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#5405 feedback defect

Problem coloring chains

Reported by:	hernando.sosa@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Depiction	Version:
Keywords:		Cc:	Tom Goddard
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

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
Using the color command to color individual chains in a mutichain model appears to behave erratically.
With one  nine chains (ABCDEFGHIJKLMNOPQRS) model opened a command like:
color /K blue
does not do anything, i.e. does not color chain K blue
However if I first open a model witho nly thre chains; (ABK) and then the model with 9 chains
then it works
i .e. the command
color /K blue
colors blue chaim K of both model #1 l #2

????
 

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:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> color /K sky blue All

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #2  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color /K sky blue All

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #2  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color #1 lightgreyl

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

> color #1 lightgrey

> color #2 lightgrey

> color /K cornflowerblue

> color /A orange

> select /B

6934 atoms, 7100 bonds, 862 residues, 2 models selected  

> color sel #ffaa00ff

> color sel #fea900ff

> color sel #f8a500ff

> color sel #ee9f00ff

> color sel #e89b00ff

> color sel #e29700ff

> color sel #dc9300ff

> color sel #d48d00ff

> color sel #ce8900ff

> color sel #c78500ff

> color sel #bc7d00ff

> color sel #b87b00ff

> color sel #b97b00ff

> color sel #bf7f00ff

> color sel #bf7900ff

> color sel #bf7901ff

> color sel #bf8602ff

> color sel #bf8a04ff

> color sel #bf9105ff

> color sel #bf9706ff

> color sel #bfaa09ff

> color sel #bfb009ff

> color sel #bfb00aff

> color sel #bfaa0aff

> color sel #bfa40aff

> color sel #bfa10aff

> color sel #bf9b0aff

> color sel #bf980aff

> color sel #bf920aff

> color sel #bf8c0aff

> color sel #bf890aff

> color sel #bf830aff

> color sel #bf7d0bff

> color sel #bf7a0bff

> color sel #bf7d0bff

> color sel #aaaaffff

> color /B #bf7d0b

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #1  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color #1 lightgrey

> color /K cornflowerblue

> color /K cornflowerblue

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> hide #1 models

> color /K red

> show #1 models

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #1  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> hide atoms

> show cartoons

> color /K red

> color /K red

> color /K red

> color /K red

> color /K red

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> color /K red

> close session

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18.pdb

Chain information for caKIP3LAAF_M18.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
K | No description available  
  

> open
> D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb

Summary of feedback from opening
D:/hsosa/Documents/Manuscripts/KIN8_2020/KIP3Long_ADPAlF_LocRef/Best_Model/caKIP3LAAF_M18_3AU.pdb  
---  
notes | Combining 2 symmetry atoms into MG /O:802 MG  
Combining 2 symmetry atoms into MG /K:802 MG  
Combining 2 symmetry atoms into MG /N:802 MG  
Combining 2 symmetry atoms into MG /F:502 MG  
Combining 2 symmetry atoms into MG /A:502 MG  
1 messages similar to the above omitted  
  
Chain information for caKIP3LAAF_M18_3AU.pdb #2  
---  
Chain | Description  
A C E F G H | No description available  
B D I J L M | No description available  
K N O P Q R | No description available  
  

> color lightgray

> color /K cornflowerblue

> color /A orange

> color /B #bf7d0b

> hide #1 models

> hide #2 models

> show #1 models

> show #2 models

> hide #2 models

> show #2 models

> hide #1 models




OpenGL version: 3.3.13596 Core Profile Forward-Compatible Context FireGL 18.50.02 27.20.1028.2002
OpenGL renderer: Radeon (TM) Pro WX 5100 Graphics
OpenGL vendor: ATI Technologies Inc.
Manufacturer: Dell Inc.
Model: Precision 5820 Tower X-Series
OS: Microsoft Windows 10 Pro (Build 19043)
Memory: 34,043,539,456
MaxProcessMemory: 137,438,953,344
CPU: 20 Intel(R) Core(TM) i9-9820X CPU @ 3.30GHz
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-Clipper: 0.16.0
    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-ISOLDE: 1.2.2
    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

Change History (2)

comment:1 by pett, 4 years ago

Cc:	Tom Goddard added
Component:	Unassigned → Depiction
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Problem coloring chains

comment:2 by pett, 4 years ago

Status:	accepted → feedback

Hi Hernando,

I cannot reproduce this. If I open 7lup, which has 17 chains (including chain K), I can color chain K blue without any problem. Can you try 7lup and see if that structure works for you? If 7lup works for you, then it is something particular about your caKIP3LAAF_M18_3AU.pdb structure and we would need access to it to figure out the problem. You could send it to me directly (pett@…) if necessary.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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