Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5928 closed defect (fixed)

"name 'stream' is not defined" opening model positions file

Reported by: jribeiro@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.14393
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
I am trying to import a posiotion matrix obtained by dali into chimeerax.

i saved the file as n:\temp\model.positions. containing 2 lines below:
JAP81880.1-Alphafold.pdb,0.803979,0.048204,0.592701,2.164986,-0.220978,-0.901117,0.373038,19.548801,0.552075,-0.430888,-0.713827,-35.291908 
pdb3uv1.ent,1,0,0,0,0,1,0,0,0,0,1,0

Then I tried to import the file with
open n:\temp\model.positions model #1

and I got the error

NameError: name 'stream' is not defined

File "d:\Program Files\ChimeraX 1.3\bin\lib\site-packages\chimerax\positions\positions.py", line 67, in _parse_places
% (line_num+1, stream.name, len(fields), line))

See log for complete Python traceback.

Log:
Startup Messages  
---  
warning | No presets found in custom preset folder D:/ChimeraX 1.2.5  
  
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open .\\\links\\\pdb\\\JAP81880.1-Alphafold.pdb

Chain information for JAP81880.1-Alphafold.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open .\\\links\\\ent\\\pdb3uv1.ent

pdb3uv1.ent title:  
Crystal structure A major allergen from dust mite [more info...]  
  
Chain information for pdb3uv1.ent #2  
---  
Chain | Description | UniProt  
A B | der F 7 allergen | A1KXH4_DERFA  
  

> view matrix

camera position: 1,0,0,-0.48368,0,1,0,8.8447,0,0,1,145.56  
model positions: #1,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0  
  

> open n:\temp\model.positions models #1

No positions specified in positions file n:\temp\model.positions.  

> select down

Nothing selected  

> select down

Nothing selected  

> open n:\temp\model.positions models

Missing "models" keyword's argument  

> open n:\temp\model.positions models #1

No positions specified in positions file n:\temp\model.positions.  

> open n:\temp\model.positions models #1

Traceback (most recent call last):  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\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 "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\\__init__.py", line 27, in open  
return positions.read_positions(session, data, file_name,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 27, in read_positions  
places = _parse_places(lines)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
NameError: name 'stream' is not defined  
  
NameError: name 'stream' is not defined  
  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
  
See log for complete Python traceback.  
  

> open n:\temp\model.positions models #1

Traceback (most recent call last):  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\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 "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\\__init__.py", line 27, in open  
return positions.read_positions(session, data, file_name,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 27, in read_positions  
places = _parse_places(lines)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
NameError: name 'stream' is not defined  
  
NameError: name 'stream' is not defined  
  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
  
See log for complete Python traceback.  
  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> open n:\temp\model.positions models #1

Traceback (most recent call last):  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\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 "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\\__init__.py", line 27, in open  
return positions.read_positions(session, data, file_name,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 27, in read_positions  
places = _parse_places(lines)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
NameError: name 'stream' is not defined  
  
NameError: name 'stream' is not defined  
  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
  
See log for complete Python traceback.  
  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> select down

Nothing selected  

> open n:\temp\model.positions models #1

Traceback (most recent call last):  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 297, in execute  
cmd.run(cmd_text)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\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 "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 432, in collated_open  
return remember_data_format()  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\open_command\cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\\__init__.py", line 27, in open  
return positions.read_positions(session, data, file_name,  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 27, in read_positions  
places = _parse_places(lines)  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
NameError: name 'stream' is not defined  
  
NameError: name 'stream' is not defined  
  
File "d:\Program Files\ChimeraX 1.3\bin\lib\site-
packages\chimerax\positions\positions.py", line 67, in _parse_places  
% (line_num+1, stream.name, len(fields), line))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3 (Core Profile) Mesa 20.2.0-devel (git-a8d28e4676)
OpenGL renderer: llvmpipe (LLVM 5.0, 256 bits)
OpenGL vendor: VMware, Inc.
Manufacturer: VMware, Inc.
Model: VMware Virtual Platform
OS: Microsoft Windows Server 2016 Standard (Build 14393)
Memory: 25,769,332,736
MaxProcessMemory: 137,438,953,344
CPU: 1 Intel(R) Xeon(R) CPU E5-2660 0 @ 2.20GHz
OSLanguage: en-US
Locale: ('en_US', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pywin32: 228
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (6)

comment:1 by Tom Goddard, 4 years ago

Component: Unassigned → Core
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → "name 'stream' is not defined" opening model positions file

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

There is a mistake in the ChimeraX code that is trying to print an error message saying a line of your file has a line that has less than 13 fields separated by commas. I've fixed that code.

I don't have your file and since the error message failed to display I don't know which line it is complaining about. But I see that the code will not even accept blank lines, so make sure you have none of those. It will allow you to put comment lines that start with a "#" character.

in reply to:  3 ; comment:3 by jribeiro@…, 4 years ago 

Thanks,

In fact my file had an empty line at the end. I removed it and the error did not show up.

Perhaps the python code could not trigger an error when an empty line appears, which can be common at the end of the file.

Many thanks,

Jose

Jose Ribeiro

Head,
Section of Vector Biology
Laboratory of Malaria and Vector Research
National Institute of Allergy and Infectious Diseases

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Friday, January 14, 2022 6:54 PM
Cc: goddard@cgl.ucsf.edu; Ribeiro, Jose (NIH/NIAID) [E] <jribeiro@niaid.nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #5928: "name 'stream' is not defined" opening model positions file

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.


#5928: "name 'stream' is not defined" opening model positions file
---------------------------------+-------------------------
          Reporter:  jribeiro@…  |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Core        |    Version:
        Resolution:  fixed       |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => fixed


Comment:

 There is a mistake in the ChimeraX code that is trying to print an error  message saying a line of your file has a line that has less than 13 fields  separated by commas.  I've fixed that code.

 I don't have your file and since the error message failed to display I  don't know which line it is complaining about.  But I see that the code  will not even accept blank lines, so make sure you have none of those.  It  will allow you to put comment lines that start with a "#" character.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5928#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  4 ; comment:4 by goddard@…, 4 years ago 

Agree.  My fixed code allows blank lines.  It is in the daily builds on the ChimeraX download page.

in reply to:  5 ; comment:5 by jribeiro@…, 4 years ago 

Hi,

I am glad to play the part of the fool to make the program foolproof!

Regards,

Jose

Jose Ribeiro

Head,
Section of Vector Biology
Laboratory of Malaria and Vector Research
National Institute of Allergy and Infectious Diseases

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Saturday, January 15, 2022 5:28 PM
To: goddard@cgl.ucsf.edu; Ribeiro, Jose (NIH/NIAID) [E] <jribeiro@niaid.nih.gov>
Subject: [EXTERNAL] Re: [ChimeraX] #5928: "name 'stream' is not defined" opening model positions file

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.


#5928: "name 'stream' is not defined" opening model positions file
---------------------------------+-------------------------
          Reporter:  jribeiro@…  |      Owner:  Tom Goddard
              Type:  defect      |     Status:  closed
          Priority:  normal      |  Milestone:
         Component:  Core        |    Version:
        Resolution:  fixed       |   Keywords:
        Blocked By:              |   Blocking:
Notify when closed:              |   Platform:  all
           Project:  ChimeraX    |
---------------------------------+-------------------------

Comment (by goddard@…):

 {{{
 Agree.  My fixed code allows blank lines.  It is in the daily builds on  the ChimeraX download page.
 }}}

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5928#comment:4>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

in reply to:  6 ; comment:6 by goddard@…, 4 years ago 

Hi Jose,

Wait, I'm the fool, the one who wrote the broken ChimeraX code!  I greatly appreciate your bug report and all the bug reports we get -- it helps make ChimeraX more reliable and easy to use.  In this case, the error message for reading position files now works, and blank lines are permitted, two nice improvements.  Keep sending ChimeraX bug reports when things goes wrong.

  I asked my wife who develops software for a large company Agilent whether they encourage bug reports from users and she pointed out to me that they have dozens of full-time staff software testers, more testers than people writing the code.  Unfortunately with our NIH funded software the users end up being the main testers.  Our lab is lucky that we have one person (Elaine) who does testing half-time, but otherwise our code only gets tested by the programmer who wrote it before it is unleashed on researchers.

	Tom
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