id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5881 Save TIFF stack: ImageJ hyperstack shape and axes do not match kimsk@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.4.dev202110301952 (2021-10-30 19:52:32 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.4.dev202110301952 (2021-10-30) © 2016-2021 Regents of the University of California. All rights reserved. > open ""/Users/katekim/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2.cxs"" format session Opened denmod_KS_AT_sharpened_map.ccp4 as #5, grid size 209,117,160, pixel 0.835,0.835,0.835, shown at level 1.99, step 1, values float32 developer warning: container ""attr_registration"" snapshot methods are missing include_state method developer warning: container ""custom_attr_preserver"" snapshot methods are missing include_state method Log from Mon Jan 3 15:17:43 2022UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2.cxs"" Exception ignored in: Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 2088, in __del__ % self.name) chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer ""stereo camera"" was not deleted before graphics.Framebuffer destroyed Exception ignored in: Traceback (most recent call last): File ""/Applications/ChimeraX-1.1.1 2.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/graphics/opengl.py"", line 2088, in __del__ % self.name) chimerax.graphics.opengl.OpenGLError: OpenGL framebuffer ""stereo camera"" was not deleted before graphics.Framebuffer destroyed Log from Mon Jan 3 11:44:57 2022UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2.cxs"" Log from Thu Dec 30 09:39:38 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens.cxs"" Log from Tue Dec 28 22:14:49 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/janetfiner-moore/KS-substrate_dens.cxs Log from Tue Dec 28 19:21:24 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open /Users/janetfiner-moore/KS_Substrate_density.cxs restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None Log from Mon Dec 27 14:32:40 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. > open ""/Users/harries/Dropbox/PKS13/MAPS and > MODELS_UPDATED/COORDSwithHETATM/density_substrate.cxs"" Log from Mon Dec 27 13:32:19 2021UCSF ChimeraX version: 1.1.1 (2020-10-07) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/harries/Dropbox/PKS13/MAPS AND > MODELS_submit/KS_AT_conformer/KSAT_real_space_refined__Q__denmod_KS_AT_sharpened_map.pdb"" Chain information for KSAT_real_space_refined__Q__denmod_KS_AT_sharpened_map.pdb #1 --- Chain | Description A B | No description available > preset ""overall look"" publication Preset expands to these ChimeraX commands: set bg white graphics silhouettes t > open ""/Users/harries/Dropbox/PKS13/MAPS AND > MODELS_submit/KS_AT_conformer/denmod_KS_AT_sharpened_map.ccp4"" Opened denmod_KS_AT_sharpened_map.ccp4, grid size 209,117,160, pixel 0.835,0.835,0.835, shown at level 4.5, step 1, values float32 > ui tool show ""Show Volume Menu"" > transparency 50 > show target ab > cartoon hide > select H 13880 atoms, 1850 residues, 1 model selected > hide sel target a > help help:user > select ::name=""DCR"" 102 atoms, 100 bonds, 2 residues, 1 model selected > color sel purple > color sel byhetero > ui tool show ""Side View"" > volume #2 level 2.657 > volume #2 level 2.045 > volume #2 level 2.096 > volume #2 level 2.198 > volume #2 level 2.249 > volume #2 level 2.3 > volume #2 level 2.249 > volume #2 level 2.198 > volume #2 level 2.147 > volume #2 level 1.994 > volume #2 level 1.943 > volume #2 level 1.739 > volume #2 level 1.483 > volume #2 level 1.483 > volume #2 level 1.177 > volume #2 level 0.6666 > volume #2 level 0.3603 > volume #2 level 0.002946 > volume #2 level 0.7686 > volume #2 level 0.8197 > volume #2 level 0.7686 > ui tool show ""Side View"" > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #2 level 1.61 > select clear > volume #2 level 1.967 > open ""/Users/harries/Dropbox/PKS13/MAPS and > MODELS_UPDATED/COORDSwithHETATM/KS_wHET_real_space_refined.pdb"" Chain information for KS_wHET_real_space_refined.pdb #3 --- Chain | Description A B | No description available > hide #!1 models > show #!1 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > volume #2 level 3.039 > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > volume #2 level 1.916 > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > select #3/A 6554 atoms, 6617 bonds, 442 residues, 1 model selected > cartoon hide sel > select #3/B 6554 atoms, 6617 bonds, 442 residues, 1 model selected > cartoon hide sel > select clear > select #3/B 6554 atoms, 6617 bonds, 442 residues, 1 model selected > hide sel target a > select ::name=""DCR"" 204 atoms, 200 bonds, 4 residues, 2 models selected > show sel target ab > volume #2 level 2.937 > volume #2 level 1.967 > hide #3 models > select #1:1101 102 atoms, 100 bonds, 2 residues, 1 model selected > hide sel target a > show #3 models > ui tool show ""Side View"" > select #3/A 6554 atoms, 6617 bonds, 442 residues, 1 model selected > hide sel target a > select ::name=""DCR"" 204 atoms, 200 bonds, 4 residues, 2 models selected > ui tool show ""Color Actions"" > color sel plum > color sel byhetero > color sel violet > color sel byhetero > color sel khaki > color sel byhetero > color sel light coral > color sel byhetero > color sel burly wood > color sel tan > color sel rosy brown > color sel dim gray > color sel dark magenta > color sel orchid > color sel byhetero > color sel dark orchid > color sel byhetero > select clear > save ""/Users/harries/Dropbox/PKS13/MAPS and > MODELS_UPDATED/COORDSwithHETATM/density_substrate.cxs"" opened ChimeraX session > select #2 2 models selected > select clear > select #3/B:1101@C1 1 atom, 1 residue, 1 model selected > ui tool show Distances > distance #1/B:267@SG #3/B:1101@C1 Distance between KSAT_real_space_refined__Q__denmod_KS_AT_sharpened_map.pdb #1/B CYS 267 SG and KS_wHET_real_space_refined.pdb #3/B DCR 1101 C1: 1.9Å > distance style color #5d00ff > distance style color #8300ff > distance style color #8400ff > distance style dashes 8 > distance style dashes 8 > distance style dashes 7 > distance style dashes 7 > distance style dashes 6 > distance style dashes 6 > distance style dashes 5 > distance style dashes 5 > distance style dashes 6 > distance style dashes 6 > distance style dashes 7 > distance style dashes 7 > distance style dashes 8 > distance style dashes 8 > distance style dashes 9 > distance style dashes 9 > distance style dashes 10 > distance style dashes 10 > distance style radius 0.19 > distance style radius 0.19 > distance style radius 0.18 > distance style radius 0.18 > distance style radius 0.17 > distance style radius 0.17 > select clear > help help:user > distance style symbol false > view clip false > view clip false > undo > undo > ui tool show Distances > style stick Changed 41557 atom styles > distance style decimalPlaces 0 > distance style decimalPlaces 0 > distance style decimalPlaces -1 Invalid ""decimalPlaces"" argument: Must be greater than or equal to 0 > distance style decimalPlaces 0 > toolshed show > ~label > distance style stick Expected a keyword > distance style dashes 11 > distance style dashes 11 > distance style dashes 10 > distance style dashes 10 > distance style dashes 9 > distance style dashes 9 > distance style dashes 8 > distance style dashes 8 > distance style dashes 7 > distance style dashes 7 > distance style dashes 6 > distance style dashes 6 > distance style dashes 5 > distance style dashes 5 > distance style dashes 4 > distance style dashes 4 > distance style dashes 3 > distance style dashes 3 > distance style dashes 2 > distance style dashes 2 > distance style dashes 1 > distance style dashes 1 > distance style dashes 0 > distance style dashes 0 > save ""/Users/harries/Dropbox/PKS13/MAPS AND > MODELS_submit/KS_AT_conformer/KS_substrate_density.png"" width 1100 height > 772 supersample 3 > save ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND > REVIEWS/FIGURES/KS_Substrate_density.cxs"" opened ChimeraX session > open /Users/janetfiner-moore/KSAT_real_space_refined-coot-2.pdb Chain information for KSAT_real_space_refined-coot-2.pdb #2 --- Chain | Description A B | No description available > hide #3 models > show #3 models > hide #3 models > select #2 28413 atoms, 28287 bonds, 4 pseudobonds, 2270 residues, 2 models selected > show (#!2 & sel) target ab > cartoon hide (#!2 & sel) > ui tool show ""Color Actions"" > color sel tan > color sel byhetero > select H 34221 atoms, 4570 residues, 3 models selected > hide (#!1-2 & sel) target a > select #2:1101 102 atoms, 100 bonds, 2 residues, 1 model selected > show sel target ab > color sel dark orchid > color sel byhetero > hide #!1 models > hide #4 models > open ""/Users/janetfiner-moore/Dropbox/PKS13/MAPS AND > MODELS_submit/KS_AT_conformer/denmod_KS_AT_sharpened_map.ccp4"" Opened denmod_KS_AT_sharpened_map.ccp4, grid size 209,117,160, pixel 0.835,0.835,0.835, shown at level 4.5, step 1, values float32 > transparency sel 50 > volume #5 level 4.495 > volume #5 level 4.444 > volume #5 level 4.393 > volume #5 level 4.24 > volume #5 level 4.087 > volume #5 level 3.882 > volume #5 level 3.831 > volume #5 level 3.678 > volume #5 level 3.474 > volume #5 level 3.168 > volume #5 level 2.913 > volume #5 level 2.708 > volume #5 level 2.453 > volume #5 level 2.147 > volume #5 level 1.943 > volume #5 level 1.687 > volume #5 level 1.483 > volume #5 level 1.381 > volume #5 level 1.33 > volume #5 level 1.381 > volume #5 level 1.432 > volume #5 level 1.483 No visible Surface models selected > select #5 4 models selected > transparency #5.1 50 > select clear > save /Users/janetfiner-moore/KS-substrate_dens.cxs opened ChimeraX session > volume #5 level 1.994 > save /Users/janetfiner-moore/KS-substrate_dens.cxs opened ChimeraX session > select #3/A 6554 atoms, 6617 bonds, 442 residues, 1 model selected > select #1/A#2/A#3/A 34527 atoms, 34873 bonds, 6 pseudobonds, 2296 residues, 5 models selected > ui tool show ""Color Actions"" > color sel tomato > color sel byhetero > color sel coral > color sel sienna > color sel indian red > color sel byhetero > select #2/B 14001 atoms, 14144 bonds, 2 pseudobonds, 929 residues, 2 models selected > color sel crimson > color sel red > color sel byhetero > color sel crimson > color sel byhetero > color sel red > color sel crimson > color sel red > color sel byhetero > ui tool show ""Color Actions"" > color sel crimson > color sel byhetero > select ::name=""DCR"" 306 atoms, 300 bonds, 6 residues, 3 models selected > color sel dark blue > color sel byhetero > select clear > close #1 > close #3 > close #4 > save ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2.cxs"" opened ChimeraX session > select ::name=""HOH"" 412 atoms, 412 residues, 1 model selected > color sel cyan > select clear > hide #!5 models > select /A 14000 atoms, 14143 bonds, 2 pseudobonds, 929 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light coral > color sel tomato > color sel coral > color sel indian red > color sel tomato > color sel byhetero > color sel salmon > color sel byhetero > color sel orange red > color sel tomato > color sel light salmon > color sel salmon > color sel byhetero > show #!5 models > select clear > save ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate-dens.tif"" width 1100 height 772 supersample 3 > save ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2.cxs"" opened ChimeraX session > select /A 14000 atoms, 14143 bonds, 2 pseudobonds, 929 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pink > color sel byhetero > select /B 14001 atoms, 14144 bonds, 2 pseudobonds, 929 residues, 2 models selected > color sel red > color sel byhetero > select ::name=""DCR"" 102 atoms, 100 bonds, 2 residues, 1 model selected > color sel dark slate blue > color sel dark blue > color sel byhetero > select clear > save ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate-dens-stereo.tif"" width 1100 height 843 supersample 3 > save ""/Users/harries/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2.cxs"" ——— End of log from Mon Jan 3 15:17:43 2022 ——— opened ChimeraX session > select #2/A:93-535 6432 atoms, 6493 bonds, 437 residues, 1 model selected > color sel #f79292 > color sel byhetero > select #2/B:93-535 6432 atoms, 6493 bonds, 437 residues, 1 model selected > color sel #ff1616 > color sel byhetero > select clear > select ::name=""HOH"" 412 atoms, 412 residues, 1 model selected > color sel cyan > select clear > select ::name=""DCR"" 102 atoms, 100 bonds, 2 residues, 1 model selected > color sel medium blue > color sel byhetero > select clear > save ""/Users/katekim/Dropbox/PKS13/POST NATURE 2ND REVIEWS/FIGURES/KS- > substrate_dens2_v2.cxs"" includeMaps true > save Fig2b.png pixelSize 0.05 supersample 24 transparentBackground false > graphics silhouettes false > graphics silhouettes true > lighting shadows true > lighting shadows false > save /Users/katekim/Desktop/Fig2b.tif models #5 format imagejtiff Traceback (most recent call last): File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 89, in provider_save saver_info.save(session, path, **provider_kw) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/__init__.py"", line 167, in save save_map(session, path, _name, **kw) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/volume.py"", line 3971, in save_map save_grid_data(grids, path, session, format_name, options) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_data/fileformats.py"", line 314, in save_grid_data ff.save_func(garg, tpath, options = options, progress = p) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_data/imagestack/imagej_write.py"", line 19, in write_imagej_tiff _write_3d_tiff(grid_data, path) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map_data/imagestack/imagej_write.py"", line 29, in _write_3d_tiff imwrite(path, array_zcyx, imagej=True, resolution=(1/xstep, 1/ystep), File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/tifffile/tifffile.py"", line 856, in imwrite result = tif.write(data, shape, dtype, **kwargs) File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/tifffile/tifffile.py"", line 1640, in write ijshape = imagej_shape( File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/tifffile/tifffile.py"", line 14066, in imagej_shape raise ValueError('ImageJ hyperstack shape and axes do not match') ValueError: ImageJ hyperstack shape and axes do not match ValueError: ImageJ hyperstack shape and axes do not match File ""/private/var/folders/jl/b36pl7px7sz1691hs9ycjs_80000gn/T/AppTranslocation/BED623A2-87A6-4D3D-BA89-01571485A281/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/tifffile/tifffile.py"", line 14066, in imagej_shape raise ValueError('ImageJ hyperstack shape and axes do not match') See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.7.21 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 650 OpenGL vendor: Intel Inc.Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro14,2 Processor Name: Dual-Core Intel Core i5 Processor Speed: 3.1 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB Boot ROM Version: 447.60.3.0.0 SMC Version (system): 2.44f6 Software: System Software Overview: System Version: macOS 10.15.7 (19H1615) Kernel Version: Darwin 19.6.0 Time since boot: 2 days 3:24 Graphics/Displays: Intel Iris Plus Graphics 650: Chipset Model: Intel Iris Plus Graphics 650 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x5927 Revision ID: 0x0006 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No 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: 1.5.1.1 charset-normalizer: 2.0.7 ChimeraX-AddCharge: 1.1.5 ChimeraX-AddH: 2.1.10 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: 4.1.6 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.1 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: 2.2.2 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: 1.4.dev202110301952 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 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-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 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: 2.0.3 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: 1.3.1 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: 1.8 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 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: 2.4.5 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-StructMeasure: 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: 1.14 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 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.5.0 html2text: 2020.1.16 idna: 3.3 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: 4.9.1 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 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: 3.0.21 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: 3.0.4 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: 1.11.2 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: 5.1.1 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 fixed all ChimeraX