id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 4280 Save movie image files numbered starting at 25 instead of 1 aalhossary@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC) Description I was trying to generate a movie using this script movie record directory c:\Temp\chim format png limit 15000;movie duplicate;coordset #1 1,;wait 30;movie encode ""C:/Users/Amr/OneDrive/Amr and Nosa/SCAsia2021/Attic/Ivermectin_ACE-2.mp4"" verbose true resetMode clear There are files, but they start with chimovie_0Txj-00025.png Log: UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. > open ""C:\Users\Amr\OneDrive\Amr and > Nosa\SCAsia2021\Attic\Ivermectin_ACE-2.cxs"" format session Log from Mon Feb 22 01:02:50 2021 Startup Messages --- warning | Your computer has Intel graphics driver 8190 with a known bug that causes all Qt user interface panels to be blank. ChimeraX can partially fix this but may make some panel titlebars and edges black. Hopefully newer Intel graphics drivers will fix this. UCSF ChimeraX version: 1.1 (2020-09-09) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Temp/mdSim_mmpbsa_7/humanACE-2/md_Ivermectin/complex_traj.pdb > coordsets true Summary of feedback from opening C:/Temp/mdSim_mmpbsa_7/humanACE-2/md_Ivermectin/complex_traj.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 3 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 9661 REMARK GENERATED BY TRJCONV Ignored bad PDB record found on line 9663 REMARK THIS IS A SIMULATION BOX Ignored bad PDB record found on line 19321 REMARK GENERATED BY TRJCONV 57 messages similar to the above omitted complex_traj.pdb title: 1R42 in water t= 0.00000 step= 0 [more info...] Chain information for complex_traj.pdb #1 --- Chain | Description A | No description available Non-standard residues in complex_traj.pdb #1 --- [00 — ([00) complex_traj.pdb has 31 coordinate sets > rainbow > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 136 atoms, 142 bonds, 1 residue, 1 model selected > view sel > ui tool show H-Bonds > ui tool show H-Bonds > hbonds sel color #ffff00 interModel false select true reveal true 94 hydrogen bonds found in 31 coordsets Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 1993, in _forward_keystroke if not self.floating and not isinstance(self.ui_area.focusWidget(), (QLineEdit, QComboBox)): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 1826, in _get_floating return self.__toolkit.dock_widget.isFloating() AttributeError: 'NoneType' object has no attribute 'dock_widget' AttributeError: 'NoneType' object has no attribute 'dock_widget' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py"", line 1826, in _get_floating return self.__toolkit.dock_widget.isFloating() See log for complete Python traceback. > label sel attribute name > label sel attribute label_specifier > label sel text ""/{0.chain_id} {0.name} {0.number}{0.insertion_code}"" > select clear > select /B:616@C17 1 atom, 1 residue, 1 model selected > select /B:616@C17 1 atom, 1 residue, 1 model selected > select up 136 atoms, 142 bonds, 1 residue, 1 model selected > ~label sel residues > set bgColor white > select clear > graphics silhouettes true > lighting shadows true > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting full > lighting shadows false > save ""C:/Users/Amr/OneDrive/Amr and > Nosa/SCAsia2021/Attic/Ivermectin_ACE-2.cxs"" opened ChimeraX session > movie record directory c:\Temp\chim format PNG limit 15000 > movie duplicate Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 275, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2805, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\movie\moviecmd.py"", line 258, in movie_duplicate session.movie.postprocess('duplicate', frames) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\movie\movie.py"", line 282, in postprocess self.capture_image() # Capture all frames right now. File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\movie\movie.py"", line 172, in capture_image self.save_duplicate_images() File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\movie\movie.py"", line 211, in save_duplicate_images image = Image.open(save_path) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\PIL\Image.py"", line 2843, in open fp = builtins.open(filename, ""rb"") FileNotFoundError: [Errno 2] No such file or directory: 'c:\\\Temp\\\chim\\\chimovie_0Txj--0001.png' FileNotFoundError: [Errno 2] No such file or directory: 'c:\\\Temp\\\chim\\\chimovie_0Txj--0001.png' File ""C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\PIL\Image.py"", line 2843, in open fp = builtins.open(filename, ""rb"") See log for complete Python traceback. Failed to send bug report. Error while sending follows: Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\bug_reporter\bug_reporter_gui.py"", line 241, in submit errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields) File ""C:\Program Files\ChimeraX 1.1\bin\lib\site- packages\chimerax\webservices\post_form.py"", line 40, in post_multipart_formdata h.request('POST', url, body=body, headers=headers) File ""C:\Program Files\ChimeraX 1.1\bin\lib\http\client.py"", line 1262, in request self._send_request(method, url, body, headers, encode_chunked) File ""C:\Program Files\ChimeraX 1.1\bin\lib\http\client.py"", line 1308, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File ""C:\Program Files\ChimeraX 1.1\bin\lib\http\client.py"", line 1257, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File ""C:\Program Files\ChimeraX 1.1\bin\lib\http\client.py"", line 1028, in _send_output self.send(msg) File ""C:\Program Files\ChimeraX 1.1\bin\lib\http\client.py"", line 968, in send self.connect() File ""C:\Program Files\ChimeraX 1.1\bin\lib\http\client.py"", line 940, in connect (self.host,self.port), self.timeout, self.source_address) File ""C:\Program Files\ChimeraX 1.1\bin\lib\socket.py"", line 707, in create_connection for res in getaddrinfo(host, port, 0, SOCK_STREAM): File ""C:\Program Files\ChimeraX 1.1\bin\lib\socket.py"", line 752, in getaddrinfo for res in _socket.getaddrinfo(host, port, family, type, proto, flags): socket.gaierror: [Errno 11001] getaddrinfo failed OpenGL version: 3.3.0 - Build 27.20.100.8190 OpenGL renderer: Intel(R) UHD Graphics OpenGL vendor: Intel Manufacturer: HP Model: HP ProBook 430 G7 OS: Microsoft Windows 10 Education (Build 19042) Memory: 17,009,516,544 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-10510U CPU @ 1.80GHz"" PyQt version: 5.12.3 Compiled Qt version: 5.12.4 Runtime Qt version: 5.12.9 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.8.0 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.6.20 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: 1.6.1 ChimeraX-AtomSearch: 2.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.0.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.0 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: 2.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-CommandLine: 1.1.3 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.1 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.0.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-DataFormats: 1.0 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: 2.0 ChimeraX-Help: 1.0 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.0 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.0 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: 2.0 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: 1.2.1 ChimeraX-PDB: 2.1 ChimeraX-PDBBio: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0 ChimeraX-PubChem: 2.0 ChimeraX-Read-Pbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.0 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.2 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.2 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 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.0.4 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: 1.2.3 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: 0.29.20 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 gdcm: 2.8.8 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.16 imagecodecs: 2020.5.30 imagecodecs-lite: 2020.1.31 imagesize: 1.2.0 ipykernel: 5.3.0 ipython: 7.15.0 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.3 jupyter-core: 4.6.3 kiwisolver: 1.2.0 line-profiler: 2.1.2 lxml: 4.5.1 MarkupSafe: 1.1.1 matplotlib: 3.2.1 MolecularDynamicsViewer: 1.1 msgpack: 1.0.0 netifaces: 0.10.9 networkx: 2.4 numexpr: 2.7.1 numpy: 1.18.5+mkl numpydoc: 1.0.0 openvr: 1.12.501 packaging: 20.4 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.1.2 pip: 20.2.2 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.7 psutil: 5.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.6.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.12.3 PyQt5-sip: 4.19.19 PyQtWebEngine-commercial: 5.12.1 python-dateutil: 2.8.1 pytz: 2020.1 pywin32: 228 pyzmq: 19.0.2 qtconsole: 4.7.4 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.4.1 setuptools: 49.4.0 sfftk-rw: 0.6.6.dev0 six: 1.15.0 snowballstemmer: 2.0.0 sortedcontainers: 2.2.2 Sphinx: 3.1.1 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 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.6.3 tinyarray: 1.2.2 tornado: 6.0.4 traitlets: 5.0.4 urllib3: 1.25.10 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.34.2 WMI: 1.5.1 }}} " defect closed normal Input/Output not a bug all ChimeraX