label-height check bad

[novakw@…]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
Set label height will not accept a decimal using the menu, e.g. 1.5. This works find on the command line: label height 1.5. But in the menu I get the error: Height must be a number.

Log:
> open 6m0j

Summary of feedback from opening 6m0j fetched from pdb  
---  
notes | Fetching compressed mmCIF 6m0j from
http://files.rcsb.org/download/6m0j.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
Fetching CCD NAG from http://ligand-expo.rcsb.org/reports/N/NAG/NAG.cif  
  
6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #1  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike protein S1  
  
Non-standard residues in 6m0j #1  
---  
CL — chloride ion  
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)  
ZN — zinc ion  
  

> select ::name="CYS"

96 atoms, 87 bonds, 16 residues, 1 model selected  

> select clear

> select :CL

1 atom, 1 residue, 1 model selected  

> show sel atoms

> close

> open 6m0j

6m0j title:  
Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2
[more info...]  
  
Chain information for 6m0j #1  
---  
Chain | Description  
A | Angiotensin-converting enzyme 2  
E | Spike protein S1  
  
Non-standard residues in 6m0j #1  
---  
CL — chloride ion  
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)  
ZN — zinc ion  
  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" cartoon

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> preset "overall look" interactive

Preset expands to these ChimeraX commands:

    
    
    ~set bg
    graphics silhouettes f

  

> select :CL

1 atom, 1 residue, 1 model selected  

> select /A

4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected  

> color (#!1 & sel) cyan

> select /E

1559 atoms, 1598 bonds, 204 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel wheat target s

> select /A:227

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

> select up

296 atoms, 303 bonds, 35 residues, 1 model selected  

> select up

4999 atoms, 5070 bonds, 674 residues, 1 model selected  

> color sel plum target s

> color sel plum

> select clear

> ui mousemode right select

> select /A:102

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

> select clear

> select /A:205

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

> ui mousemode right rotate

> ui mousemode right "translate selected models"

> view matrix models #1,1,0,0,1.5715,0,1,0,-0.76563,0,0,1,-3.4477

> select clear

> select /E

1559 atoms, 1598 bonds, 204 residues, 1 model selected  

> color sel wheat

> select clear

> color byhetero

> select up

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

> select up

70 atoms, 70 bonds, 5 residues, 1 model selected  

> select down

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

> select up

70 atoms, 70 bonds, 5 residues, 1 model selected  

> select up

6558 atoms, 6668 bonds, 878 residues, 1 model selected  

> select down

70 atoms, 70 bonds, 5 residues, 1 model selected  

> name frozen glycans sel

> select clear

> select ::name="CL"

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select add /A:901@ZN

2 atoms, 2 residues, 1 model selected  

> select clear

> ui tool show "Color Actions"

> select /A

4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected  

> color sel lawn green target a

> color sel byhetero

> select clear

> select helix

3942 atoms, 4019 bonds, 476 residues, 1 model selected  

> color sel purple target c

> select strand

580 atoms, 580 bonds, 70 residues, 1 model selected  

> color sel yellow target c

> select clear

> select /A

4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected  

> color sel plum target c

> select clear

> select /A:901@ZN

1 atom, 1 residue, 1 model selected  

> select add /A:902@CL

2 atoms, 2 residues, 1 model selected  

> name frozen ions sel

"ions" is reserved and cannot be redefined  

> select clear

> select ions

2 atoms, 2 residues, 1 model selected  

> color sel gray target c

> color sel gray target a

> select glycans

70 atoms, 70 bonds, 5 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel chartreuse target a

> color sel byhetero

> style sel sphere

Changed 70 atom styles  

> color sel medium aquamarine target a

> color sel byhetero

> select clear

> save "/Users/novakw/Box/_novakw/molvis/jan 2022 workshop/task3_chimera.cxs"

> save "/Users/novakw/Box/_novakw/molvis/jan 2022 workshop/task3c.png" width
> 1211 height 885 supersample 3

> close all

> open 1xwww

'1xwww' has no suffix  

> open 1xww

1xww title:  
Crystal Structure of Human B-form Low Molecular Weight Phosphotyrosyl
Phosphatase at 1.6 Angstrom Resolution [more info...]  
  
Chain information for 1xww #1  
---  
Chain | Description  
A | Low molecular weight phosphotyrosine protein phosphatase  
  
Non-standard residues in 1xww #1  
---  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
SO4 — sulfate ion  
  

> color byss

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> color ss

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword  

> hide atoms

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select /A:12

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:12-27

120 atoms, 121 bonds, 16 residues, 1 model selected  

> select /A:17-33,35-37,56-66,78-85,92-105,117-120,134-156

646 atoms, 649 bonds, 80 residues, 1 model selected  

> select /A:6-12,39-45,87-90,112-115

174 atoms, 174 bonds, 22 residues, 1 model selected  

> select /A:12-27

120 atoms, 121 bonds, 16 residues, 1 model selected  

> select /A:17-33,35-37,56-66,78-85,92-105,117-120,134-156

646 atoms, 649 bonds, 80 residues, 1 model selected  

> select /A:12

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select /A:12-18

51 atoms, 50 bonds, 7 residues, 1 model selected  

> name frozen PLoop sel

> show sel atoms

> label sel text "/{0.chain_id} {0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> label sel text "/{0.chain_id} {0.name} {0.number}{0.insertion_code}"

Height must be a number  
Height must be a number  
Height must be a number  
Height must be a number  

> label height 1

> label color yellow

> color sel green target l

> label color white

> label height 2

Height must be a number  
Height must be a number  
Height must be a number  

> label height 1

> label height 1.5

Height must be a number  




OpenGL version: 4.1 ATI-3.10.21
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac19,2
      Processor Name: 6-Core Intel Core i5
      Processor Speed: 3 GHz
      Number of Processors: 1
      Total Number of Cores: 6
      L2 Cache (per Core): 256 KB
      L3 Cache: 9 MB
      Memory: 16 GB
      Boot ROM Version: 1554.120.15.0.0
      SMC Version (system): 2.47f3

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1217)
      Kernel Version: Darwin 19.6.0
      Time since boot: 4:03

Graphics/Displays:

    Radeon Pro 560X:

      Chipset Model: Radeon Pro 560X
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x67ef
      Revision ID: 0x00c2
      ROM Revision: 113-C981AA-042
      VBIOS Version: 113-C9819A1X-009
      EFI Driver Version: 01.B1.042
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: 4096 x 2304 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        DELL U2212HM:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: PF48H246082L
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version:  e.1d

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    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: 2.5.2
    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: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    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: 1.2.1
    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: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    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: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    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: 5.0.9
    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: 0.17
    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: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    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: 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: 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: 1.3.0

[pett]

Hi Wally!

Thanks for reporting this. I've fixed the problem and the fix will be in tomorrow's daily build.

Happy Holidays!

--Eric