id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5411 Hung saving TIFF? chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.4.0-210-generic-x86_64-with-glibc2.14 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) 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 > /scratch2/jrai/hpc_mountoint/jrai/21may22d/Refine3D/job050/run_ct13_class001.mrc Opened run_ct13_class001.mrc as #1, grid size 256,256,256, pixel 1.07, shown at level 0.00917, step 1, values float32 > set bgColor white > volume #1 level 0.006097 > volume #1 level 0.003599 > open /disks/li/d1/Jay/19sep13a/Finalstructures/run_ct14_class001.mrc Opened run_ct14_class001.mrc as #2, grid size 256,256,256, pixel 1.07, shown at level 0.0149, step 1, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 8010, resource id: 11625610, major code: 40 (TranslateCoords), minor code: 0 > close #1 > volume #2 level 0.01076 > graphics silhouettes true width 5 depthJump 0.2 colorblack Expected a keyword > graphics silhouettes true width 5 depthJump 0.2 color black > transparency #2 100 > graphics silhouettes true width 5 depthJump 0.3 color black > graphics silhouettes true width 5 depthJump 0.5 color black > graphics silhouettes true width 5 depthJump 0.1 color black > graphics silhouettes true width 5 depthJump 0.05 color black > open > /scratch2/jrai/mountpoint12tb/21may/P19/J148/cryosparc_P19_J148_class_00_00122_volume.mrc > /scratch2/jrai/mountpoint12tb/21may/P19/J148/cryosparc_P19_J148_class_01_00122_volume.mrc > /scratch2/jrai/mountpoint12tb/21may/P19/J148/cryosparc_P19_J148_class_02_00122_volume.mrc Opened cryosparc_P19_J148_class_00_00122_volume.mrc as #1.1, grid size 128,128,128, pixel 2.15, shown at level 0.444, step 1, values float32 Opened cryosparc_P19_J148_class_01_00122_volume.mrc as #1.2, grid size 128,128,128, pixel 2.15, shown at level 0.65, step 1, values float32 Opened cryosparc_P19_J148_class_02_00122_volume.mrc as #1.3, grid size 128,128,128, pixel 2.15, shown at level 0.383, step 1, values float32 > volume #2 level 0.006831 > volume #1.1 level 0.2766 > color #1 gray > lighting soft > lighting simple > lighting full > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > show #!1.1 models > lighting simple > lighting soft > lighting full > lighting soft > hide #!1.1 models > show #!1.2 models > hide #!1.2 models > show #!1.3 models > close #1.1 > close #1.2 > close #1.3 > open > /scratch2/jrai/mountpoint12tb/21may/P19/J150/cryosparc_P19_J150_class_00_00122_volume.mrc Opened cryosparc_P19_J150_class_00_00122_volume.mrc as #3, grid size 128,128,128, pixel 2.15, shown at level 0.615, step 1, values float32 > color #3 gray > open > /scratch2/jrai/mountpoint12tb/21may/P19/J150/cryosparc_P19_J150_class_01_00122_volume.mrc Opened cryosparc_P19_J150_class_01_00122_volume.mrc as #4, grid size 128,128,128, pixel 2.15, shown at level 0.681, step 1, values float32 > open > /scratch2/jrai/mountpoint12tb/21may/P19/J150/cryosparc_P19_J150_class_02_00122_volume.mrc Opened cryosparc_P19_J150_class_02_00122_volume.mrc as #5, grid size 128,128,128, pixel 2.15, shown at level 0.653, step 1, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 51241, resource id: 11633465, major code: 40 (TranslateCoords), minor code: 0 > volume #4 level 0.3291 > volume #3 level 0.4265 > volume #5 level 0.3788 > hide #!3 models > hide #!4 models > hide #!5 models > show #!3 models No map chosen to save QXcbConnection: XCB error: 3 (BadWindow), sequence: 60790, resource id: 11634744, major code: 40 (TranslateCoords), minor code: 0 > save /scratch2/jrai/mountpoint12tb/21may/Images/J150_class00.tiff > show #!4 models > hide #!3 models > color #4 gray > save /scratch2/jrai/mountpoint12tb/21may/Images/J150_class01.tiff > hide #!4 models > show #!5 models > color #5 gray > save /scratch2/jrai/mountpoint12tb/21may/Images/J150_class02.tiff > close #3 > close #4 > close #5 > open > /scratch2/jrai/hpc_mountoint/jrai/21may22d/PostProcess/job040/postprocess.mrc Opened postprocess.mrc as #3, grid size 256,256,256, pixel 1.07, shown at level 0.0103, step 1, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 6072, resource id: 11648632, major code: 40 (TranslateCoords), minor code: 0 > fitmap #3 #2 Missing required ""in_map"" argument > fitmap #3 inMap #2 Fit map postprocess.mrc in map run_ct14_class001.mrc using 167668 points correlation = 0.9119, correlation about mean = 0.4922, overlap = 65.27 steps = 236, shift = 12.1, angle = 20.6 degrees Position of postprocess.mrc (#3) relative to run_ct14_class001.mrc (#2) coordinates: Matrix rotation and translation 0.96813892 -0.17382027 -0.18025968 54.28506092 0.12273318 0.95682775 -0.26347150 28.82644944 0.21827415 0.23295317 0.94767569 -43.90133347 Axis 0.70686609 -0.56747794 0.42226664 Axis point 0.00000000 213.16701708 81.96713191 Rotation angle (degrees) 20.55735072 Shift along axis 3.47582605 > surface dust #3 > volume #3 level 0.007796 > color #3 gray > save /scratch2/jrai/mountpoint12tb/21may/Images/pp_job40.tiff > hide #!3 models > close #3 > open > /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class005.mrc > /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class004.mrc > /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class003.mrc > /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class002.mrc > /scratch2/jrai/hpc_mountoint/jrai/21may22d/Class3D/job039/run_it025_class001.mrc Opened run_it025_class005.mrc as #3.1, grid size 256,256,256, pixel 1.07, shown at level 0.0119, step 1, values float32 Opened run_it025_class004.mrc as #3.2, grid size 256,256,256, pixel 1.07, shown at level 0.0102, step 1, values float32 Opened run_it025_class003.mrc as #3.3, grid size 256,256,256, pixel 1.07, shown at level 0.0111, step 1, values float32 Opened run_it025_class002.mrc as #3.4, grid size 256,256,256, pixel 1.07, shown at level 0.0127, step 1, values float32 Opened run_it025_class001.mrc as #3.5, grid size 256,256,256, pixel 1.07, shown at level 0.00887, step 1, values float32 > fitmap #3 inMap #2 Multiple maps for #3 > fitmap #3.1-3.5 inMap #2 No atoms or maps for #3.1-3.5 > fitmap #2 inMap #3.1 Fit map run_ct14_class001.mrc in map run_it025_class005.mrc using 342747 points correlation = 0.8839, correlation about mean = 0.5114, overlap = 76.99 steps = 212, shift = 11.4, angle = 20.4 degrees Position of run_ct14_class001.mrc (#2) relative to run_it025_class005.mrc (#3.1) coordinates: Matrix rotation and translation 0.96918677 0.11999885 0.21512153 -45.59826548 -0.17061000 0.95694219 0.23484862 -8.41701514 -0.17767730 -0.26431406 0.94792872 58.72385164 Axis -0.71461679 0.56234302 -0.41604467 Axis point 0.00000000 211.25372010 82.76188668 Rotation angle (degrees) 20.44157025 Shift along axis 3.42029095 > hide #!3.1 models > hide #!3.2 models > hide #!3.3 models > hide #!3.4 models > hide #!3.5 models > color #3 gray > show #!3.1 models > volume #3.1 level 0.005417 > hide #!3.1 models > show #!3.2 models > volume #3.2 level 0.005712 > hide #!3.2 models > show #!3.3 models > volume #3.2 level 0.003187 > hide #!3.2 models > volume #3.3 level 0.005126 > volume #3.4 level 0.006421 > hide #!3.3 models > hide #!3.4 models > show #!3.5 models > volume #3.5 level 0.004892 > hide #!3.5 models > show #!3.4 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > show #!3.1 models > show #!3.2 models > show #!3.3 models > show #!3.4 models > show #!3.5 models > hide #!3.4 models > hide #!3.3 models > hide #!3.2 models > hide #!3.1 models > save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class001.tiff > hide #!3.5 models > show #!3.4 models > save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class002.tiff > hide #!3.4 models > show #!3.3 models > save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class003.tiff > hide #!3.3 models > show #!3.2 models > save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class004.tiff > hide #!3.2 models > show #!3.1 models > volume #3.1 level 0.001018 > save /scratch2/jrai/mountpoint12tb/21may/Images/class3D_job039_class005.tiff > close #3.1-5 > close #3 > close #1 > open > /scratch2/jrai/hpc_mountoint/jrai/21may22d/PostProcess/job052/postprocess.mrc Opened postprocess.mrc as #1, grid size 256,256,256, pixel 1.07, shown at level 0.0115, step 1, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 48992, resource id: 11010712, major code: 40 (TranslateCoords), minor code: 0 > surface dust #2 > volume #1 level 0.01319 > surface undust Missing or invalid ""surfaces"" argument: empty atom specifier > surface undust #1 > surface dust #1 > volume #1 level 0.004617 > volume #1 level 0.01295 > volume #1 level 0.008901 > volume #1 level 0.005807 > surface dust #1 > volume #1 level 0.01104 > save /scratch2/jrai/mountpoint12tb/21may/Images/pp_job052.tiff > color #1 gray > save /scratch2/jrai/mountpoint12tb/21may/Images/pp_job052.tiff > close #1 > open > /scratch2/jrai/mountpoint12tb/21may/P19/J151/cryosparc_P19_J151_class_02_00102_volume.mrc > /scratch2/jrai/mountpoint12tb/21may/P19/J151/cryosparc_P19_J151_class_01_00102_volume.mrc > /scratch2/jrai/mountpoint12tb/21may/P19/J151/cryosparc_P19_J151_class_00_00102_volume.mrc Opened cryosparc_P19_J151_class_02_00102_volume.mrc as #1.1, grid size 128,128,128, pixel 2.15, shown at level 0.583, step 1, values float32 Opened cryosparc_P19_J151_class_01_00102_volume.mrc as #1.2, grid size 128,128,128, pixel 2.15, shown at level 0.617, step 1, values float32 Opened cryosparc_P19_J151_class_00_00102_volume.mrc as #1.3, grid size 128,128,128, pixel 2.15, shown at level 0.681, step 1, values float32 QXcbConnection: XCB error: 3 (BadWindow), sequence: 31565, resource id: 11018261, major code: 40 (TranslateCoords), minor code: 0 > volume #1.1 level 0.5834 > volume #1.1 level 0.3244 > fitmap #group 1 in_map #2 Missing or invalid ""atomsOrMap"" argument: invalid objects specifier > fitmap #1.1 inMap #2 Fit map cryosparc_P19_J151_class_02_00102_volume.mrc in map run_ct14_class001.mrc using 44317 points correlation = 0.8378, correlation about mean = 0.3813, overlap = 437.1 steps = 148, shift = 3.68, angle = 12.7 degrees Position of cryosparc_P19_J151_class_02_00102_volume.mrc (#1.1) relative to run_ct14_class001.mrc (#2) coordinates: Matrix rotation and translation 0.99555142 -0.02488321 -0.09087465 19.05868236 0.01479670 0.99381863 -0.11002542 15.49379655 0.09305071 0.10819132 0.98976573 -18.13420011 Axis 0.75734292 -0.63833127 0.13771307 Axis point 0.00000000 183.68491337 142.37342037 Rotation angle (degrees) 8.28327388 Shift along axis 2.04646702 > fitmap #1.2 inMap #2 Fit map cryosparc_P19_J151_class_01_00102_volume.mrc in map run_ct14_class001.mrc using 20969 points correlation = 0.8771, correlation about mean = 0.341, overlap = 359.4 steps = 140, shift = 3.87, angle = 11.7 degrees Position of cryosparc_P19_J151_class_01_00102_volume.mrc (#1.2) relative to run_ct14_class001.mrc (#2) coordinates: Matrix rotation and translation 0.99515919 -0.04477703 -0.08748257 21.35221386 0.03383829 0.99186110 -0.12274575 15.02259506 0.09226675 0.11919130 0.98857487 -18.49021696 Axis 0.77671808 -0.57706972 0.25238771 Axis point 0.00000000 174.09914329 126.11793630 Rotation angle (degrees) 8.95989931 Shift along axis 3.24886237 > fitmap #1.3 inMap #2 Fit map cryosparc_P19_J151_class_00_00102_volume.mrc in map run_ct14_class001.mrc using 20966 points correlation = 0.8807, correlation about mean = 0.3437, overlap = 398.7 steps = 128, shift = 4.3, angle = 11.9 degrees Position of cryosparc_P19_J151_class_00_00102_volume.mrc (#1.3) relative to run_ct14_class001.mrc (#2) coordinates: Matrix rotation and translation 0.99454544 -0.05773828 -0.08686572 24.09498810 0.04820837 0.99297420 -0.10806565 10.56549857 0.09249495 0.10328855 0.99034144 -17.27927847 Axis 0.71220969 -0.60439967 0.35701316 Axis point 0.00000000 193.58614204 110.94411937 Rotation angle (degrees) 8.53301011 Shift along axis 4.60597055 > color #1 gray > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > show #!1.3 models > volume #1.3 level 0.3866 > hide #!1.3 models > show #!1.2 models > volume #1.2 level 0.3959 > show #!1.3 models > hide #!1.3 models > hide #!1.1 models > show #!1.1 models > hide #!1 models > show #!1 models > show #!1.2 models > hide #!1.1 models > hide #!1.2 models > show #!1.3 models > hide #!1.3 models > show #!1.2 models > hide #!1.2 models > show #!1.1 models > show #!1.3 models > show #!1.2 models > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > show #!1.1 models > save /scratch2/jrai/mountpoint12tb/21may/Images/J151_class002.tiff > hide #!1.1 models > show #!1.2 models > save /scratch2/jrai/mountpoint12tb/21may/Images/J151_class001.tiff > hide #!1.2 models > show #!1.3 models > save /scratch2/jrai/mountpoint12tb/21may/Images/J151_class000.tiff Traceback (most recent call last): File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. Traceback (most recent call last): File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): KeyboardInterrupt KeyboardInterrupt File ""/scratch/users/Jay/chimerax-1.2.5-rc-2021.05.24/lib/python3.8/site- packages/chimerax/core/updateloop.py"", line 128, in _redraw_timer_callback def _redraw_timer_callback(self): See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 460.32.03 OpenGL renderer: GeForce GTX 1080/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: ASUS Model: All Series OS: Ubuntu 16.04 xenial Architecture: 64bit ELF Virutal Machine: none CPU: 16 Intel(R) Core(TM) i7-6900K CPU @ 3.20GHz Cache Size: 20480 KB Memory: total used free shared buff/cache available Mem: 62G 7.3G 23G 320M 31G 54G Swap: 15G 3.5G 12G Graphics: 01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:1b80] (rev a1) Subsystem: ASUSTeK Computer Inc. Device [1043:859b] Kernel driver in use: nvidia Locale: ('en_US', 'UTF-8') 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-LinuxSupport: 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 distro: 1.5.0 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 pexpect: 4.8.0 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 ptyprocess: 0.7.0 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 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: 1.2.0 }}} " defect closed normal Input/Output can't reproduce all ChimeraX