Trying to save Color object as setting

[fcofas@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.19041
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
auto_awesome
Quizás quisiste decir: Estaba intentando mostrar contactos y cambié el color del pseudo enlace. El siguiente error apareció:
volume_up
100 / 5000
Resultados de traducción
I was trying to show contacts and changed the color of the pseudobond. The following error appeared:

Illegal contacts 'color' attribute value (Color([0.78431374, 0.69803923, 0.19607843, 1.0])), leaving attribute unchanged

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "D:\\\OneDrive - UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO\\\ongoing-
> work\\\disenno\\\CV07-250\\\test_rosetta\\\fixbb\\\roundA\\\6xkq\\\6xkq_ok.pdb"

Chain information for 6xkq_ok.pdb #1  
---  
Chain | Description  
A | No description available  
H | No description available  
L | No description available  
  

> set bgColor white

> ui mousemode right zoom

> rainbow chains

> select /A:157

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 3 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  

> ui tool show Contacts

> contacts sel interModel false intraMol false makePseudobonds false reveal
> true

90 contacts  

> select clear

> color byhetero

> ~display element.H

> hide element.H

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

> hide element.H

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

> select clear

> select H

4451 atoms, 611 residues, 1 model selected  

> hide H

> select clear

> select /A:65

19 atoms, 18 bonds, 1 residue, 1 model selected  

> select up

59 atoms, 58 bonds, 3 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel indigo

> color sel plum

> select /H:60

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

39 atoms, 38 bonds, 3 residues, 1 model selected  

> select /H:60

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

39 atoms, 38 bonds, 3 residues, 1 model selected  

> select up

3268 atoms, 3311 bonds, 222 residues, 1 model selected  

> color sel light salmon

> color sel dodger blue

> color sel cornflower blue

> color sel royal blue

> color sel cyan

> color sel deep sky blue

> select /L:73

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

> select up

84 atoms, 83 bonds, 6 residues, 1 model selected  

> select up

3080 atoms, 3123 bonds, 212 residues, 1 model selected  

> color sel purple

> color sel medium purple

> select clear

> select /H:60

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

39 atoms, 38 bonds, 3 residues, 1 model selected  

> select up

3268 atoms, 3311 bonds, 222 residues, 1 model selected  

> color sel light coral

> select clear

> select /A:157

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 3 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  

> select clear

> select /L:74

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 83 bonds, 6 residues, 1 model selected  

> select up

3080 atoms, 3123 bonds, 212 residues, 1 model selected  

> color sel pale violet red

> color sel light cyan

> color sel light sky blue

> select add /A:149@CG

1 atom, 3 bonds, 1 residue, 1 model selected  

> select add /A:152@CZ

2 atoms, 3 bonds, 2 residues, 1 model selected  

> select add /A:118@CD1

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

> select add /A:147@CD

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

> select add /A:156@CD

5 atoms, 4 bonds, 5 residues, 1 model selected  

> select add /A:161@CD

6 atoms, 6 bonds, 6 residues, 1 model selected  

> select add /A:164@CG

7 atoms, 6 bonds, 7 residues, 1 model selected  

> select up

19 atoms, 6 bonds, 13 residues, 1 model selected  

> select up

224 atoms, 219 bonds, 13 residues, 1 model selected  

> color sel magenta

> color sel byhetero

> color sel hot pink

> color sel byhetero

> select clear

> select add /L:34@CE2

1 atom, 2 bonds, 1 residue, 1 model selected  

> select add /L:32@OH

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

> select add /L:33@CG

3 atoms, 2 bonds, 3 residues, 1 model selected  

> select up

9 atoms, 3 bonds, 6 residues, 1 model selected  

> select up

107 atoms, 106 bonds, 6 residues, 1 model selected  

> color sel dodger blue

> color sel byhetero

> select clear

> select /H:31@CD2

1 atom, 1 residue, 1 model selected  

> select up

7 atoms, 3 bonds, 4 residues, 1 model selected  

> select up

67 atoms, 65 bonds, 4 residues, 1 model selected  

> select clear

> select add /H:31@CD2

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /H:101@CG

2 atoms, 1 bond, 2 residues, 1 model selected  

> select add /H:110@CD2

3 atoms, 1 bond, 3 residues, 1 model selected  

> select add /H:107@CG

4 atoms, 1 bond, 4 residues, 1 model selected  

> select up

6 atoms, 1 bond, 5 residues, 1 model selected  

> select up

80 atoms, 77 bonds, 5 residues, 1 model selected  

> color sel salmon

> color sel pale violet red

> color sel blue violet

> select /A:119

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select up

576 atoms, 585 bonds, 37 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  

> ui tool show H-Bonds

> hbonds sel color #000000 intraMol false intraRes false reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6xkq_ok.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A GLN 156 NE2  /L ASP 33 OD2  /A GLN 156 HE21  3.112  2.198
    /H ASN 107 N    /A TYR 152 OH  /H ASN 107 H     3.459  2.471
    /L GLY 70 N     /A TYR 112 OH  /L GLY 70 H      3.314  2.401
    

  
3 hydrogen bonds found  

> hbonds sel color #000000 radius 0.105 intraMol false intraRes false reveal
> true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6xkq_ok.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A GLN 156 NE2  /L ASP 33 OD2  /A GLN 156 HE21  3.112  2.198
    /H ASN 107 N    /A TYR 152 OH  /H ASN 107 H     3.459  2.471
    /L GLY 70 N     /A TYR 112 OH  /L GLY 70 H      3.314  2.401
    

  
3 hydrogen bonds found  

> select clear

> select clear

> select /A:83

12 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

84 atoms, 84 bonds, 5 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  

> hbonds sel color #000000 radius 0.105 dashes 5 intraMol false intraRes false
> reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6xkq_ok.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A GLN 156 NE2  /L ASP 33 OD2  /A GLN 156 HE21  3.112  2.198
    /H ASN 107 N    /A TYR 152 OH  /H ASN 107 H     3.459  2.471
    /L GLY 70 N     /A TYR 112 OH  /L GLY 70 H      3.314  2.401
    

  
3 hydrogen bonds found  

> hbonds sel color #000000 radius 0.105 dashes 5 intraMol false intraRes false
> select true reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6xkq_ok.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A GLN 156 NE2  /L ASP 33 OD2  /A GLN 156 HE21  3.112  2.198
    /H ASN 107 N    /A TYR 152 OH  /H ASN 107 H     3.459  2.471
    /L GLY 70 N     /A TYR 112 OH  /L GLY 70 H      3.314  2.401
    

  
3 hydrogen bonds found  

> select clear

> select clear

> select clear

> hide H

> select clear

> select /A:157

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 3 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  

> hbonds sel color #000000 radius 0.105 dashes 5 intraMol false intraRes false
> reveal true log true
    
    
    Finding intermodel H-bonds
    Finding intramodel H-bonds
    Constraints relaxed by 0.4 angstroms and 20 degrees
    Models used:
    	1 6xkq_ok.pdb
    
    3 H-bonds
    H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
    /A GLN 156 NE2  /L ASP 33 OD2  /A GLN 156 HE21  3.112  2.198
    /H ASN 107 N    /A TYR 152 OH  /H ASN 107 H     3.459  2.471
    /L GLY 70 N     /A TYR 112 OH  /L GLY 70 H      3.314  2.401
    

  
3 hydrogen bonds found  

> select /A:156@HG3

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select /A:156@HB3

1 atom, 1 residue, 1 model selected  

> select add /A:156@HG2

2 atoms, 1 residue, 1 model selected  

> hide sel atoms

> select /A:156@HB2

1 atom, 1 residue, 1 model selected  

> hide sel atoms

> select clear

> select /H:106

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

> hide sel cartoons

> show sel atoms

> select clear

> color byhetero

> select /H:106@CA

1 atom, 1 residue, 1 model selected  

> select up

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

> show sel cartoons

> select /H:107

14 atoms, 13 bonds, 1 residue, 1 model selected  

> hide sel cartoons

> select /A:152@OH

1 atom, 1 residue, 1 model selected  

> select add /H:107@N

2 atoms, 2 residues, 1 model selected  

> distance /A:152@OH /H:107@N

Distance between /A TYR 152 OH and /H ASN 107 N: 3.459Å  

> select /L:33@OD2

1 atom, 1 residue, 1 model selected  

> select add /A:156@NE2

2 atoms, 2 residues, 1 model selected  

> distance /L:33@OD2 /A:156@NE2

Distance between /L ASP 33 OD2 and /A GLN 156 NE2: 3.112Å  

> select /L:70

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

> hide sel cartoons

> show sel atoms

> select /A:112@OH

1 atom, 1 residue, 1 model selected  

> select add /L:70@N

2 atoms, 2 residues, 1 model selected  

> distance /A:112@OH /L:70@N

Distance between /A TYR 112 OH and /L GLY 70 N: 3.314Å  

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> show sel cartoons

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

14 atoms, 13 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select clear

> hide H

> hide #2.1 models

> select clear

> hbonds sel color #000000 radius 0.105 dashes 5 intraMol false intraRes false
> reveal true log true

Atom specifier selects no atoms  

> close #1.1

> select clear

> select clear

> select /A:156

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select up

47 atoms, 46 bonds, 3 residues, 1 model selected  

> select up

2753 atoms, 2794 bonds, 177 residues, 1 model selected  
Illegal contacts 'color' attribute value (Color([1.0, 1.0, 0.0, 1.0])),
leaving attribute unchanged  
Illegal contacts 'color' attribute value (Color([0.0, 0.0, 0.0, 1.0])),
leaving attribute unchanged  
Illegal contacts 'color' attribute value (Color([0.33333334, 0.6666667, 0.0,
1.0])), leaving attribute unchanged  
Illegal contacts 'color' attribute value (Color([0.78431374, 0.69803923,
0.19607843, 1.0])), leaving attribute unchanged  




OpenGL version: 3.3.0 NVIDIA 472.12
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 68,626,759,680
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 3800X 8-Core Processor             
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: 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
    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
    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
    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
    pywin32: 228
    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
    WMI: 1.5.1

[Eric Pettersen]

Hi Luis,

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

--Eric

Eric Pettersen
UCSF Computer Graphics Lab