id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8235 Crash saving image in Pillow, ChimeraX 1.3, Linux 3.10 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-3.10.0-1160.62.1.el7.x86_64-x86_64-with-glibc2.17 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007f6138334740 (most recent call first): File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/ImageFile.py"", line 518 in _save File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/PngImagePlugin.py"", line 1349 in _save File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/PIL/Image.py"", line 2235 in save File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/image_formats/save.py"", line 123 in save_image File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/image_formats/__init__.py"", line 45 in save File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py"", line 89 in provider_save File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2856 in run File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/save_command/cmd.py"", line 75 in cmd_save File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/cli.py"", line 2856 in run File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/commands/run.py"", line 36 in run File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py"", line 512 in run File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py"", line 1254 in save_image File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py"", line 327 in run File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py"", line 408 in run_shortcut File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py"", line 390 in try_shortcut File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/shortcuts.py"", line 1334 in run_provider File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/shortcuts/__init__.py"", line 52 in run_provider File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/__init__.py"", line 1284 in run_provider File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/core/toolshed/info.py"", line 381 in run_provider File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/toolbar/tool.py"", line 165 in callback File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py"", line 87 in _run_code File ""/programs/x86_64-linux/chimerax/1.3/libexec/UCSF-ChimeraX/lib/python3.9/runpy.py"", line 197 in _run_module_as_main ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/PRC26U1T_1G4L_20220317/Phenix_final/final_figure.cxs format > session Opened 1G4_RNA.mrc as #1.1, grid size 300,300,300, pixel 1.06, shown at level 0.0164, step 1, values float32 Opened Body1_postproposs_RNAandOverlapping_removed.mrc as #1.2, grid size 300,300,300, pixel 1.06, shown at level 0.015, step 1, values float32 Opened Body2_postproposs_RNAandOverlapping_removed.mrc as #1.3, grid size 300,300,300, pixel 1.06, shown at level 0.0164, step 1, values float32 opened ChimeraX session > lighting intensity 0.25 > material dull > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > view > lighting intensity 0.2 > lighting intensity 0.25 > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > open > /data/PRC26U1T_1G4L_20220317/Phenix_final/Body1_final_final3_real_space_refined_028.pdb > /data/PRC26U1T_1G4L_20220317/Phenix_final/Body2_final_final3_real_space_refined_027.pdb > /data/PRC26U1T_1G4L_20220317/Phenix_final/RNA_G4_aligned.pdb Chain information for Body1_final_final3_real_space_refined_028.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available Chain information for Body2_final_final3_real_space_refined_027.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available RNA_G4_aligned.pdb title: Structure of stacked G-quadruplex formed by human terra sequence In potassium solution [more info...] Chain information for RNA_G4_aligned.pdb #4 --- Chain | Description A B | RNA (5'-R(*GP*GP*GP*up*up*ap*GP*GP*GP*U)-3') > hide #!1 models > hide #2.2 models > hide #3.2 models > show cartoons > hide atoms > hide surfaces > select #2/A:31 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 244 atoms, 246 bonds, 39 residues, 1 model selected > select up 3434 atoms, 3498 bonds, 521 residues, 1 model selected > select up 12550 atoms, 12851 bonds, 1853 residues, 1 model selected > select up 25732 atoms, 26382 bonds, 3722 residues, 4 models selected > select up 25732 atoms, 26382 bonds, 3722 residues, 4 models selected > select down 12550 atoms, 12851 bonds, 1853 residues, 1 model selected > select down 3434 atoms, 3498 bonds, 521 residues, 1 model selected > select down 244 atoms, 246 bonds, 39 residues, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2 12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected > rainbow sel > color sel bychain > show sel atoms > style sel stick Changed 12550 atom styles > style sel ball Changed 12550 atom styles > style sel sphere Changed 12550 atom styles > style sel stick Changed 12550 atom styles > style sel ball Changed 12550 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel tube/slab shape box > nucleotides sel ladder > hide sel atoms > ~select #2 Nothing selected > select #4 592 atoms, 638 bonds, 18 residues, 1 model selected > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 592 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 592 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 592 atom styles > nucleotides sel tube/slab shape box > nucleotides sel slab > style nucleic & sel stick Changed 592 atom styles > nucleotides sel tube/slab shape box > nucleotides sel tube/slab shape ellipsoid > nucleotides sel tube/slab shape muffler > nucleotides sel tube/slab shape box > nucleotides sel ladder > nucleotides sel stubs > nucleotides sel tube/slab shape box > nucleotides sel slab > style nucleic & sel stick Changed 592 atom styles > nucleotides sel tube/slab shape box > color sel bynucleotide > ui tool show ""Color Actions"" > color sel orange > save /data/PRC26U1T_1G4L_20220317/Phenix_final/final_figure.cxs > select #2/A#3/A 6862 atoms, 6990 bonds, 68 pseudobonds, 1042 residues, 6 models selected > select #2/B#3/B 5844 atoms, 5964 bonds, 20 pseudobonds, 866 residues, 4 models selected > color sel forest green > color sel green > color sel forest green > select #2/C#3/C 5255 atoms, 5401 bonds, 732 residues, 2 models selected > color sel cyan > color sel deep sky blue > color sel cyan > select #2/D#3/D 5444 atoms, 5612 bonds, 2 pseudobonds, 784 residues, 4 models selected > color sel yellow > color sel purple > color sel cornflower blue > color sel medium purple > select #2/E#3/E 358 atoms, 362 bonds, 62 residues, 2 models selected > color sel magenta > select #2/F#3/F 1377 atoms, 1415 bonds, 2 pseudobonds, 218 residues, 4 models selected > color sel red > help help:user/findseq.html > select #2 12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected > ui tool show ""Blast Protein"" > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #3/A Alignment identifier is 1 > select #2/A:22-23 #3/A:22-23 20 atoms, 18 bonds, 4 residues, 2 models selected > select #2/A:22-124 #3/A:22-124 1381 atoms, 1407 bonds, 206 residues, 2 models selected Seqview [ID: 1] region 2 chains [1-103] RMSD: 144.512 > select #2/A:741 #3/A:741 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:598-741 #3/A:598-741 2047 atoms, 2089 bonds, 288 residues, 2 models selected Seqview [ID: 1] region 2 chains [370-513] RMSD: 59.124 > select #2/A:742 #3/A:742 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:23-742 #3/A:23-742 6838 atoms, 6980 bonds, 12 pseudobonds, 1026 residues, 4 models selected Seqview [ID: 1] region 2 chains [2-514] RMSD: 95.556 > select #2/A:712-742 #3/A:712-742 444 atoms, 450 bonds, 62 residues, 2 models selected > select #2/A:577-742 #3/A:577-742 2336 atoms, 2384 bonds, 332 residues, 2 models selected Seqview [ID: 1] region 2 chains [349-514] RMSD: 55.917 > color sel blue > select #2/A:577 #3/A:577 14 atoms, 14 bonds, 2 residues, 2 models selected > select #2/A:540-577 #3/A:540-577 534 atoms, 544 bonds, 76 residues, 2 models selected Seqview [ID: 1] region 2 chains [312-349] RMSD: 26.025 > color sel blue > select #2/A:540 #3/A:540 14 atoms, 14 bonds, 2 residues, 2 models selected > select #2/A:481-540 #3/A:481-540 312 atoms, 322 bonds, 2 pseudobonds, 46 residues, 4 models selected Seqview [ID: 1] region 2 chains [290-312] RMSD: 49.257 > color sel blue > select #2/A:479-480 #3/A:479-480 20 atoms, 18 bonds, 4 residues, 2 models selected > select #2/A:479-481 #3/A:479-481 30 atoms, 28 bonds, 6 residues, 2 models selected Seqview [ID: 1] region 2 chains [288-290] RMSD: 110.420 > color sel blue > select #2/A:481 #3/A:481 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:481-522 #3/A:481-522 54 atoms, 50 bonds, 2 pseudobonds, 10 residues, 4 models selected Seqview [ID: 1] region 2 chains [290-294] RMSD: 73.704 > select #2/A:482-520 #3/A:482-520 20 atoms, 16 bonds, 2 pseudobonds, 4 residues, 4 models selected > select #2/A:482-524 #3/A:482-524 84 atoms, 82 bonds, 2 pseudobonds, 12 residues, 4 models selected Seqview [ID: 1] region 2 chains [291-296] RMSD: 52.564 > select #2/A:520 #3/A:520 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:520-525 #3/A:520-525 98 atoms, 100 bonds, 12 residues, 2 models selected Seqview [ID: 1] region 2 chains [292-297] RMSD: 31.845 > select #2/A:481-482 #3/A:481-482 20 atoms, 18 bonds, 4 residues, 2 models selected > select #2/A:274-482 #3/A:274-482 1731 atoms, 1775 bonds, 2 pseudobonds, 264 residues, 4 models selected Seqview [ID: 1] region 2 chains [160-291] RMSD: 91.364 > color sel hot pink > select #2/A:273 #3/A:273 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:269-273 #3/A:269-273 60 atoms, 58 bonds, 10 residues, 2 models selected Seqview [ID: 1] region 2 chains [155-159] RMSD: 103.180 > select #2/A:273 #3/A:273 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:250-273 #3/A:250-273 224 atoms, 228 bonds, 2 pseudobonds, 36 residues, 4 models selected Seqview [ID: 1] region 2 chains [142-159] RMSD: 104.862 > select #2/A:257 #3/A:257 14 atoms, 14 bonds, 2 residues, 2 models selected > select #2/A:257-277 #3/A:257-277 266 atoms, 272 bonds, 42 residues, 2 models selected Seqview [ID: 1] region 2 chains [143-163] RMSD: 100.469 > color sel hot pink > select #2/A:250 #3/A:250 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:22-250 #3/A:22-250 1769 atoms, 1789 bonds, 6 pseudobonds, 284 residues, 4 models selected Seqview [ID: 1] region 2 chains [1-142] RMSD: 141.653 > color sel gold > select #2/A:742 #3/A:742 10 atoms, 8 bonds, 2 residues, 2 models selected > select #2/A:577-742 #3/A:577-742 2336 atoms, 2384 bonds, 332 residues, 2 models selected Seqview [ID: 1] region 2 chains [349-514] RMSD: 55.917 > select #3 12590 atoms, 12893 bonds, 46 pseudobonds, 1851 residues, 3 models selected > select #2 12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected > ~select #2 Nothing selected > show #!1 models > hide #!1 models > ui tool show ""Surface Color"" > show #!1 models > color radial #1.1.1 palette #ff0000:#ffffff:#0000ff > color single #1.1.1 > ui tool show ""Color Zone"" > color zone #1.2 near #2 distance 6.38 > color zone #1.2 near #2 distance 17.05 > color zone #1.2 near #2 distance 16.94 > color zone #1.2 near #2 distance 17.05 > color zone #1.2 near #2 distance 16.94 > color zone #1.2 near #2 distance 11.33 > color zone #1.2 near #2 distance 11.25 > color zone #1.2 near #2 distance 11.17 > color zone #1.2 near #2 distance 11.24 > color zone #1.2 near #2 distance 8.85 > color zone #1.2 near #2 distance 8.75 > color single #1.2 > color zone #1.2 near #2 distance 6 > color zone #1.2 near #2 distance 8 > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #3/A Alignment identifier is 1 > hide #!1 models > lighting depthCue false > open > /data/PRC26U1T_1G4L_20220317/Phenix_final/Body1_final_final1_real_space_refined_023-coot-1.pdb Chain information for Body1_final_final1_real_space_refined_023-coot-1.pdb #5 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available > hide atoms > hide #!5 models > show #!5 models > show cartoons > hide #!2 models > show #!2 models > hide #!5 models > show #!5 models > close #5 > show #!1 models > color zone #1.2 near #2 distance 7 > lighting depthCue false > volume #1.2 level 0.01512 > volume #1.2 level 0.015 > volume #1.2 level 0.0155 > volume #1.2 level 0.015 > select #1.2 2 models selected > select #1 7 models selected > ~select #1 Nothing selected > select #1.2 2 models selected > select #1 7 models selected > ~select #1 Nothing selected > volume #1.2 level 0.0155 > volume #1.2 level 0.015 > color zone #1.2 near #2 distance 6 > lighting depthCue false > color zone #1.3 near #3 distance 6.38 > volume #1.3 level 0.0164 > color zone #1.3 near #3 distance 7 > lighting depthCue false > color zone #1.3 near #3 distance 8 > lighting depthCue false > color zone #1.1 near #4 distance 6.38 > color zone #1.1 near #4 distance 8 > color zone #1.1 near #4 distance 9 > hide #!2 models > hide #!3 models > hide #4 models > lighting intensity 0.4 > lighting intensity 0.3 > color #1 #eeeeec models transparency 0 > color #1 white models transparency 0 > color #1 #d3d7cf models transparency 0 > color zone #1.1 near #4 distance 9 > color zone #1.2 near #2 distance 6.38 > ui tool show ""Hide Dust"" > surface dust #1.1 size 1.06 > surface dust #1.2 size 6.13 > surface dust #1.2 size 11.03 > select #2 12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected > ~select #2 Nothing selected > select #2 12550 atoms, 12851 bonds, 46 pseudobonds, 1853 residues, 3 models selected > ~select #2 Nothing selected > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > surface dust #1.2 size 11.13 > surface dust #1.1 size 5.97 > color zone #1.3 near #3 distance 6.38 > color zone #1.3 near #3 distance 7.97 > color zone #1.3 near #3 distance 7 > lighting intensity 0.3 > surface dust #1.3 size 14.46 > surface dust #1.3 size 8.41 > save /data/PRC26U1T_1G4L_20220317/Phenix_final/final_figure_map.cxs > view > save /home/spuser/Desktop/image1.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 3.3.0 NVIDIA 470.63.01 OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: SYS-7049GP-TRT OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 96 Intel(R) Xeon(R) Gold 5220R CPU @ 2.20GHz Cache Size: 36608 KB Memory: total used free shared buff/cache available Mem: 251G 11G 238G 40M 1.7G 239G Swap: 31G 0B 31G Graphics: 04:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41) Subsystem: Super Micro Computer Inc Device [15d9:096d] Kernel driver in use: ast 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: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 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: 2.6.1 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: 2.2.2 ChimeraX-Clipper: 0.17.0 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 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 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: 2.1.2 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-LinuxSupport: 1.0 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: 2.0.4 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: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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: 2.4.6 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: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 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: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 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: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 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: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 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: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 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: 2.2.0 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 tables: 3.6.1 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Input/Output nonchimerax all ChimeraX