id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
4391	view matrix: 'tuple' object has no attribute 'matrix'	ben.tatman@…	Eric Pettersen	"{{{
The following bug report has been submitted:
Platform:        Linux-5.10.19-200.fc33.x86_64-x86_64-with-glibc2.14
ChimeraX Version: 1.2.dev202103220641 (2021-03-22 06:41:31 UTC)
Description
I'm trying to get my view matrix so I can put this into a script. The manual says that 'view matrix' should give the current view in matrix form but instead I get an attribute error? I might just be doing something wrong though.

Log:
UCSF ChimeraX version: 1.2.dev202103220641 (2021-03-22)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open gen_water.cxc

> cd /home/ben/Documents/Projects/Teixobactin/Data/1GHz_50ms/vis

Current working directory is:
/home/ben/Documents/Projects/Teixobactin/Data/1GHz_50ms/vis  

> open 6yfy

6yfy title:  
Solid-state NMR structure of the D-Arg4,L10-teixobactin - Lipid II complex in
lipid bilayers [more info...]  
  
Chain information for 6yfy  
---  
Chain | Description  
1.1/A 1.1/B 1.1/E 1.1/F | D-Arg4,Leu10-Teixobactin  
1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A
1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A 1.22/A 1.23/A 1.24/A
1.25/A 1.26/A 1.2/B 1.3/B 1.4/B 1.5/B 1.6/B 1.7/B 1.8/B 1.9/B 1.10/B 1.11/B
1.12/B 1.13/B 1.14/B 1.15/B 1.16/B 1.17/B 1.18/B 1.19/B 1.20/B 1.21/B 1.22/B
1.23/B 1.24/B 1.25/B 1.26/B 1.2/E 1.3/E 1.4/E 1.5/E 1.6/E 1.7/E 1.8/E 1.9/E
1.10/E 1.11/E 1.12/E 1.13/E 1.14/E 1.15/E 1.16/E 1.17/E 1.18/E 1.19/E 1.20/E
1.21/E 1.22/E 1.23/E 1.24/E 1.25/E 1.26/E 1.2/F 1.3/F 1.4/F 1.5/F 1.6/F 1.7/F
1.8/F 1.9/F 1.10/F 1.11/F 1.12/F 1.13/F 1.14/F 1.15/F 1.16/F 1.17/F 1.18/F
1.19/F 1.20/F 1.21/F 1.22/F 1.23/F 1.24/F 1.25/F 1.26/F |
D-Arg4,Leu10-Teixobactin  
1.1/C 1.1/D 1.1/G 1.1/H | Lipid II  
1.2/C 1.3/C 1.4/C 1.5/C 1.6/C 1.7/C 1.8/C 1.9/C 1.10/C 1.11/C 1.12/C 1.13/C
1.14/C 1.15/C 1.16/C 1.17/C 1.18/C 1.19/C 1.20/C 1.21/C 1.22/C 1.23/C 1.24/C
1.25/C 1.26/C 1.2/D 1.3/D 1.4/D 1.5/D 1.6/D 1.7/D 1.8/D 1.9/D 1.10/D 1.11/D
1.12/D 1.13/D 1.14/D 1.15/D 1.16/D 1.17/D 1.18/D 1.19/D 1.20/D 1.21/D 1.22/D
1.23/D 1.24/D 1.25/D 1.26/D 1.2/G 1.3/G 1.4/G 1.5/G 1.6/G 1.7/G 1.8/G 1.9/G
1.10/G 1.11/G 1.12/G 1.13/G 1.14/G 1.15/G 1.16/G 1.17/G 1.18/G 1.19/G 1.20/G
1.21/G 1.22/G 1.23/G 1.24/G 1.25/G 1.26/G 1.2/H 1.3/H 1.4/H 1.5/H 1.6/H 1.7/H
1.8/H 1.9/H 1.10/H 1.11/H 1.12/H 1.13/H 1.14/H 1.15/H 1.16/H 1.17/H 1.18/H
1.19/H 1.20/H 1.21/H 1.22/H 1.23/H 1.24/H 1.25/H 1.26/H | Lipid II  
  

> select ~#1.1

36500 atoms, 36600 bonds, 2300 residues, 26 models selected  

> delete sel

> select #1.1

1460 atoms, 1464 bonds, 92 residues, 1 model selected  

> open water_50msN.defattr

Summary of feedback from opening water_50msN.defattr  
---  
note | Assigned attribute 'satN_Swater' to 48 atoms using match mode: any  
  

> open water_50msC.defattr

Summary of feedback from opening water_50msC.defattr  
---  
note | Assigned attribute 'satC_Swater' to 108 atoms using match mode: any  
  

> hide cartoons

> hide atoms

> style ball

Changed 1460 atom styles  

> delete H

> color grey

> set bgColor white

> select /C/D/G/H

132 atoms, 128 bonds, 20 residues, 1 model selected  

> hide sel cartoons

> show sel surfaces

> color sel white

> select /A/B/E/F

348 atoms, 352 bonds, 44 residues, 1 model selected  

> show sel atoms

> color byattribute satC_Swater palette blues-7

704 atoms, 92 residues, 4 surfaces, atom satC_Swater range 0.35 to 1.01  

> lighting soft

> key ^blues-7 :unsaturated : : : : : :saturated

> ~select

Nothing selected  

> graphics silhouettes true

> view matrix camera
> -0.54428,0.12604,0.82938,60.729,0.16128,0.98593,-0.043995,-0.27895,-0.82326,0.10981,-0.55695,-21.737

executed gen_water.cxc  

> view

> view

> view matrix

Traceback (most recent call last):  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py"", line 275, in execute  
cmd.run(cmd_text)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2852, in run  
result = ci.function(session, **kw_args)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 472, in view_matrix  
report_positions(session)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 479, in report_positions  
lines.append('model positions: %s\n' % model_positions_string(mlist))  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 483, in model_positions_string  
mpos = ','.join('#%s,%s' % (m.id_string, _position_string(m.position)) for m
in models)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 483, in <genexpr>  
mpos = ','.join('#%s,%s' % (m.id_string, _position_string(m.position)) for m
in models)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 487, in _position_string  
return ','.join('%.5g' % x for x in tuple(p.matrix.flat))  
AttributeError: 'tuple' object has no attribute 'matrix'  
  
AttributeError: 'tuple' object has no attribute 'matrix'  
  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 487, in _position_string  
return ','.join('%.5g' % x for x in tuple(p.matrix.flat))  
  
See log for complete Python traceback.  
  

> view matrixggh

Expected an objects specifier or a view name or a keyword  

> view matrix

Traceback (most recent call last):  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py"", line 275, in execute  
cmd.run(cmd_text)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/core/commands/cli.py"", line 2852, in run  
result = ci.function(session, **kw_args)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 472, in view_matrix  
report_positions(session)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 479, in report_positions  
lines.append('model positions: %s\n' % model_positions_string(mlist))  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 483, in model_positions_string  
mpos = ','.join('#%s,%s' % (m.id_string, _position_string(m.position)) for m
in models)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 483, in <genexpr>  
mpos = ','.join('#%s,%s' % (m.id_string, _position_string(m.position)) for m
in models)  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 487, in _position_string  
return ','.join('%.5g' % x for x in tuple(p.matrix.flat))  
AttributeError: 'tuple' object has no attribute 'matrix'  
  
AttributeError: 'tuple' object has no attribute 'matrix'  
  
File ""/opt/UCSF/ChimeraX-daily/lib/python3.8/site-
packages/chimerax/std_commands/view.py"", line 487, in _position_string  
return ','.join('%.5g' % x for x in tuple(p.matrix.flat))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 20.3.4
OpenGL renderer: Mesa Intel(R) UHD Graphics (ICL GT1)
OpenGL vendor: Intel
Manufacturer: LENOVO
Model: 81YH
OS: Fedora 33 
Architecture: 64bit ELF
Virutal Machine: none
CPU: 8 Intel(R) Core(TM) i5-1035G1 CPU @ 1.00GHz
Cache Size: 6144 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          7.4Gi       4.4Gi       1.1Gi       1.5Gi       2.0Gi       1.3Gi
	Swap:         3.7Gi       197Mi       3.5Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation Iris Plus Graphics G1 (Ice Lake) [8086:8a56] (rev 07)	
	Subsystem: Lenovo Device [17aa:3f0a]	
	Kernel driver in use: i915
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.4
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.11.2
    ChimeraX-AtomicLibrary: 2.0
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.dev202103220641
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0.1
    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
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.3
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    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: 0.29.21
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    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: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.2.0

}}}
"	defect	closed	normal		Graphics		fixed						all	ChimeraX