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#4489 assigned defect

SEQCROW: No such file or directory: '/Users/sethmartinez/AARON_libs/citations.txt'

Reported by:	sisimalandrin@…	Owned by:	Tony Schaefer
Priority:	normal	Milestone:
Component:	Third Party	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Darwin-20.3.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show

Downloading bundle SEQCROW-0.25.1-py3-none-any.whl  
Successfully installed SEQCROW-0.25.1 Send2Trash-1.5.0  
Installed SEQCROW (0.25.1)  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 353, in init_manager  
return api._api_caller.init_manager(api, session, self, name, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1269, in init_manager  
return cls._get_func(api, "init_manager")(session, bi, name, **kw)  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/__init__.py", line 90, in init_manager  
from .managers import FileReaderManager  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/managers/__init__.py", line 3, in <module>  
from .job_manager import JobManager  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/managers/job_manager.py", line 3, in <module>  
from AaronTools.fileIO import FileReader  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/fileIO.py", line 10, in <module>  
from AaronTools.atoms import Atom  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/atoms.py", line 73, in <module>  
@addlogger  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 232, in addlogger  
cls.LOG = ATLogger(name, level=level, override=override)  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 148, in __init__  
handlers += [(CitationHandler(SAVE_CITATIONS), True)]  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 116, in __init__  
super().__init__(filename, **kwargs)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/__init__.py",
line 1087, in __init__  
StreamHandler.__init__(self, self._open())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/__init__.py",
line 1116, in _open  
return open(self.baseFilename, self.mode, encoding=self.encoding)  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/sethmartinez/Aaron_libs/citations.txt'  
  

SEQCROW (installed) [version: 0.25.1] [api package: SEQCROW] [category:
General, Input/Output, External Program] [tool: Build QM Input [categories:
AaronTools] [synopsis: Create Gaussian, ORCA, or Psi4 input file]] [tool:
Structure Modification [categories: AaronTools] [synopsis: Modify
substituents, swap ligands, and fuse rings]] [tool: Change Substituents
[categories: Structure Editing] [synopsis: Modify substituents, swap ligands,
and fuse rings]] [tool: Swap Transition Metal Ligands [categories: Structure
Editing] [synopsis: Modify substituents, swap ligands, and fuse rings]] [tool:
Fuse Ring [categories: Structure Editing] [synopsis: Modify substituents, swap
ligands, and fuse rings]] [tool: Browse AaronTools Libraries [categories:
AaronTools] [synopsis: Browse the AaronTools ligand, substituent, and ring
libraries]] [tool: Process QM Thermochemistry [categories: AaronTools]
[synopsis: Compute the free energy of a molecule with frequency data]] [tool:
Managed Models [categories: SEQCROW] [synopsis: see models managed by
SEQCROW]] [tool: Add to Personal Library [categories: AaronTools] [synopsis:
Add to your personal ligand, substituent, and ring libraries]] [tool:
Visualize Normal Modes [categories: AaronTools] [synopsis: Visualize normal
modes from a frequency output file as displacement vectors or as an
animation]] [tool: Job Queue [categories: SEQCROW] [synopsis: View status of
jobs]] [tool: Substituent Sterimol [categories: Structure Analysis] [synopsis:
Calculate L, B1, and B5 Sterimol parameters for a substituent]] [tool: Bond
Editor [categories: Structure Editing] [synopsis: Draw or erase bonds]] [tool:
Change Element [categories: Structure Editing] [synopsis: Modify substituents,
swap ligands, and fuse rings]] [tool: Rotate Atoms [categories: Structure
Editing] [synopsis: Rotate all or part of a molecular structure]] [tool:
Buried Volume [categories: Structure Analysis] [synopsis: Calculate percent
buried volume]] [tool: File Info [categories: AaronTools] [synopsis:
Miscellaneous file data]] [command: rmsdAlign [categories: Structure Analysis]
[synopsis: Calculate RMSD between structures]] [command: substitute
[categories: Structure Editing] [synopsis: change substiuents]] [command:
fuseRing [categories: Structure Editing] [synopsis: fuse a ring]] [command:
tsbond [categories: Structure Editing] [synopsis: display a forming/breaking
bond as semi-transparent]] [command: ~tsbond [categories: Structure Editing]
[synopsis: remove a forming/breaking bond]] [command: sterimol [categories:
Structure Analysis] [synopsis: calculate L, B1, and B5 Sterimol parameters]]
[command: percentVolumeBuried [categories: Structure Analysis] [synopsis:
calculate percent volume buried by ligands around a metal center]] [command:
highlight [categories: General] [synopsis: make some atoms or bonds stand
out]] [command: ~highlight [categories: General] [synopsis: remove
highlights]]: manager initialization failed  

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 342, in initialize  
api._api_caller.initialize(api, session, self)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1265, in initialize  
return cls._get_func(api, "initialize")(session, bi)  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/__init__.py", line 37, in initialize  
from AaronTools.substituent import Substituent  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/substituent.py", line 14, in <module>  
from AaronTools.fileIO import FileReader, read_types  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/fileIO.py", line 10, in <module>  
from AaronTools.atoms import Atom  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/atoms.py", line 73, in <module>  
@addlogger  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 232, in addlogger  
cls.LOG = ATLogger(name, level=level, override=override)  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 148, in __init__  
handlers += [(CitationHandler(SAVE_CITATIONS), True)]  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 116, in __init__  
super().__init__(filename, **kwargs)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/__init__.py",
line 1087, in __init__  
StreamHandler.__init__(self, self._open())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/__init__.py",
line 1116, in _open  
return open(self.baseFilename, self.mode, encoding=self.encoding)  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/sethmartinez/AARON_libs/citations.txt'  
  

SEQCROW (installed) [version: 0.25.1] [api package: SEQCROW] [category:
General, Input/Output, External Program] [tool: Build QM Input [categories:
AaronTools] [synopsis: Create Gaussian, ORCA, or Psi4 input file]] [tool:
Structure Modification [categories: AaronTools] [synopsis: Modify
substituents, swap ligands, and fuse rings]] [tool: Change Substituents
[categories: Structure Editing] [synopsis: Modify substituents, swap ligands,
and fuse rings]] [tool: Swap Transition Metal Ligands [categories: Structure
Editing] [synopsis: Modify substituents, swap ligands, and fuse rings]] [tool:
Fuse Ring [categories: Structure Editing] [synopsis: Modify substituents, swap
ligands, and fuse rings]] [tool: Browse AaronTools Libraries [categories:
AaronTools] [synopsis: Browse the AaronTools ligand, substituent, and ring
libraries]] [tool: Process QM Thermochemistry [categories: AaronTools]
[synopsis: Compute the free energy of a molecule with frequency data]] [tool:
Managed Models [categories: SEQCROW] [synopsis: see models managed by
SEQCROW]] [tool: Add to Personal Library [categories: AaronTools] [synopsis:
Add to your personal ligand, substituent, and ring libraries]] [tool:
Visualize Normal Modes [categories: AaronTools] [synopsis: Visualize normal
modes from a frequency output file as displacement vectors or as an
animation]] [tool: Job Queue [categories: SEQCROW] [synopsis: View status of
jobs]] [tool: Substituent Sterimol [categories: Structure Analysis] [synopsis:
Calculate L, B1, and B5 Sterimol parameters for a substituent]] [tool: Bond
Editor [categories: Structure Editing] [synopsis: Draw or erase bonds]] [tool:
Change Element [categories: Structure Editing] [synopsis: Modify substituents,
swap ligands, and fuse rings]] [tool: Rotate Atoms [categories: Structure
Editing] [synopsis: Rotate all or part of a molecular structure]] [tool:
Buried Volume [categories: Structure Analysis] [synopsis: Calculate percent
buried volume]] [tool: File Info [categories: AaronTools] [synopsis:
Miscellaneous file data]] [command: rmsdAlign [categories: Structure Analysis]
[synopsis: Calculate RMSD between structures]] [command: substitute
[categories: Structure Editing] [synopsis: change substiuents]] [command:
fuseRing [categories: Structure Editing] [synopsis: fuse a ring]] [command:
tsbond [categories: Structure Editing] [synopsis: display a forming/breaking
bond as semi-transparent]] [command: ~tsbond [categories: Structure Editing]
[synopsis: remove a forming/breaking bond]] [command: sterimol [categories:
Structure Analysis] [synopsis: calculate L, B1, and B5 Sterimol parameters]]
[command: percentVolumeBuried [categories: Structure Analysis] [synopsis:
calculate percent volume buried by ligands around a metal center]] [command:
highlight [categories: General] [synopsis: make some atoms or bonds stand
out]] [command: ~highlight [categories: General] [synopsis: remove
highlights]]: custom initialization failed  

> toolshed show

> open /Users/sethmartinez/Desktop/Development/Software/source/@emerald-
> organics:SerturnerX/SerturnerX/Data/Conformer3D_CID_4980.sdf

PubChem entry 4980  
  
Downloading file toolshed.html  

> ui tool show "Add to Personal Library"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 531, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/__init__.py", line 1312, in start_tool  
return cls._get_func(api, "start_tool")(session, bi, ti)  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/__init__.py", line 169, in start_tool  
from .tools import LibAdd  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/tools/__init__.py", line 1, in <module>  
from .browse_aarontools import AaronTools_Library, key_atom_highlight,
ghost_connection_highlight, show_walk_highlight  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/SEQCROW/tools/browse_aarontools.py", line 15, in <module>  
from AaronTools.component import Component  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/component.py", line 9, in <module>  
from AaronTools.fileIO import read_types  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/fileIO.py", line 10, in <module>  
from AaronTools.atoms import Atom  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/atoms.py", line 73, in <module>  
@addlogger  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 232, in addlogger  
cls.LOG = ATLogger(name, level=level, override=override)  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 148, in __init__  
handlers += [(CitationHandler(SAVE_CITATIONS), True)]  
File "/Users/sethmartinez/Library/Application Support/ChimeraX/1.1/site-
packages/AaronTools/__init__.py", line 116, in __init__  
super().__init__(filename, **kwargs)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/__init__.py",
line 1087, in __init__  
StreamHandler.__init__(self, self._open())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/logging/__init__.py",
line 1116, in _open  
return open(self.baseFilename, self.mode, encoding=self.encoding)  
FileNotFoundError: [Errno 2] No such file or directory:
'/Users/sethmartinez/AARON_libs/citations.txt'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1501, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.1.1.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-1.1.1.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-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/cmd.py", line 187, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Add to
Personal Library in bundle SEQCROW:  
[Errno 2] No such file or directory:
'/Users/sethmartinez/AARON_libs/citations.txt'  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Add to
Personal Library in bundle SEQCROW:  
[Errno 2] No such file or directory:
'/Users/sethmartinez/AARON_libs/citations.txt'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 537, in start_tool  
"start_tool() failed for tool %s in bundle %s:\n%s" % (tool_name, self.name,
str(e)))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.1.12
OpenGL renderer: Intel HD Graphics 5000 OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir6,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1.3 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: 4 GB
      System Firmware Version: 430.0.0.0.0
      SMC Version (system): 2.13f15

Software:

    System Software Overview:

      System Version: macOS 11.2.3 (20D91)
      Kernel Version: Darwin 20.3.0
      Time since boot: 12:03

Graphics/Displays:

    Intel HD Graphics 5000:

      Chipset Model: Intel HD Graphics 5000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x0a26
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

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: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    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: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    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
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    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
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    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: 1.2.3
    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
    Send2Trash: 1.5.0
    SEQCROW: 0.25.1
    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

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component:	Unassigned → Third Party
Owner:	set to Tony Schaefer
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → SEQCROW: No such file or directory: '/Users/sethmartinez/AARON_libs/citations.txt'

in reply to: 2 ; follow-up: 2 comment:2 by Tony Schaefer, 5 years ago

Sorry about that, AaronTools recently added the option to log recommended citations (e.g. for structure analysis methods) to a file. You don't have the default folder for that log file, but it shouldn't have tried to set up the logger if that folder doesn't exist. I've uploaded a fix in SEQCROW version 0.25.2.

Tony
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Monday, April 12, 2021 1:11 PM
Cc: sisimalandrin@outlook.com <sisimalandrin@outlook.com>; Anthony James Schaefer <tony.schaefer@uga.edu>
Subject: Re: [ChimeraX] #4489: SEQCROW: No such file or directory: '/Users/sethmartinez/AARON_libs/citations.txt' (was: ChimeraX bug report submission)

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


#4489: SEQCROW: No such file or directory:
'/Users/sethmartinez/AARON_libs/citations.txt'
--------------------------------------+---------------------------
          Reporter:  sisimalandrin@…  |      Owner:  Tony Schaefer
              Type:  defect           |     Status:  assigned
          Priority:  normal           |  Milestone:
         Component:  Third Party      |    Version:
        Resolution:                   |   Keywords:
        Blocked By:                   |   Blocking:
Notify when closed:                   |   Platform:  all
           Project:  ChimeraX         |
--------------------------------------+---------------------------
Changes (by Eric Pettersen):

 * status:  new => assigned
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tony Schaefer


--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4489#comment:1>
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