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#4121 closed defect (fixed)
Surface cap not transparent
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Surface | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| 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.dev202011140750 (2020-11-14 07:50:08 UTC)
Description
Clipped transparent density surface is not transparent in clipped side
Log:
UCSF ChimeraX version: 1.2.dev202011140750 (2020-11-14)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/models/Chimeric_GDP-1-sw1-v2-RSR-0-coot-14.pdb
Chain information for Chimeric_GDP-1-sw1-v2-RSR-0-coot-14.pdb #1
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> style stick
Changed 153138 atom styles
> set bgColor white
> show cartoons
> select /x:537
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
60 atoms, 61 bonds, 7 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> hbonds
The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /I PRO 19 N; /I PRO 22 N; /I PRO 25 N; /I PRO 53 N; /I PRO 21
N; /I PRO 55 N; /5 PRO 68 N; /5 PRO 79 N; /I PRO 73 N; /I PRO 74 N; /5 PRO 89
N; /5 PRO 130 N; /I PRO 92 N; /5 PRO 119 N
16031 hydrogen bonds found
> lighting simple
> view sel
> ui tool show "Side View"
> hide sel cartoons
> color sel byhetero
> select /A:1915
21 atoms, 22 bonds, 1 residue, 1 model selected
> select up
62336 atoms, 69815 bonds, 2903 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
121 atoms, 122 bonds, 16 residues, 1 model selected
> select up
5473 atoms, 5576 bonds, 704 residues, 1 model selected
> open
> X:/Work/Projects/EF-G/g3/Final_Modelling/chimeric_GDP1/sharpened/chimeric_GDP1_job1099_3d512_31A_sharpened.mrc
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc as #2, grid size
512,512,512, pixel 0.652, shown at level 4.2, step 2, values float32
> volume #2 step 1
> volume zone #2 nearAtoms sel newMap true
Opened chimeric_GDP1_job1099_3d512_31A_sharpened.mrc zone as #3, grid size
512,512,512, pixel 0.652, shown at step 1, values float32
> volume #3 level 2.88
> volume #3 color white
> volume #3 color #ffffff98
> ui mousemode right pivot
> volume #3 level 2.122
> volume #3 level 1.253
> volume #3 level 1.253
OpenGL version: 3.3.0 NVIDIA 461.09
OpenGL renderer: GeForce GTX 1070/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Micro-Star International Co., Ltd.
Model: GE73VR 7RF
OS: Майкрософт Windows 10 Pro (Build 19042)
Memory: 17,056,964,608
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-7700HQ CPU @ 2.80GHz
OSLanguage: uk-UA
Locale: ('uk_UA', 'cp1251')
PyQt version: 5.15.1
Compiled Qt version: 5.15.1
Runtime Qt version: 5.15.1
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.9.0
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2020.11.8
cftime: 1.2.1
chardet: 3.0.4
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.1
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.9.3
ChimeraX-AtomicLibrary: 1.1
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: 2.2
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.0
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-CommandLine: 1.1.3
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.2.dev202011140750
ChimeraX-CoreFormats: 1.0
ChimeraX-coulombic: 1.0.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-DataFormats: 1.0.1
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: 1.0
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.0
ChimeraX-ImageFormats: 1.1
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0
ChimeraX-Label: 1.0
ChimeraX-ListInfo: 1.1
ChimeraX-Log: 1.1.1
ChimeraX-LookingGlass: 1.1
ChimeraX-Map: 1.0.1
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: 2.1
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.0
ChimeraX-mmCIF: 2.2
ChimeraX-MMTF: 2.0
ChimeraX-Modeller: 1.0
ChimeraX-ModelPanel: 1.0
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.0
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0
ChimeraX-OpenCommand: 1.3.1
ChimeraX-PDB: 2.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.0.1
ChimeraX-Read-Pbonds: 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: 1.2.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SeqView: 2.2.1
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: 1.2.2
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.0
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.0
ChimeraX-ToolshedUtils: 1.0
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.3.1
ChimeraX-uniprot: 2.0
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
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
imagecodecs-lite: 2020.1.31
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: 4.6.3
kiwisolver: 1.3.1
line-profiler: 2.1.2
lxml: 4.5.2
lz4: 3.1.0
MarkupSafe: 1.1.1
matplotlib: 3.3.2
msgpack: 1.0.0
netCDF4: 1.5.4
netifaces: 0.10.9
networkx: 2.5
numexpr: 2.7.1
numpy: 1.19.2
numpydoc: 1.1.0
openvr: 1.14.1501
packaging: 20.4
parso: 0.7.1
pickleshare: 0.7.5
Pillow: 7.2.0
pip: 20.2.3
pkginfo: 1.5.0.1
prompt-toolkit: 3.0.8
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: 5.15.1
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.1
python-dateutil: 2.8.1
pytz: 2020.4
pywin32: 228
pyzmq: 20.0.0
qtconsole: 4.7.7
QtPy: 1.9.0
RandomWords: 0.3.0
requests: 2.24.0
scipy: 1.5.2
setuptools: 50.3.0
sfftk-rw: 0.6.7.dev1
six: 1.15.0
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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
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tables: 3.6.1
tifffile: 2020.9.3
tinyarray: 1.2.3
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traitlets: 5.0.5
urllib3: 1.25.11
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.35.1
WMI: 1.5.1
File attachment: Screenshot_1.png
Attachments (1)
Change History (5)
by , 5 years ago
| Attachment: | Screenshot_1.png added |
|---|
comment:1 by , 5 years ago
| Component: | Unassigned → Surface |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Surface cap not transparent |
comment:2 by , 5 years ago
The clip cap on the volume is a separate model. When you change the volume color or transparency with the color button on the volume viewer panel in only changes the volume color and not the clip cap. You could change the transparency of both or color of both with command "transparency #3 50" or "color #3 tan transparency 50". Also in Model Panel you can see your volume model, and under that the surface model, and under that the clip cap model, and you can change the color of just the clip cap or just the surface with the color buttons in the model panel.
I think the volume viewer panel color button should change the clip cap color and transparency to match the surface. I will see if I can change it to do that.
In mesh display the cap is not shown at all, and you may prefer that.
comment:3 by , 5 years ago
| Cc: | added |
|---|---|
| Resolution: | → fixed |
| Status: | assigned → closed |
Fixed.
I made coloring the a volume surface or changing its transparency always make the clip cap match. If it is desired to give the clip cap a different color from the surface then you have to color specifically the cap.
comment:4 by , 5 years ago
Thank you! Respectfully yours, Valentyn Petrychenko сб, 9 січ. 2021 о 01:34 ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> пише:
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