.11 on MacOS 10.15.

cheers,
Caillan

Log:
UCSF ChimeraX version: 1.2.dev202010080457 (2020-10-08)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1ehz

Summary of feedback from opening 1ehz fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ehz from
http://files.rcsb.org/download/1ehz.cif  
Fetching CCD MN from http://ligand-expo.rcsb.org/reports/M/MN/MN.cif  
Fetching CCD H2U from http://ligand-expo.rcsb.org/reports/H/H2U/H2U.cif  
Fetching CCD OMC from http://ligand-expo.rcsb.org/reports/O/OMC/OMC.cif  
Fetching CCD YYG from http://ligand-expo.rcsb.org/reports/Y/YYG/YYG.cif  
Fetching CCD 1MA from http://ligand-expo.rcsb.org/reports/1/1MA/1MA.cif  
  
1ehz title:  
The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution [more
info...]  
  
Chain information for 1ehz #1  
---  
Chain | Description  
A | transfer RNA (phe)  
  
Non-standard residues in 1ehz #1  
---  
MG — magnesium ion  
MN — manganese (II) ion  
  

> open 1ttt

Summary of feedback from opening 1ttt fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "PHE" near line 16567  
notes | Fetching compressed mmCIF 1ttt from
http://files.rcsb.org/download/1ttt.cif  
Fetching CCD GNP from http://ligand-expo.rcsb.org/reports/G/GNP/GNP.cif  
  
1ttt title:  
Phe-tRNA, elongation factoR EF-TU:GDPNP ternary complex [more info...]  
  
Chain information for 1ttt #2  
---  
Chain | Description  
A B C | of elongation factor tu (ef-tu)  
D E F | transfer ribonucleic acid (yeast, phe)  
  
Non-standard residues in 1ttt #2  
---  
GNP — phosphoaminophosphonic acid-guanylate ester  
MG — magnesium ion  
  
1ttt mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
  

> rename #1-2 id #3

> hide #3.2 models

> hide #3.1 models

> show #3.1 models

> show #3.2 models

> hide #!3 models

> show #!3 models

> close session

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 914, in <lambda>  
close_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_close_cb(sess))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 633, in file_close_cb  
run(session, 'close session')  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2835, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/std_commands/close.py", line 60, in close_session  
session.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/session.py", line 502, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 570, in reset_state  
self.close([m for m in self.list() if not m.SESSION_ENDURING])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 888, in close  
self.remove(mopen)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 864, in remove  
del self._models[model_id]  
KeyError: (3, 1)  
  
KeyError: (3, 1)  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/models.py", line 864, in remove  
del self._models[model_id]  
  
See log for complete Python traceback.  
  

> hide # models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide #3.2 models

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 165, in <lambda>  
lambda *args, ft=self._fill_tree, ar=always_rebuild: ft(always_rebuild=ar))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 202, in _fill_tree  
len_id = len(model_id)  
TypeError: object of type 'NoneType' has no len()  
  
Error processing trigger "new frame":  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/model_panel/tool.py", line 202, in _fill_tree  
len_id = len(model_id)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.18
OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,1
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3.7 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 32 GB
      Boot ROM Version: 1037.140.50.0.0
      SMC Version (system): 2.46f13

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H2)
      Kernel Version: Darwin 19.6.0
      Time since boot: 13 days 2:44

Graphics/Displays:

    Radeon Pro 580X:

      Chipset Model: Radeon Pro 580X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 8 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67df
      Revision ID: 0x00c0
      ROM Revision: 113-D0008A-042
      VBIOS Version: 113-D0008A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 5120 x 2880 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2412M:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: YPPY075J05DS
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: Thunderbolt/DisplayPort

Locale: (None, 'UTF-8')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
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    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    cftime: 1.2.1
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    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.8.2
    ChimeraX-AtomicLibrary: 1.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
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    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
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    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202010080457
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
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    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 1.0
    ChimeraX-Hbonds: 2.1
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    ChimeraX-Log: 1.1.1
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    ChimeraX-MatchMaker: 1.1
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    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
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    wheel: 0.34.2

[Eric Pettersen]

Reported by Caillan Crowe-McAuliffe

[Tom Goddard]

Fixed.

Moving a model which has child models to a lower position in the model hierarchy goofed up the model ids. When moving #1 to #3.1, instead of #1.1 becoming #3.1.1 it became #3.1.