Opened 5 months ago
Closed 5 months ago
#17714 closed defect (duplicate)
Regular PDB file opened in MD Viewer
Reported by: | Owned by: | Eric Pettersen | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Third Party | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.26100 ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Registration file 'C:\\\Users\\\Amy Oo\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has expired UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open D:/CB2/CB2_Homodimerization/Simulations/Analysis/lastframe.pdb Summary of feedback from opening D:/CB2/CB2_Homodimerization/Simulations/Analysis/lastframe.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK BIOVIA PDB file Ignored bad PDB record found on line 2 REMARK Created: 2025-05-17T14:53:51Z Chain information for lastframe.pdb #1 --- Chain | Description P R | No description available > select > :199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302 1113 atoms, 1089 bonds, 72 residues, 1 model selected > select > :199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302/P 6197 atoms, 6253 bonds, 396 residues, 1 model selected > select > /P:199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302 557 atoms, 545 bonds, 36 residues, 1 model selected > set bgColor white > lighting flat > lighting soft > show sel atoms > select > /O:199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302 Nothing selected > select > /P:199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302 557 atoms, 545 bonds, 36 residues, 1 model selected > select > /R:199,202,203,206,207,209,210,213,214,216,218,220,238,241,242,244,245,248,249,252,255,256,259,262,263,266,269,270,271,302 490 atoms, 477 bonds, 30 residues, 1 model selected > show sel atoms > select > /R:199,202,203,206,207,209,210,213,214,216,218,220,238,241,242,244,245,248,249,252,255,256,259,262,263,266,269,270,271 466 atoms, 454 bonds, 29 residues, 1 model selected > show sel surfaces > hide sel atoms > mlp sel Map values for surface "lastframe.pdb_R SES surface": minimum -1252, mean 1.237e+32, maximum 5.12e+34 To also show corresponding color key, enter the above mlp command and add key true > select > /R:199,202,203,206,207,209,210,213,214,216,218,220,238,241,242,244,245,248,249,252,255,256,259,262,263,266,269,270,271,302 490 atoms, 477 bonds, 30 residues, 1 model selected > show sel surfaces > select > /P:199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302 557 atoms, 545 bonds, 36 residues, 1 model selected > show sel surfaces > mlp sel Map values for surface "lastframe.pdb_P SES surface": minimum -28.42, mean 5.558e+32, maximum 3.831e+35 To also show corresponding color key, enter the above mlp command and add key true > hide sel atoms > hide sel surfaces > select clear > hide surfaces > show cartoons > hide atoms > select ::name="9JU" 132 atoms, 140 bonds, 2 residues, 1 model selected > show sel atoms > select clear > select /P 5641 atoms, 5709 bonds, 360 residues, 1 model selected > show sel surfaces > select /R 5639 atoms, 5708 bonds, 360 residues, 1 model selected > select clear > lighting flat > lighting soft > select > /P:199,202,203,206,207,209,210,213,214,216,220,221,223,224,225,234,238,241,244,245,248,249,252,255,256,259,262,263,266-272,302 557 atoms, 545 bonds, 36 residues, 1 model selected > select > /R:199,202,203,206,207,209,210,213,214,216,218,220,238,241,242,244,245,248,249,252,255,256,259,262,263,266,269,270,271,302 490 atoms, 477 bonds, 30 residues, 1 model selected > select > /R:199,202,203,206,207,209,210,213,214,216,218,220,238,241,242,244,245,248,249,252,255,256,259,262,263,266,269,270,271 466 atoms, 454 bonds, 29 residues, 1 model selected > show sel atoms > view > view sel > style sel ball Changed 466 atom styles > style sel ball Changed 466 atom styles > select clear > show surfaces > preset "overall look" "publication 1 (silhouettes)" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset "overall look" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > set bgColor white > toolshed show > ui tool show Contacts > hide surfaces > select :233-271 1259 atoms, 1267 bonds, 78 residues, 1 model selected > contacts sel restrict both interModel false intraMol false > ignoreHiddenModels true dashes 5 radius 0.3 reveal true 28 contacts > hide sel atoms > select clear > hide atoms > select ::name="9JU" 132 atoms, 140 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 132 atom styles > select clear > select :233-271 1259 atoms, 1267 bonds, 28 pseudobonds, 78 residues, 2 models selected > contacts sel restrict both interModel false intraMol false > ignoreHiddenModels true dashes 5 radius 0.3 reveal true 28 contacts > ui tool show H-Bonds > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 3.0 angleSlop 120.0 twoColors true saltOnly true intraMol false > intraRes false select true reveal true 0 hydrogen bonds found 0 strict hydrogen bonds found > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 3.5 angleSlop 120.0 twoColors true saltOnly true intraMol false > intraRes false select true reveal true Atom specifier selects no atoms > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 3.5 angleSlop 120.0 twoColors true saltOnly true intraMol false > intraRes false select true reveal true Atom specifier selects no atoms > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 3.5 angleSlop 120.0 saltOnly true intraMol false intraRes false > select true reveal true Atom specifier selects no atoms > select :233-271 1259 atoms, 1267 bonds, 28 pseudobonds, 78 residues, 2 models selected > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 3.5 angleSlop 120.0 twoColors true saltOnly true intraMol false > intraRes false select true reveal true 0 hydrogen bonds found 0 strict hydrogen bonds found > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 4.0 angleSlop 120.0 twoColors true saltOnly true intraMol false > intraRes false select true reveal true Atom specifier selects no atoms > select :233-271 1259 atoms, 1267 bonds, 28 pseudobonds, 78 residues, 2 models selected > hbonds sel color #00ff00 showDist true restrict both interModel false > distSlop 4.0 angleSlop 120.0 twoColors true saltOnly true intraMol false > intraRes false select true reveal true 0 hydrogen bonds found 0 strict hydrogen bonds found > select :233-271 1259 atoms, 1267 bonds, 28 pseudobonds, 78 residues, 2 models selected > toolshed show Downloading bundle MolecularDynamicsViewer-1.6-py3-none-any.whl Installed MolecularDynamicsViewer (1.6) QWebEngineUrlScheme::registerScheme: Scheme "kmd" already registered > toolshed show > ui tool show "Molecular Dynamics Viewer" > select clear > show surfaces Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\ui\htmltool.py", line 112, in _navigate self.session.ui.thread_safe(self.handle_scheme, url) File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 375, in thread_safe func(*args, **kw) File "C:\Users\Amy Oo\AppData\Local\UCSF\ChimeraX\1.7\Python311\site- packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme self.openFile() File "C:\Users\Amy Oo\AppData\Local\UCSF\ChimeraX\1.7\Python311\site- packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] ~~~~~~~~~~~~~~~~~^^^ IndexError: list index out of range IndexError: list index out of range File "C:\Users\Amy Oo\AppData\Local\UCSF\ChimeraX\1.7\Python311\site- packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] ~~~~~~~~~~~~~~~~~^^^ See log for complete Python traceback. > close session > ui tool show "Molecular Dynamics Viewer" Traceback (most recent call last): File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 320, in interceptRequest self._callback(info) File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\ui\widgets\htmlview.py", line 93, in _intercept return interceptor(request_info, *args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "C:\Program Files\ChimeraX\bin\Lib\site- packages\chimerax\ui\htmltool.py", line 112, in _navigate self.session.ui.thread_safe(self.handle_scheme, url) File "C:\Program Files\ChimeraX\bin\Lib\site-packages\chimerax\ui\gui.py", line 375, in thread_safe func(*args, **kw) File "C:\Users\Amy Oo\AppData\Local\UCSF\ChimeraX\1.7\Python311\site- packages\com\kdiller\dynamics\viewer\gui.py", line 57, in handle_scheme self.openFile() File "C:\Users\Amy Oo\AppData\Local\UCSF\ChimeraX\1.7\Python311\site- packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] ~~~~~~~~~~~~~~~~~^^^ IndexError: list index out of range IndexError: list index out of range File "C:\Users\Amy Oo\AppData\Local\UCSF\ChimeraX\1.7\Python311\site- packages\com\kdiller\dynamics\viewer\gui.py", line 239, in openFile self.atomStruct.atoms.coords = self.atomLocation[0] ~~~~~~~~~~~~~~~~~^^^ See log for complete Python traceback. OpenGL version: 3.3.0 Core Profile Context 22.20.20.06.231106 OpenGL renderer: AMD Radeon RX 640 OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: en_CA.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: Dell Inc. Model: OptiPlex 7000 OS: Microsoft Windows 11 Pro (Build 26100) Memory: 16,853,479,424 MaxProcessMemory: 137,438,953,344 CPU: 20 12th Gen Intel(R) Core(TM) i7-12700 OSLanguage: en-US Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-Cytoscape: 0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBImages: 1.2 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 comtypes: 1.1.14 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 llvmlite: 0.42.0 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 MolecularDynamicsViewer: 1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numba: 0.59.1 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 23.2 pandas: 2.2.1 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 plotly: 5.20.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tenacity: 8.2.3 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (2)
comment:1 by , 5 months ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Regular PDB file opened in MD Viewer |
comment:2 by , 5 months ago
Resolution: | → duplicate |
---|---|
Status: | accepted → closed |
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