![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 4 years ago
Closed 4 years ago
#5361 closed defect (fixed)
Trying to save Color object as setting
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Analysis | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19041
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
Change History (2)
comment:1 by , 4 years ago
| Component: | Unassigned → Structure Analysis |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Trying to save Color object as setting |
comment:2 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | accepted → closed |
Note:
See TracTickets
for help on using tickets.
Hi Luis,
--Eric