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Opened 4 years ago
Closed 4 years ago
#5320 closed defect (fixed)
Tile command layout is wrong if one model is rotated
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Depiction | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-11.5.2-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202109201808 (2021-09-20 18:08:56 UTC)
Description
Tile command after rotating a model produces wrong layout with models far apart and not in a rectangular grid. Reported by Pranav Shah on ChimeraX mailing list.
Log:
UCSF ChimeraX version: 1.3.dev202109201808 (2021-09-20)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/goddard/ucsf/people/vorlander/shortdist.py format python
executed shortdist.py
> open 1080 format ccp4 fromDatabase emdb
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> open 1080 format ccp4 fromDatabase emdb
Opened emdb 1080 as #2, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> open /Users/goddard/ucsf/people/vorlander/shortdist.py format python
FYI: command is replacing existing command: "closest"
executed shortdist.py
> open /Users/goddard/ucsf/people/vorlander/shortdist.py format python
FYI: command is replacing existing command: "closest"
executed shortdist.py
> ui mousemode right "move picked models"
> view matrix models
> #1,0.79116,-0.13273,0.59704,22.398,-0.13849,0.91194,0.38625,2.6825,-0.59573,-0.38827,0.7031,-0.92921
> view matrix models
> #2,0.26328,0.27248,-0.92544,-1.1491,0.37929,0.8528,0.359,0.59157,0.88703,-0.44552,0.12118,1.3835
> open 1080 format ccp4 fromDatabase emdb
Opened emdb 1080 as #3, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> view matrix models
> #3,0.033677,0.83987,-0.54174,24.34,-0.11834,0.54158,0.83228,11.772,0.9924,0.03608,0.11763,16.583
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> volume showOutlineBox true
> view initial #1-3
> tile #1.3
No models found for tiling.
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> close
> open 1080 fromDatabase emdb
Opened emdb 1080 as #1, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> open 1080 fromDatabase emdb
Opened emdb 1080 as #2, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> open 1080 fromDatabase emdb
Opened emdb 1080 as #3, grid size 100,100,100, pixel 2.7, shown at level 1.68,
step 1, values float32
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> view matrix models
> #1,0.2173,0.88296,0.41613,0.47876,0.55509,0.23889,-0.79675,-1.3412,-0.80291,0.40412,-0.43821,-5.8287
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> close
> open 1a0m
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #1
---
Chain | Description | UniProt
A B | α-conotoxin [TYR15]-epi | CXA1_CONEP
Non-standard residues in 1a0m #1
---
NH2 — amino group
> open 1a0m
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #2
---
Chain | Description | UniProt
A B | α-conotoxin [TYR15]-epi | CXA1_CONEP
Non-standard residues in 1a0m #2
---
NH2 — amino group
> open 1a0m
1a0m title:
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]
Chain information for 1a0m #3
---
Chain | Description | UniProt
A B | α-conotoxin [TYR15]-epi | CXA1_CONEP
Non-standard residues in 1a0m #3
---
NH2 — amino group
> tile #1-3
3 models tiled
> turn y 45 models #1
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile #1-3
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> tile
3 models tiled
> view matrix models
> #1,0.064767,-0.76261,-0.64361,27.69,-0.06455,0.64041,-0.76532,9.2889,0.99581,0.091112,-0.0077494,0.61478
> tile
3 models tiled
> tile
3 models tiled
> view initial
> view
> view orient
> tile
3 models tiled
> tile
3 models tiled
> turn y 140 models #1
> tile
3 models tiled
> tile
3 models tiled
OpenGL version: 4.1 ATI-4.6.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: MacBookPro15,3
Processor Name: 8-Core Intel Core i9
Processor Speed: 2.4 GHz
Number of Processors: 1
Total Number of Cores: 8
L2 Cache (per Core): 256 KB
L3 Cache: 16 MB
Hyper-Threading Technology: Enabled
Memory: 32 GB
System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)
Software:
System Software Overview:
System Version: macOS 11.5.2 (20G95)
Kernel Version: Darwin 20.6.0
Time since boot: 29 days 3:25
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0002
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Radeon Pro Vega 20:
Chipset Model: Radeon Pro Vega 20
Type: GPU
Bus: PCIe
PCIe Lane Width: x8
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x69af
Revision ID: 0x00c0
ROM Revision: 113-D2060I-087
VBIOS Version: 113-D20601MA0T-016
Option ROM Version: 113-D20601MA0T-016
EFI Driver Version: 01.01.087
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 2880 x 1800 Retina
Framebuffer Depth: 24-Bit Color (ARGB8888)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
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: 2021.5.30
cftime: 1.5.0
charset-normalizer: 2.0.6
ChimeraX-AddCharge: 1.1.4
ChimeraX-AddH: 2.1.10
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.30.1
ChimeraX-AtomicLibrary: 4.1.4
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.1
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3.dev202109201808
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.1
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.1
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
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: 1.1
ChimeraX-Hbonds: 2.1.1
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.1
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2
ChimeraX-ModelPanel: 1.2
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: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.2
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: 2.1
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: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6
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: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.13.2
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 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: 0.4.4
cxservices: 1.1
cycler: 0.10.0
Cython: 0.29.24
decorator: 5.1.0
distlib: 0.3.2
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.4.0
html2text: 2020.1.16
idna: 3.2
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.2.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.8.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
pandas: 1.3.2
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.20
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 2.4.7
PyQt5: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.1
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.1
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.1.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
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
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.0
urllib3: 1.26.6
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (7)
comment:1 by , 4 years ago
| Component: | Unassigned → Depiction |
|---|---|
| Platform: | → all |
| Project: | → ChimeraX |
| Reporter: | changed from to |
| Summary: | ChimeraX bug report submission → Tile command layout is wrong if one model is rotated |
comment:2 by , 4 years ago
comment:3 by , 4 years ago
| Cc: | added |
|---|---|
| Resolution: | → fixed |
| Status: | new → closed |
Fixed.
The tile command did not handle models with different rotations correctly. Also it strangely only handle structures and volumes. I made it handle all models. More properly it handles all "top models". For instance if #1 and #2 are structures with submodels that are surfaces and pseudobonds then the "tile #1,2" only tiles the two parent models, not the submodels. So for an NMR ensemble where there are 20 models #1.1, #1.2, ..., #1.20 the command "tile #1.*" will tile the 20 models, but "tile #1" will only tile the top level model (which does nothing since it is only one model).
comment:4 by , 4 years ago
One more detail for documentation. The first model specified is left in its current position and the others are moved relative to that first model to create a grid parallel to the screen in the current view.
comment:5 by , 4 years ago
| Resolution: | fixed |
|---|---|
| Status: | closed → reopened |
comment:6 by , 4 years ago
| Owner: | set to |
|---|---|
| Status: | reopened → assigned |
comment:7 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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I have seen similar bad layout from the tile command. If I open 3 copies of a model the tile them it works, then rotate just one and try to tile several times and it gives all kinds of weird wrong positions.