Write failure raises OSError instead of IOError

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.2.dev202009150003 (2020-09-15 00:03:23 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.dev202009150003 (2020-09-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  

> open "/Users/Bruce/Desktop/ADAM17/B0AT1/6m17_Coulomic electrostatic
> RQYFLKVK-RS on ACE2-chain A copy.cxs"

Log from Wed Sep 16 09:52:10 2020UCSF ChimeraX version: 1.2.dev202009150003
(2020-09-15)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

Error installing 'ChimeraX-UI==1.2.1'  

Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
  

ERROR: Could not find a version that satisfies the requirement ChimeraX-
LeapMotion==1.1  
ERROR: No matching distribution found for ChimeraX-LeapMotion==1.1  
WARNING: You are using pip version 20.2.2; however, version 20.2.3 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
  

> /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install
> --upgrade pip

Unknown command: /Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m
pip install --upgrade pip  

> Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m pip install
> --upgrade pip

Unknown command: Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX -m
pip install --upgrade pip  

> ui tool show Toolbar

> open "/Users/Bruce/Desktop/ADAM17/6M17 6M18/6m17 copy.pdb" format pdb

6m17 copy.pdb title:  
The 2019-ncov RBD/ACE2-B0AT1 complex [more info...]  
  
Chain information for 6m17 copy.pdb #1  
---  
Chain | Description  
A C | sodium-dependent neutral amino acid transporter B(0)AT1  
B D | angiotensin-converting enzyme 2  
E F | sars-cov-2 receptor binding domain  
  
Non-standard residues in 6m17 copy.pdb #1  
---  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
ZN — zinc ion  
  

> coulombic

Coulombic values for 6m17 copy.pdb_A SES surface #1.2: minimum, -20.86, mean
-3.52, maximum 13.62  
Coulombic values for 6m17 copy.pdb_B SES surface #1.3: minimum, -20.90, mean
-4.10, maximum 13.79  
Coulombic values for 6m17 copy.pdb_C SES surface #1.4: minimum, -21.33, mean
-3.54, maximum 13.33  
Coulombic values for 6m17 copy.pdb_D SES surface #1.5: minimum, -19.88, mean
-4.08, maximum 13.77  
Coulombic values for 6m17 copy.pdb_E SES surface #1.6: minimum, -11.73, mean
-0.27, maximum 10.37  
Coulombic values for 6m17 copy.pdb_F SES surface #1.7: minimum, -28.99, mean
-0.26, maximum 10.12  

> select :NAG

616 atoms, 634 bonds, 44 residues, 1 model selected  

> select ::name="HOH"::name="NAG"::name="ZN"

626 atoms, 634 bonds, 54 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> hide surfaces

> hide cartoons

> hide atoms

> hide atoms

> show atoms

> preset cartoons/nucleotides licorice/ovals

Changed 24700 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /B

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:708

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:708-709

17 atoms, 16 bonds, 2 residues, 1 model selected  

> style sel stick

Changed 17 atom styles  

> show sel atoms

> color sel byhetero

> select /B:652

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:652-659

76 atoms, 77 bonds, 8 residues, 1 model selected  

> style sel stick

Changed 76 atom styles  

> style sel stick

Changed 76 atom styles  

> show sel atoms

> color sel byhetero

> select clear

> save "/Users/Bruce/Desktop/ADAM17/B0AT1/6m17_Coulomic electrostatic
> RQYFLKVK-RS on ACE2-chain A.cxs" includeMaps true

> set bgColor white

> select /B

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select /A/C

9616 atoms, 9900 bonds, 1212 residues, 1 model selected  

> color (#!1 & sel) dark gray

> color (#!1 & sel) dim gray

> select clear

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> color (#!1 & sel) medium blue

> color (#!1 & sel) blue

> color (#!1 & sel) cornflower blue

> ui tool show "Color Actions"

> color sel medium blue

> select clear

> ui tool show "Show Sequence Viewer"

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> select clear

> select /D:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> color (#!1 & sel) medium blue

> select /E:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel gold

> color sel goldenrod

> color sel dark goldenrod

> color sel dark goldenrod

> select clear

> select /F:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> color sel dark goldenrod

> select clear

> ui mousemode right select

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select /B:708

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:708-709

17 atoms, 16 bonds, 2 residues, 1 model selected  

> color (#!1 & sel) red

> color sel byhetero

> select /B:652

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:652-659

76 atoms, 77 bonds, 8 residues, 1 model selected  

> color (#!1 & sel) red

> color sel byhetero

> save "/Users/Bruce/Desktop/ADAM17/B0AT1/6m17_Coulomic electrostatic
> RQYFLKVK-RS on ACE2-chain A.cxs" includeMaps true

> select clear

> lighting simple

> lighting soft

> lighting simple

> lighting full

> lighting simple

> lighting full

> lighting simple

> select /D:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> color (#!1 & sel) cornflower blue

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> color (#!1 & sel) medium blue

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select clear

> select /B:708

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:708-709

17 atoms, 16 bonds, 2 residues, 1 model selected  

> color (#!1 & sel) red

> style sel stick

Changed 17 atom styles  

> color sel byhetero

> select /B:652

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:652-659

76 atoms, 77 bonds, 8 residues, 1 model selected  

> color (#!1 & sel) red

> color sel byhetero

> label (#!1 & sel) attribute name

> label (#!1 & sel) text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

> label (#!1 & sel) attribute label_specifier

> label (#!1 & sel) attribute name

> ~label (#!1 & sel) residues

> select /B:709

6 atoms, 5 bonds, 1 residue, 1 model selected  

> ui mousemode right label

> label #1/B:709

> label #1/B:708

> label #1/B:657

> label #1/B:658

> label #1/B:656

> label #1/B:659

> label #1/B:654

> label #1/B:655

> label #1/B:652

> label #1/B:653

> save /Users/Bruce/Desktop/image1.png supersample 3

> label #1/D:638

> label #1/D:670

> ~label (#!1 & sel) residues

> label delete residues

> save /Users/Bruce/Desktop/image2.png supersample 3

> ui mousemode right select

> ui mousemode right "translate selected models"

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> coulombic sel

Coulombic values for 6m17 copy.pdb_B SES surface #1.3: minimum, -20.90, mean
-4.10, maximum 13.79  

> select /A:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> show sel surfaces

> transparency (#!1 & sel) 50

> transparency (#!1 & sel) 0

> color (#!1 & sel) light gray

> color (#!1 & sel) gray

> color (#!1 & sel) light gray

> color (#!1 & sel) dim gray

> ui tool show "Color Actions"

> color sel light gray

> color sel silver

> color sel light gray

> color sel silver

> color sel light gray

> color sel silver

> select clear

> select /A:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> select /C:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> color sel silver

> select /C:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> select /C:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> select clear

> select /A:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> select /C:5-609

4799 atoms, 4942 bonds, 605 residues, 1 model selected  

> show sel surfaces

> select /D:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> show sel surfaces

> select /E:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> show sel surfaces

> select /E:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> select /E:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> select /F:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> show sel surfaces

> lighting full

> select clear

> save /Users/Bruce/Desktop/image3.png supersample 3

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> transparency (#!1 & sel) 40

> select /E:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> select /F:336-518

1462 atoms, 1506 bonds, 183 residues, 1 model selected  

> hide sel cartoons

> hide sel atoms

> transparency (#!1 & sel) 40

> transparency (#!1 & sel) 0

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select backbone

12288 atoms, 12282 bonds, 3072 residues, 1 model selected  

> select clear

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> save "/Users/Bruce/Desktop/ADAM17/B0AT1/6m17_Coulomic electrostatic
> RQYFLKVK-RS on ACE2-chain A.cxs"

> select clear

> ui mousemode right select

> select /B:709@N

1 atom, 1 residue, 1 model selected  

> color (#!1 & sel) lime

> show sel cartoons

> hide sel cartoons

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> show sel cartoons

> hide sel cartoons

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 1/B  

> select clear

> select /B:708

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:708-709

17 atoms, 16 bonds, 2 residues, 1 model selected  

> color (#!1 & sel) lime

> style sel stick

Changed 17 atom styles  

> show sel atoms

> color sel byhetero

> style sel ball

Changed 17 atom styles  

> style sel stick

Changed 17 atom styles  

> color sel byhetero

> hide sel atoms

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> undo

> select /B:708

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:708-709

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select clear

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> coulombic sel

Coulombic values for 6m17 copy.pdb_B SES surface #1.3: minimum, -20.90, mean
-4.10, maximum 13.79  

> hide sel surfaces

> color (#!1 & sel) lime

> select clear

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> select /B:21-768

6089 atoms, 6255 bonds, 748 residues, 1 model selected  

> coulombic sel

Coulombic values for 6m17 copy.pdb_B SES surface #1.3: minimum, -20.90, mean
-4.10, maximum 13.79  

> hide sel surfaces

> show sel surfaces

> transparency (#!1 & sel) 50

> select clear

> save /Users/Bruce/Desktop/image4.png supersample 3

> save /Users/Bruce/Desktop/image5.png supersample 3

> save "/Users/Bruce/Desktop/ADAM17/B0AT1/6m17_Coulomic electrostatic
> RQYFLKVK-RS on ACE2-chain A.cxs"

> save "/Users/Bruce/Desktop/ADAM17/B0AT1/6m17_Coulomic electrostatic
> RQYFLKVK-RS on ACE2-chain A.cxs" includeMaps true

opened ChimeraX session  

> save "/Users/Bruce/Desktop/ADAM17/ADAM17 PDB 3LGP/B0AT1/6m17_Coulomic
> electrostatic RQYFLKVK-RS on ACE2-chain A_trial2.pdb" relModel #1

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/pdb/__init__.py", line 71, in save  
pdb.save_pdb(session, path, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/pdb/pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
OSError: Unable to open file '/Users/Bruce/Desktop/ADAM17/ADAM17 PDB
3LGP/B0AT1/6m17_Coulomic electrostatic RQYFLKVK-RS on ACE2-chain A_trial2.pdb'
for writing  
  
OSError: Unable to open file '/Users/Bruce/Desktop/ADAM17/ADAM17 PDB
3LGP/B0AT1/6m17_Coulomic electrostatic RQYFLKVK-RS on ACE2-chain A_trial2.pdb'
for writing  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/pdb/pdb.py", line 119, in save_pdb  
(serial_numbering == "h36"), polymeric_res_names)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel Iris OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: Mac mini
      Model Identifier: Macmini7,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2.6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 249.0.0.0.0
      SMC Version (system): 2.24f32

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 10 days 19:51

Graphics/Displays:

    Intel Iris:

      Chipset Model: Intel Iris
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a2e
      Revision ID: 0x0009
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        DELL U3014:
          Resolution: 2560 x 1600
          UI Looks like: 2560 x 1600 @ 60 Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: J3Y9N63G634L
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    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-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    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
    ChimeraX-Centroids: 1.1
    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.dev202009150003
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    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
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    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
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0.1
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2.1
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[pett]

Despite the C++ explicitly setting IOError

[pett]

testing Trac

[pett]

Test of update from mail