Opened 3 years ago

Closed 3 years ago

#8606 closed defect (fixed)

No sequences in file

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Sequence Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /output_mature.fasta" format
> fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/output_mature.fasta  
---  
note | Alignment identifier is output_mature.fasta  
  
Opened 1 sequences from output_mature.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /output_mature.fasta"

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/output_mature.fasta  
---  
notes | Destroying pre-existing alignment with identifier output_mature.fasta  
Alignment identifier is output_mature.fasta  
  
Opened 1 sequences from output_mature.fasta  

> help help:credits.html

> show # target m

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

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta" format fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
note | Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta" format fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
notes | Destroying pre-existing alignment with identifier I6YB54.fasta  
Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta"

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
notes | Destroying pre-existing alignment with identifier I6YB54.fasta  
Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /A0R4L5.fasta"

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/A0R4L5.fasta  
---  
note | Alignment identifier is A0R4L5.fasta  
  
Opened 1 sequences from A0R4L5.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /AF-I6YB54-F1-model_v4.pdb"

AF-I6YB54-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (I6YB54) [more
info...]  
  
Chain information for AF-I6YB54-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | uncharacterized protein | I6YB54_MYCTU  
  
Associated AF-I6YB54-F1-model_v4.pdb chain A to tr_I6YB54_I6YB54_MYCTU with 0
mismatches  

> select /A:28-32

40 atoms, 40 bonds, 5 residues, 1 model selected  

> select /A:28-36

73 atoms, 75 bonds, 9 residues, 1 model selected  

> select /A:28-31

29 atoms, 29 bonds, 4 residues, 1 model selected  

> select /A:28-51

202 atoms, 211 bonds, 24 residues, 1 model selected  

> select /A:379

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:28-379

2868 atoms, 2962 bonds, 352 residues, 1 model selected  

> select add #1

3063 atoms, 3160 bonds, 379 residues, 1 model selected  

> select subtract #1

Nothing selected  

> view clip false

> select /A:28-379

2868 atoms, 2962 bonds, 352 residues, 1 model selected  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /AF-I6YB54-F1-model_v4.pdb"

AF-I6YB54-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (I6YB54) [more
info...]  
  
Chain information for AF-I6YB54-F1-model_v4.pdb #2  
---  
Chain | Description | UniProt  
A | uncharacterized protein | I6YB54_MYCTU  
  

> select add #2

5931 atoms, 6122 bonds, 731 residues, 2 models selected  

> select add #1

6126 atoms, 6320 bonds, 758 residues, 2 models selected  

> select subtract #1

3063 atoms, 3160 bonds, 379 residues, 1 model selected  

> hide #1 models

> close #2

> close

> ui windowfill toggle

[Repeated 1 time(s)]

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta" format fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
note | Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta" format fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
notes | Destroying pre-existing alignment with identifier I6YB54.fasta  
Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> ui tool show "Selection Inspector"

>

Incomplete command: alphafold  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta"

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
note | Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta" format fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
notes | Destroying pre-existing alignment with identifier I6YB54.fasta  
Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /I6YB54.fasta" format fasta

Summary of feedback from opening /Users/Camille/Desktop/td SAV2 DARDENNE
/I6YB54.fasta  
---  
notes | Destroying pre-existing alignment with identifier I6YB54.fasta  
Alignment identifier is I6YB54.fasta  
  
Opened 1 sequences from I6YB54.fasta  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /AF-I6YB54-F1-model_v4.pdb"
> format pdb

AF-I6YB54-F1-model_v4.pdb title:  
Alphafold monomer V2.0 prediction for uncharacterized protein (I6YB54) [more
info...]  
  
Chain information for AF-I6YB54-F1-model_v4.pdb #1  
---  
Chain | Description | UniProt  
A | uncharacterized protein | I6YB54_MYCTU  
  
Associated AF-I6YB54-F1-model_v4.pdb chain A to tr|I6YB54|I6YB54_MYCTU
1,4-beta-xylanase OS=Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
OX=83332 GN=Rv3096 PE=1 SV=1 with 0 mismatches  

> sequence align I6YB54.fasta program clustalOmega

Must specify 2 or more protein sequences  

> select /A:29-30

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

> select /A:1-30

220 atoms, 223 bonds, 30 residues, 1 model selected  

> select /A:31

4 atoms, 3 bonds, 1 residue, 1 model selected  

> select /A:31-379

2843 atoms, 2936 bonds, 349 residues, 1 model selected  

>

Incomplete command: alphafold  

>

Incomplete command: alphafold  

> close session

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /mature.rtf"

Unrecognized file suffix '.rtf'  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /mature.fasta"

Traceback (most recent call last):  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/__init__.py", line 61, in open  
return open_file(session, data, file_name,  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/parse.py", line 35, in open_file  
raise ValueError("No sequences found in %s file '%s'!" % (format_name, fname))  
ValueError: No sequences found in FASTA file 'mature.fasta'!  
  
ValueError: No sequences found in FASTA file 'mature.fasta'!  
  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/parse.py", line 35, in open_file  
raise ValueError("No sequences found in %s file '%s'!" % (format_name, fname))  
  
See log for complete Python traceback.  
  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /mature.fasta"

Failed opening file /Users/Camille/Desktop/td SAV2 DARDENNE /mature.fasta:  
No sequences found in FASTA file 'mature.fasta'!  

> open "/Users/Camille/Desktop/td SAV2 DARDENNE /mature.fasta"

Traceback (most recent call last):  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 193, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 457, in collated_open  
return remember_data_format()  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 428, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/__init__.py", line 61, in open  
return open_file(session, data, file_name,  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/parse.py", line 35, in open_file  
raise ValueError("No sequences found in %s file '%s'!" % (format_name, fname))  
ValueError: No sequences found in FASTA file 'mature.fasta'!  
  
ValueError: No sequences found in FASTA file 'mature.fasta'!  
  
File
"/private/var/folders/c9/82flpt392n15m2r37cr9c92c0000gp/T/AppTranslocation/EBBDB09C-0DDF-4811-B0CA-D7C11DFE0CB0/d/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/seqalign/parse.py", line 35, in open_file  
raise ValueError("No sequences found in %s file '%s'!" % (format_name, fname))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-18.4.6
OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
OpenGL vendor: Intel Inc.

Python: 3.9.11
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: MacBook Pro
      Model Identifier: MacBookPro12,1
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 2,7 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: 8 GB
      System Firmware Version: 428.60.3.0.0
      OS Loader Version: 540.80.2~11
      SMC Version (system): 2.28f7

Software:

    System Software Overview:

      System Version: macOS 12.2.1 (21D62)
      Kernel Version: Darwin 21.3.0
      Time since boot: 52 days 19:50

Graphics/Displays:

    Intel Iris Graphics 6100:

      Chipset Model: Intel Iris Graphics 6100
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x162b
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Sequence
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → No sequences in file

Should probably convert to UserError

comment:2 by Eric Pettersen, 3 years ago

Resolution: → fixed
Status: accepted → closed

Converted no-sequences error to UserError

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