id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15921 Could not instantiate StructureSeq.structure jacques.van-Helden@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000382313000 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001ffaacc00 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py"", line 91 in get_prop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1255 in _changes_cb File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 1069 in proxy_handler File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/changes.py"", line 54 in check_for_changes File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/__init__.py"", line 77 in File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3318 in command_trigger File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/contextlib.py"", line 144 in __exit__ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3203 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py"", line 225 in delete File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/tool.py"", line 308 in _key_closed File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/color_key/model.py"", line 105 in delete File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/models.py"", line 1010 in close File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/close.py"", line 43 in close File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3213 in run File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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""45f4e2a5-551b-4bc2-a2dc-19c244dda8f8"", ""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van- > Helden@univ-amu.fr/My > Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin/1MBN_myoglobin_rolling.cxc"" > cd /Users/jvanheld/structures/1MBN_myoglobin/ Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin > close session > open 1MBN 1mbn title: The stereochemistry of the protein myoglobin [more info...] Chain information for 1mbn #1 --- Chain | Description | UniProt A | MYOGLOBIN | MYG_PHYCA 1-153 Non-standard residues in 1mbn #1 --- HEM — protoporphyrin IX containing Fe (HEME) OH — hydroxide ion > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > view orient > color byelement > movie record > wait 20 > roll axis y angle 3 frames 120 > wait > roll axis x angle 3 frames 120 > wait > view orient > 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 > save 1MBN_myoglobin_white-bg.png width 1984 height 1240 supersample 3 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > save 1MBN_myoglobin_black-bg.png width 1984 height 1240 supersample 3 > movie encode output 1MBN_myoglobin_rolling.mov Movie saved to 1MBN_myoglobin_rolling.mov > view orient > movie record > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > transparency 50 > wait 50 > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLY 153 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09, maximum 9.92 > transparency 50 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 50 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 50 > wait 100 > view orient > roll axis y angle 1 frames 25 > wait > wait 30 > roll axis z angle 1 frames 10 > wait > wait 30 > roll axis x angle 3 frames 36 > wait > wait 30 > roll axis y angle -1 frames 10 > wait > wait 30 > transparency 0 > wait 50 > zoom 2.0 frames 100 > wait 100 > rock y 20 400 > wait 400 > zoom 0.5 frames 100 > wait 100 > roll axis x angle 3 frames 120 > wait 200 > 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 > save 1MBN_myoglobin_heme-pocket_white-bg.png width 1984 height 1240 > supersample 3 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > save 1MBN_myoglobin_heme-pocket_black-bg.png width 1984 height 1240 > supersample 3 > save 1MBN_myoglobin_rolling.cxs executed 1MBN_myoglobin_rolling.cxc > view orient > movie record Already recording a movie > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > transparency 50 > wait 50 > coulombic Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09, maximum 9.92 > transparency 50 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 50 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 30 > wait 100 > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > transparency 30 > wait 50 > coulombic Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09, maximum 9.92 > transparency 30 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 30 > wait 100## Show hydrostatic profile Expected an integer >= 1 or a keyword > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 30 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 30 > wait 100 > view orient > roll axis y angle 1 frames 25 > wait > wait 30 > roll axis z angle 1 frames 10 > wait > wait 30 > roll axis x angle 3 frames 36 > wait > wait 30 > roll axis y angle -1 frames 10 > wait > wait 30 > transparency 0 > wait 50 > zoom 2.0 frames 100 > wait 100 > zoom 2.0 frames 60 > wait > wait 30 > zoom 0.25 > zoom 2.0 frames 30 > wait > wait 30 > rock y 20 300 > rock y 20 180 > wait > wait 30 > rock y 20 80 > wait > wait 30 > rock y 20 80 > wait > wait 30 > rock y 20 80 > wait > wait 30 > rock y 20 240 > wait > wait 30 > zoom 0.5 frames 100 > wait 100 > zoom 2.0 frames 30 > wait > wait 30 > zoom 0.5 frames 30 > wait > wait 30 > zoom 2.0 frames 60 > wait > wait 30 > zoom 0.5 frames 30 > wait > wait 30 > roll axis x angle 3 frames 120 > wait > wait 30 > open ""/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van- > Helden@univ-amu.fr/My > Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin/1MBN_myoglobin_rolling.cxc"" > cd /Users/jvanheld/structures/1MBN_myoglobin/ Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin > close session > open 1MBN 1mbn title: The stereochemistry of the protein myoglobin [more info...] Chain information for 1mbn #1 --- Chain | Description | UniProt A | MYOGLOBIN | MYG_PHYCA 1-153 Non-standard residues in 1mbn #1 --- HEM — protoporphyrin IX containing Fe (HEME) OH — hydroxide ion > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > view orient > color byelement > movie record Already recording a movie > movie stop > close session > open ""/Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van- > Helden@univ-amu.fr/My > Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin/1MBN_myoglobin_rolling.cxc"" > cd /Users/jvanheld/structures/1MBN_myoglobin/ Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin > close session > open 1MBN 1mbn title: The stereochemistry of the protein myoglobin [more info...] Chain information for 1mbn #1 --- Chain | Description | UniProt A | MYOGLOBIN | MYG_PHYCA 1-153 Non-standard residues in 1mbn #1 --- HEM — protoporphyrin IX containing Fe (HEME) OH — hydroxide ion > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > view orient > color byelement > movie record > wait 20 > roll axis y angle 3 frames 120 > wait > wait 30 > roll axis x angle 3 frames 120 > wait > wait 30 > view orient > wait 180 > 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 > save 1MBN_myoglobin_white-bg.png width 1984 height 1240 supersample 3 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > save 1MBN_myoglobin_black-bg.png width 1984 height 1240 supersample 3 > movie encode output 1MBN_myoglobin_rolling.mov Movie saved to 1MBN_myoglobin_rolling.mov > view orient > movie record > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > transparency 30 > wait 50 > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLY 153 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09, maximum 9.92 > transparency 30 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 30 > wait 100 > view orient > roll axis y angle 1 frames 25 > wait > wait 30 > roll axis z angle 1 frames 10 > wait > wait 30 > roll axis x angle 3 frames 36 > wait > wait 30 > roll axis y angle -1 frames 10 > wait > wait 30 > transparency 0 > wait 50 > zoom 2.0 frames 60 > wait > wait 30 > rock y 20 260 > wait > wait 30 > zoom 0.5 frames 30 > wait > wait 30 > roll axis x angle 3 frames 120 > wait > wait 30 > 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 > save 1MBN_myoglobin_heme-pocket_white-bg.png width 1984 height 1240 > supersample 3 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > save 1MBN_myoglobin_heme-pocket_black-bg.png width 1984 height 1240 > supersample 3 > movie encode output 1MBN_myoglobin_heme-pocket.mov Movie saved to 1MBN_myoglobin_heme-pocket.mov > save 1MBN_myoglobin_rolling.cxs executed 1MBN_myoglobin_rolling.cxc > close session The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > close session > cd /Users/jvanheld/structures/1MBN_myoglobin/ Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/1MBN_myoglobin > close session > open 1MBN 1mbn title: The stereochemistry of the protein myoglobin [more info...] Chain information for 1mbn #1 --- Chain | Description | UniProt A | MYOGLOBIN | MYG_PHYCA 1-153 Non-standard residues in 1mbn #1 --- HEM — protoporphyrin IX containing Fe (HEME) OH — hydroxide ion > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > view orient > color byelement > movie record > wait 20 > roll axis y angle 3 frames 120 > wait > wait 30 > roll axis x angle 3 frames 120 > wait > wait 30 > view orient > wait 180 > 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 > save 1MBN_myoglobin_white-bg.png width 1984 height 1240 supersample 3 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > save 1MBN_myoglobin_black-bg.png width 1984 height 1240 supersample 3 > movie encode output 1MBN_myoglobin_rolling.mov Movie saved to 1MBN_myoglobin_rolling.mov > movie stop No movie being recorded. > close session > open 1MBN 1mbn title: The stereochemistry of the protein myoglobin [more info...] Chain information for 1mbn #1 --- Chain | Description | UniProt A | MYOGLOBIN | MYG_PHYCA 1-153 Non-standard residues in 1mbn #1 --- HEM — protoporphyrin IX containing Fe (HEME) OH — hydroxide ion > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > view orient > color byelement > movie record > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > transparency 30 > wait 50 > coulombic The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /A GLY 153 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 1mbn_A SES surface #1.2: minimum, -11.83, mean -0.09, maximum 9.92 > transparency 30 > wait 100 > mlp Map values for surface ""1mbn_A SES surface"": minimum -28.73, mean -3.303, maximum 24.18 > transparency 30 > wait 100 > view orient > roll axis y angle 1 frames 25 > wait > wait 30 > roll axis z angle 1 frames 10 > wait > wait 30 > roll axis x angle 3 frames 36 > wait > wait 30 > roll axis y angle -1 frames 10 > wait > wait 30 > transparency 0 > wait 50 > zoom 2.0 frames 60 > wait > wait 30 > rock y 20 260 > wait > wait 30 > zoom 0.5 frames 30 > wait > wait 30 > roll axis x angle 3 frames 120 > wait > wait 30 > 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 > save 1MBN_myoglobin_heme-pocket_white-bg.png width 1984 height 1240 > supersample 3 > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > save 1MBN_myoglobin_heme-pocket_black-bg.png width 1984 height 1240 > supersample 3 > movie encode output 1MBN_myoglobin_heme-pocket.mov Movie saved to 1MBN_myoglobin_heme-pocket.mov > movie stop No movie being recorded. > save 1MBN_myoglobin_rolling.cxs > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS Summary of feedback from opening 2HBS fetched from pdb --- note | Fetching compressed mmCIF 2hbs from http://files.rcsb.org/download/2hbs.cif 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > show atoms > hide atoms > hide cartoons > hide surfaces > show cartoons > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view > view orient > select #1 4993 atoms, 4686 bonds, 4 pseudobonds, 1027 residues, 2 models selected > view matrix models #1,1,0,0,-50,0,1,0,+25,0,0,1,0 > wait 20 > close session > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #1 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #1 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > cd ""/Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT"""" Expected name of a folder to open/read; a name of 'browse' will bring up a file browser or a keyword > cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS- vs-1A3N_haemoglibin_mutant-vs-WT > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides ribbons/slabspreset cartoons/nucleotides > ribbons/slabs No preset name in category 'Cartoons/Nucleotides' matches 'ribbons/slabspreset cartoons/nucleotides ribbons/slabs' > view orient > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > select #2/A 1167 atoms, 1147 bonds, 1 pseudobond, 197 residues, 2 models selected > select down 1167 atoms, 1147 bonds, 1 pseudobond, 197 residues, 2 models selected > view matrix models #1,1,0,0,-100,0,1,0,0,0,0,1,0 > wait 20 > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-100,0,1,0,+25,0,0,1,0 > wait 20 > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E 1174 atoms, 1147 bonds, 1 pseudobond, 204 residues, 2 models selected > select #2/Eselect #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > hide sel > select #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > hide sel > cartoon hide (#!2 & sel) > cartoon hide (#!2 & sel)view orient ; Expected an atoms specifier or a keyword > view matrix models #1,1,0,0,1,0,1,0,+75,0,0,1,0 > wait 20 > view orient > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > cartoon hide (#!2 & sel) > view orient > hide (#!2 & sel) target a > cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS- vs-1A3N_haemoglibin_mutant-vs-WT > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > cartoon hide (#!2 & sel) > hide (#!2 & sel) target a > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > color red #1:.A,.B # Colorer les chaînes A et B de l'hémoglobine normale en > rouge Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > All hide (#!2 & sel) Unknown command: All hide (#!2 & sel) > All hide (#!2 & sel)# Charger les structures d'hémoglobine sauvage et mutée Unknown command: All hide (#!2 & sel)# Charger les structures d'hémoglobine sauvage et mutée > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #3 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #3 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #4 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #4 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > color green #1/A /B /C /D Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color green #1/A /B /C /D# Charger les structures d'hémoglobine sauvage et > mutée Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #5 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #5 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #6 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #6 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > color green #1/A /B /C /D Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color green #1/A /B /C /D Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS- vs-1A3N_haemoglibin_mutant-vs-WT > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > cartoon hide (#!2 & sel) > hide (#!2 & sel) target a > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS- vs-1A3N_haemoglibin_mutant-vs-WT > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > cartoon hide (#!2 & sel) > hide (#!2 & sel) target a > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > color green #1/A /B /C /Dcolor green #1/A /B /C /D ; Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color green #1/A /B /C /Dcolor green #1/A /B /C /D ; color green #1/A /B /C > /D ; Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color green #1 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color green #1 cartoons Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > cartoons color green #1 Unknown command: cartoons color green #1 > ui tool show ""Color Actions"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #1 4993 atoms, 4686 bonds, 4 pseudobonds, 1027 residues, 2 models selected > color sel forest green > color sel bychain > color sel forest green > select #1/A 1235 atoms, 1147 bonds, 1 pseudobond, 265 residues, 2 models selected > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color green sel ; # WT alpha chains Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel cyan > color sel cornflower blue > select down 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green > select #1/B #1/D 2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected > color sel cornflowerblue > select none Expected an objects specifier or a keyword > select noneselect clear Expected an objects specifier or a keyword > select noneselect clear Expected an objects specifier or a keyword > select clear > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green > select clear > select #1/B #1/D 2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected > color sel cornflowerblue > select clear > select #2/A #2/C 2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected > color sel red > select clear > select #2/B #2/D 2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected > color sel yellow > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select #2:.B at 6 # Sélectionner la position 6 de la chaîne B (mutation E6V) Expected an objects specifier or a keyword > select #2/B:6 # Sélectionner la position 6 de la chaîne B (mutation E6V) Expected a keyword > select #2/B 1240 atoms, 1201 bonds, 1 pseudobond, 223 residues, 2 models selected > select #2/B:6 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/B:6-6 # Sélectionner la position 6 de la chaîne B (mutation E6V) Expected a keyword > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color green #2:.A,.B ; # Colorer les chaînes A et B de l'hémoglobine mutée > en vert Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color magenta sel ; # Colorer ce résidu en magenta Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select clear > color sel magenta > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel magenta > select clear > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green > select clear > select #1/B #1/D 2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected > color sel cornflowerblue > select clear > select #2/A #2/C 2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected > color sel purple > select clear > select #2/B #2/D 2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected > color sel yellow > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select clear > matchmaker #1 to #2 computeSS true # Calculer les RMSD pour chaque résidu Expected a keyword > matchmaker #1 to #2 computeSS true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon > la RMSD par rapport à la structure normale Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon la RMSD par rapport à la structure normale > rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon > la RMSD par rapport à la structure normaleview Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon la RMSD par rapport à la structure normaleview > rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon > la RMSD par rapport à la structure normaleviewview orient Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon la RMSD par rapport à la structure normaleviewview orient > view orient > transparency 0.5 > transparency 0.5 All > select 14670 atoms, 14078 bonds, 12 pseudobonds, 2756 residues, 4 models selected > ui tool show ""Color Actions"" > transparency 70,s #0 Missing or invalid ""percent"" argument: Expected a number > transparency 70 #0 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 70 > transparency 70 cartoons > select clear > transparency 100,s #0 Missing or invalid ""percent"" argument: Expected a number > transparency 100 #0 Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 100 > transparency 100 cartoons > transparency 70 cartoons > transparency 70 All > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 111 atoms, 113 bonds, 15 residues, 1 model selected > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 111 atoms, 113 bonds, 15 residues, 1 model selected > transparency 0 sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 0s Missing or invalid ""percent"" argument: Expected a number > transparency 0 > transparency 0 > transparency 0 target sel Invalid ""target"" argument: Character 'e' is not an allowed target, must be one of acrsbmpfl > transparency 0 target s > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #3 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #3 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #4 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #4 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E #2/F #2/G #2/H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > cartoon hide (#!2 & sel) > hide (#!2 & sel) target a > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green transparency 50 > select clear > cd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT Current working directory is: /Users/jvanheld/Library/CloudStorage/GoogleDrive-Jacques.van-Helden@univ- amu.fr/My Drive/enseignements_JvH/AMU_enseignements/AMU_2024-2025/SSV3U15_bioinfo_L2-SV_AMU_2024/materiel_didactique_SSV3U15/structures/2HBS- vs-1A3N_haemoglibin_mutant-vs-WT > close session > open 1A3N 1a3n title: Deoxy human hemoglobin [more info...] Chain information for 1a3n #1 --- Chain | Description | UniProt A C | HEMOGLOBIN (ALPHA CHAIN) | HBA_HUMAN 1-141 B D | HEMOGLOBIN (BETA CHAIN) | HBB_HUMAN 1-146 Non-standard residues in 1a3n #1 --- HEM — protoporphyrin IX containing Fe (HEME) 4 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open 2HBS 2hbs title: The high resolution crystal structure of deoxyhemoglobin S [more info...] Chain information for 2hbs #2 --- Chain | Description | UniProt A C E G | HEMOGLOBIN S (DEOXY), ALPHA CHAIN | HBA_HUMAN 1-141 B D F H | HEMOGLOBIN S (DEOXY), BETA CHAIN | HBB_HUMAN 1-146 Non-standard residues in 2hbs #2 --- HEM — protoporphyrin IX containing Fe (HEME) 2hbs mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 8760 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #2/E-H 4850 atoms, 4696 bonds, 4 pseudobonds, 876 residues, 2 models selected > cartoon hide (#!2 & sel) > hide (#!2 & sel) target a > view orient > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > view matrix models #1,1,0,0,-75,0,1,0,+25,0,0,1,0 > wait 20 > view orient > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green transparency 50 > select clear > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green transparency 40 > select clear > select #1/B #1/D 2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected > color sel cornflowerblue transparency 40 > select clear > select #2/A #2/C 2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected > color sel purple transparency 40 > select clear > select #2/B #2/D 2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected > color sel yellow transparency 40 > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select clear > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > matchmaker #1 to #2 computeSS true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon > la RMSD par rapport à la structure normale Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon la RMSD par rapport à la structure normale > matchmaker mmaker Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green transparency 40 > select clear > select #1/B #1/D 2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected > color sel cornflowerblue transparency 40 > select clear > select #2/A #2/C 2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected > color sel purple transparency 40 > select clear > select #2/B #2/D 2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected > color sel yellow transparency 40 > select clear > select #2/A #2/C 2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected > color sel purple transparency 40 > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select clear > transparency 70 All > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 111 atoms, 113 bonds, 15 residues, 1 model selected > transparency 0 target sel Invalid ""target"" argument: Character 'e' is not an allowed target, must be one of acrsbmpfl > transparency 0 target selsel up ; Invalid ""target"" argument: Character 'e' is not an allowed target, must be one of acrsbmpfl > transparency 0 target selsel up ; sel up ; Invalid ""target"" argument: Character 'e' is not an allowed target, must be one of acrsbmpfl > transparency 0 target s > select up 1121 atoms, 1151 bonds, 146 residues, 1 model selected > transparency 0 target s > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > view orient > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 111 atoms, 113 bonds, 15 residues, 1 model selected > transparency 0 target s > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow transparency 0 > select clear > transparency 70 All > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow transparency 0 > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow transparency 0 > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select clear > select #1/A #1/C 2447 atoms, 2294 bonds, 2 pseudobonds, 507 residues, 2 models selected > color sel green transparency 40 > select clear > select #1/B #1/D 2546 atoms, 2392 bonds, 2 pseudobonds, 520 residues, 2 models selected > color sel cornflowerblue transparency 40 > select clear > select #2/A #2/C 2359 atoms, 2294 bonds, 2 pseudobonds, 419 residues, 2 models selected > color sel purple transparency 40 > select clear > select #2/B #2/D 2468 atoms, 2402 bonds, 2 pseudobonds, 434 residues, 2 models selected > color sel yellow transparency 40 > select clear > transparency 70 All > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel yellow transparency 0 > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 111 atoms, 113 bonds, 15 residues, 1 model selected > color sel yellow transparency 0 > select clear > select #2/B:6-6 7 atoms, 6 bonds, 1 residue, 1 model selected > color sel red > select clear > matchmaker #1 to #2 computeSS true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon > la RMSD par rapport à la structure normale Unknown command: rangecolor bfactor min white max red #2 ; # Colorer la structure mutée selon la RMSD par rapport à la structure normale > rmsd #2 to #1 Number of atoms from first atom spec (9677) differs from number in second (4993) > matchmaker #1 to #2 computeSS true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2hbs, chain D (#2) with 1a3n, chain D (#1), sequence alignment score = 774 RMSD between 145 pruned atom pairs is 0.475 angstroms; (across all 145 pairs: 0.475) > color byattribute rmsd palette white:red range 0,2 #2 Expected a keyword > color byattribute rmsd palette white:red range 0,2 #2color #2 byattribute > ""rmsd"" palette white:red range 0,2 Expected a keyword > color #2 byattribute ""rmsd"" palette white:red range 0,2 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > close > open 4bql Summary of feedback from opening 4bql fetched from pdb --- note | Fetching compressed mmCIF 4bql from http://files.rcsb.org/download/4bql.cif 4bql title: Crystal structure of archaeal actin [more info...] Chain information for 4bql #1 --- Chain | Description | UniProt A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432 Non-standard residues in 4bql #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion 4bql mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > open 4bql 4bql title: Crystal structure of archaeal actin [more info...] Chain information for 4bql #2 --- Chain | Description | UniProt A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432 Non-standard residues in 4bql #2 --- ADP — adenosine-5'-diphosphate MG — magnesium ion 4bql mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > delete /B,C,D > open 1j6z Summary of feedback from opening 1j6z fetched from pdb --- note | Fetching compressed mmCIF 1j6z from http://files.rcsb.org/download/1j6z.cif 1j6z title: Uncomplexed actin [more info...] Chain information for 1j6z #3 --- Chain | Description | UniProt A | ACTIN ALPHA 1 | ACTS_RABIT 2-375 Non-standard residues in 1j6z #3 --- ADP — adenosine-5'-diphosphate CA — calcium ion HIC — 4-methyl-histidine RHO — tetramethylrhodamine-5-maleimide (TMR) 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > matchmaker #2 to #1 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4bql, chain A (#1) with 4bql, chain A (#2), sequence alignment score = 2308.8 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 4bql #1/A, 4bql #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 436 pruned atom pairs is 0.000 angstroms; (across all 436 pairs: 0.000) > select add #1 3465 atoms, 3539 bonds, 437 residues, 1 model selected > close > open 4bql 4bql title: Crystal structure of archaeal actin [more info...] Chain information for 4bql #1 --- Chain | Description | UniProt A B C D | ACTIN/ACTIN FAMILY PROTEIN | A3MWN5_PYRCJ 1-432 Non-standard residues in 4bql #1 --- ADP — adenosine-5'-diphosphate MG — magnesium ion 4bql mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly Associated 4bql chain A to 4bql, chain A with 0 mismatches Associated 4bql chain B to 4bql, chain A with 0 mismatches Associated 4bql chain C to 4bql, chain A with 0 mismatches Associated 4bql chain D to 4bql, chain A with 0 mismatches > delete /B,C,D > open 1j6z 1j6z title: Uncomplexed actin [more info...] Chain information for 1j6z #2 --- Chain | Description | UniProt A | ACTIN ALPHA 1 | ACTS_RABIT 2-375 Non-standard residues in 1j6z #2 --- ADP — adenosine-5'-diphosphate CA — calcium ion HIC — 4-methyl-histidine RHO — tetramethylrhodamine-5-maleimide (TMR) 5 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > matchmaker #2 to #1 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 4bql, chain A (#1) with 1j6z, chain A (#2), sequence alignment score = 412.6 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 4bql #1/A, 1j6z #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 177 pruned atom pairs is 1.198 angstroms; (across all 349 pairs: 4.965) > ui tool show ""Render/Select by Attribute"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Render/Select by Attribute"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color byattribute r:seq_rmsd #!1-2 target csab palette > 1,#0433ff:3,white:5,red noValueColor #80b180 6810 atoms, 1218 residues, atom seq_rmsd range 0.179 to 25.6 > key #0433ff:1 white:3 red:5 showTool true > ui mousemode right ""color key"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key #0433ff:1 white:3 red:5 showTool true > ui mousemode right translate > key #0433ff:1 white:3 red:5 showTool true > ui mousemode right ""color key"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key #0433ff:1 white:3 red:5 showTool true > key pos 0.433902,0.375647 size 0.00997586,0.00432396 > undo Undo failed, probably because structures have been modified. > show target m The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > show #3 target m > hide #3 target m > show #3 target m > open 4bqlcd /Users/jvanheld/structures/2HBS-vs-1A3N_haemoglibin_mutant-vs-WT '4bqlcd' has no suffix > close > ui mousemode right translate Traceback (most recent call last): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 1069, in proxy_handler s._changes_cb(*args) File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molobject.py"", line 1255, in _changes_cb if self.structure == None: ^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molc.py"", line 91, in get_prop cget(self._c_pointer_ref, 1, v_ref) TypeError: Cannot instantiate Python class corresponding to C++ N10atomstruct9StructureE Error processing trigger ""changes"": TypeError: Cannot instantiate Python class corresponding to C++ N10atomstruct9StructureE File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/molc.py"", line 91, in get_prop cget(self._c_pointer_ref, 1, v_ref) See log for complete Python traceback. ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,7 Model Number: Z1AF00123FN/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 11 days, 43 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PHL 272B7QU: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 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: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 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: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 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-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 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: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect feedback normal Core Tom Goddard all ChimeraX