Cannot write into Modeller temporary folder

[robertperezmd@…]

The following bug report has been submitted:
Platform:        macOS-12.7.4-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Unable to model TAPV sequence usong alignment with pdb file 5F1B Chain A.

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 5F1B format mmcif fromDatabase pdb

5f1b title:  
Structural basis of Ebola virus entry: viral glycoprotein bound to its
endosomal receptor Niemann-Pick C1 [more info...]  
  
Chain information for 5f1b #1  
---  
Chain | Description | UniProt  
A | GP1 | VGP_EBOZ5 32-188  
B | GP2 | VGP_EBOZ5 509-632  
C | Niemann-Pick C1 protein | NPC1_HUMAN 2-248  
  
Non-standard residues in 5f1b #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  

> open "/Users/rickricketson/Desktop/TAPV-5F1B Chain A MSA.fasta"

Summary of feedback from opening /Users/rickricketson/Desktop/TAPV-5F1B Chain
A MSA.fasta  
---  
notes | Alignment identifier is TAPV-5F1B Chain A MSA.fasta  
Associated 5f1b chain A to 5F1B_1|Chain/1-132 A|GP1|Zaire ebolavirus (128951)
with 0 mismatches  
Showing conservation header ("seq_conservation" residue attribute) for
alignment TAPV-5F1B Chain A MSA.fasta  
  
Opened 2 sequences from TAPV-5F1B Chain A MSA.fasta  

> ui tool show "Modeller Comparative"

> modeller comparative "TAPV-5F1B Chain A MSA.fasta:2" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false

Webservices job id: 4BI53R9CPI9THYUT  
Modeller job (ID 4BI53R9CPI9THYUT) finished  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5f1b, chain A (#1) with
5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence
alignment score = 636.1  
RMSD between 117 pruned atom pairs is 0.589 angstroms; (across all 132 pairs:
1.041)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5f1b, chain A (#1) with
5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence
alignment score = 636.1  
RMSD between 128 pruned atom pairs is 0.730 angstroms; (across all 132 pairs:
0.904)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5f1b, chain A (#1) with
5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence
alignment score = 636.1  
RMSD between 127 pruned atom pairs is 0.928 angstroms; (across all 132 pairs:
1.033)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5f1b, chain A (#1) with
5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence
alignment score = 628.9  
RMSD between 121 pruned atom pairs is 0.556 angstroms; (across all 132 pairs:
0.957)  
  
Parameters  
---  
Chain pairing | ss  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker 5f1b, chain A (#1) with
5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951), chain A (#), sequence
alignment score = 636.1  
RMSD between 131 pruned atom pairs is 0.368 angstroms; (across all 132 pairs:
0.417)  
  
Associated 5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951) chain A to
5F1B_1|Chain/1-132 A|GP1|Zaire ebolavirus (128951) with 0 mismatches  
[Repeated 4 time(s)] Chain information for
5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)  
---  
Chain | Description  
2.1/A 2.2/A 2.3/A 2.4/A 2.5/A | No description available  
  

> ui tool show "Show Sequence Viewer"

> ui tool show "Modeller Comparative"

> modeller comparative "TAPV-5F1B Chain A MSA.fasta:1" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 311, in launch_modeller  
run(  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/cmd.py", line 48, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/comparative.py", line 303, in model  
save_pdb(session, pdb_file_name, models=[structure],
polymeric_res_names=ATOM_res_names)  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 224, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
OSError: Unable to open file
'/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmp42hlpdsl/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb'
for writing  
  
OSError: Unable to open file
'/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmp42hlpdsl/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb'
for writing  
  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 224, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
  
See log for complete Python traceback.  
  

> modeller comparative "TAPV-5F1B Chain A MSA.fasta:1" numModels 5 fast false
> multichain true hetPreserve false hydrogens false waterPreserve false

Traceback (most recent call last):  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/tool.py", line 311, in launch_modeller  
run(  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/cmd.py", line 48, in sequence_model  
comparative.model(session, targets, block=block, multichain=multichain,  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/modeller/comparative.py", line 303, in model  
save_pdb(session, pdb_file_name, models=[structure],
polymeric_res_names=ATOM_res_names)  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 224, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
OSError: Unable to open file
'/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmpfsciswuo/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb'
for writing  
  
OSError: Unable to open file
'/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmpfsciswuo/template_struc/5F1B_1_Chain/1-132_A_GP1_Zaire_ebolavirus_(128951)_2.4.pdb'
for writing  
  
File
"/private/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/AppTranslocation/86C366D9-172E-4933-BB9A-E788EE4B19A9/d/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/pdb/pdb.py", line 224, in save_pdb  
_pdbio.write_pdb_file([m.cpp_pointer for m in models], output, selected_only,  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac17,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 32 GB
      System Firmware Version: 526.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.33f12

Software:

    System Software Overview:

      System Version: macOS 12.7.4 (21H1123)
      Kernel Version: Darwin 21.6.0
      Time since boot: 18 minutes

Graphics/Displays:

    AMD Radeon R9 M380:

      Chipset Model: AMD Radeon R9 M380
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6640
      Revision ID: 0x0080
      ROM Revision: 113-C6005R-800
      VBIOS Version: 113-C6005T-009
      EFI Driver Version: 01.00.800
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 5K (5120 x 2880)
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
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    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.2.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
File attachment: TAPV-5F1B Chain A MSA.fasta

TAPV-5F1B Chain A MSA.fasta​

[chimerax-bug-report@…]

Added by email2trac

[Eric Pettersen]

Hi Robert,

If you do not specify a specific folder for Modeller to use for temporary files and results, it creates one. For some reason, ChimeraX could not create files in the temporary folder it created (/var/folders/2d/_cyz5n8x4kx8h1216fjhp2c00000gn/T/tmp42hlpdsl/template_struc/5F1B_1_Chain/).
My suggestion would be to tell Modeller to use a specific folder that you know you have permission to create files in (such as your Desktop or Documents folders). You do that by switching to the "Advanced" tab of the Modeller tool and enter a value for the "Temporary folder location" option (probably easiest to use its "Browse" button, since you have to provide the full path to the folder).

--Eric

Eric Pettersen
UCSF Computer Graphics Lab