id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15364 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000098fe000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff84dea5b80 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py"", line 717 in __call__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/enum.py"", line 1512 in __and__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 798 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 798 in decode_modifier_bits File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 790 in key_modifiers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 555 in _event_type File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 534 in _dispatch_mouse_event File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py"", line 651 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 61 in event File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, 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Bytes before following region: 140737488076631\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffbc000-7ffffffbd000 [ 4K] r-x\/r-x SM=SHM "", ""exception"" : {""codes"":""0x0000000000000001, 0x00000000000000a9"",""rawCodes"":[1,169],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x00000000000000a9""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":78490}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0xa9 is not in any region. 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displayId=4128833, ) with displayId 4128833 Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 [Repeated 1 time(s)] > open > /Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Summary of feedback from opening /Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- warning | Ignored bad PDB record found on line 1 REMARK The PDB FILE IS CREATED BY CY's PROGRAM CurvatureSurface AT Mon Jun 3 23:17:28 2024 Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 [Repeated 1 time(s)] > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > color bfactor protein palette viridis 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > select #1.1/A 308 atoms, 312 bonds, 40 residues, 1 model selected > hbonds sel #1.2/A Expected a keyword Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > hbonds #1.1/A #1.2/A 40 hydrogen bonds found > ~hbonds > hbonds #1.1/A restrict #1.2/A 0 hydrogen bonds found > ~hbonds > hbonds sel reveal true 38 hydrogen bonds found > close > open > /Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb > format pdb Summary of feedback from opening /Users/APCamargo-M55/Downloads/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- warning | Ignored bad PDB record found on line 1 REMARK The PDB FILE IS CREATED BY CY's PROGRAM CurvatureSurface AT Mon Jun 3 23:17:28 2024 Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > hbonds reveal true 40 hydrogen bonds found > ~hbonds > hbonds #1.1/A #1.2/A 40 hydrogen bonds found > hbonds #1.1/A restrict #1.2/A 0 hydrogen bonds found > hbonds reveal true 40 hydrogen bonds found > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > color bfactor protein palette viridis 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > lighting soft > color bfactor protein palette viridis 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > color bfactor protein palette rocket Fetching compressed palette rocket from https://www.colourlovers.com/api/palettes?keywords=rocket&format=json&numResults=100 Found 2 ColourLover palettes with name ""rocket"", using palette id 110215 by author vipanchi with most views (458). To choose a different one use ""name by author"" or id number. 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > color bfactor protein palette araucaria 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > color bfactor protein palette tokyo 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > color bfactor protein palette sunset 308 atoms, 40 residues, atom bfactor range 0.81 to 4.32 > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 12 color #363644 depthJump 0.05 > color bfactor protein palette viridis 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 12 color #363644 depthJump 0.05 > color bfactor protein palette viridis 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 82 target s > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 4 color #363644 depthJump 0.05 > color bfactor protein palette viridis 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 82 target s > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette sunset 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 85 target s > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette tokyo 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > hbonds reveal true 40 hydrogen bonds found > ~hbonds > nucleotides atoms > style nucleic stick Changed 0 atom styles > nucleotides atoms > style nucleic stick Changed 0 atom styles > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette araucaria 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette burg 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette tokyo 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > select ::name=""ALA"" 20 atoms, 16 bonds, 4 residues, 1 model selected > select 271 Expected an objects specifier or a keyword Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > select #1.1 271 Expected a keyword Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > select #1.1 residues 271 Invalid ""residues"" argument: Expected true or false (or 1 or 0) Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > select residues #1.1 271 Invalid ""residues"" argument: Expected true or false (or 1 or 0) Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > select clear > hide #1.2 models > show #1.2 models > hide #2 models > show #2 models > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette tokyo 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette tokyo 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > ui tool show ""Show Sequence Viewer"" > sequence chain #1.1/A Alignment identifier is 1.1/A Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > select #1.1/A:265 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1.1/A:265 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1.1/A:265,271 25 atoms, 25 bonds, 2 residues, 1 model selected > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 91 atoms, 86 bonds, 11 residues, 1 model selected > select clear > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 91 atoms, 86 bonds, 11 residues, 1 model selected > hbonds sel & /1.2 distance 3.5 angle 30 Expected a keyword > hbonds sel & #1.2/A distance 3.5 angle 30 Expected a keyword Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 91 atoms, 86 bonds, 11 residues, 1 model selected > select #1.2/A 58 atoms, 59 bonds, 1 residue, 1 model selected > hbonds selRestrict any reveal true Expected a keyword Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > hbonds selRestrict any reveal true Expected a keyword > findhbond selRestrict any reveal true Unknown command: findhbond selRestrict any reveal true > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 91 atoms, 86 bonds, 11 residues, 1 model selected > select #1.2/A 58 atoms, 59 bonds, 1 residue, 1 model selected > select clear > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 91 atoms, 86 bonds, 11 residues, 1 model selected > select #1.2/A 58 atoms, 59 bonds, 1 residue, 1 model selected > select ~sel & ##selected Nothing selected > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 149 atoms, 145 bonds, 12 residues, 2 models selected > hbonds selRestrict any reveal true Expected a keyword > makePseudobonds selRestrict any reveal true Unknown command: makePseudobonds selRestrict any reveal true > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 149 atoms, 145 bonds, 12 residues, 2 models selected > hbonds sel ::#1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A Expected a keyword > hbonds sel::#1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A Expected a keyword > hbonds sel:: select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 > #1.2/A Expected a keyword > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 149 atoms, 145 bonds, 12 residues, 2 models selected > hbonds sel #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A Expected a keyword > hbonds cutoffDistance 3.5 cutoffAngle 30 Expected a keyword > hbonds cutoffDistance 3.5 cutoffAngle 30 Expected a keyword Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 20 hydrogen bonds found > hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A restrict > cross 12 hydrogen bonds found > hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 20 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal > true showDist true Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal > true showDist true Atom specifier selects no atoms > ~hbonds > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal > true showDist true Atom specifier selects no atoms > addh #1.1/A Summary of feedback from adding hydrogens to cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1 --- notes | No usable SEQRES records for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb (#1.1) chain A; guessing termini instead Chain-initial residues that are actual N termini: cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1/A THR 254 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1/A LEU 293 36 hydrogen bonds cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.1/A LEU 293 is not terminus, removing H atom from 'C' 291 hydrogens added > addh #1.B/A Expected a keyword > addh #1.2/A Summary of feedback from adding hydrogens to cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb #1.2 --- notes | Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: 2 hydrogen bonds 31 hydrogens added > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) reveal > true showDist true Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) Atom specifier selects no atoms > hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 20 hydrogen bonds found Could not find virtual screen for QCocoaScreen(0x600000d3ca50, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 > hbonds #1.1/A:260,261,267,268,269,271,272,286,289,290,293 #1.2/A 20 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius > 2 Atom specifier selects no atoms > ~hbonds > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius > 2 Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius > 10 Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius > 10 reveal true Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & 1.2/A) radius > 10 reveal t Expected a keyword > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293 & #1.2/A) radius > 10 reveal true Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293@H & #1.2/A) > radius 10 reveal true Atom specifier selects no atoms > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@H 11 atoms, 11 residues, 1 model selected > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@CA 11 atoms, 11 residues, 1 model selected > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@N 11 atoms, 11 residues, 1 model selected > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@H,CA 22 atoms, 11 residues, 1 model selected > select #1.1/A:260,261,267,268,269,271,272,286,289,290,293@H 11 atoms, 11 residues, 1 model selected > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293@H & #1.2/A@H) > radius 10 reveal true Atom specifier selects no atoms > select #1.2/A@H Nothing selected > select #1.2@H Nothing selected > select #1.2/A 89 atoms, 90 bonds, 1 residue, 1 model selected > select #1.2/A@HC 1 atom, 1 residue, 1 model selected > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_3.-5.6.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette tokyo 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > select #1.2/A@H Nothing selected > select H 13 atoms, 1 residue, 1 model selected > select @H Nothing selected > select H 13 atoms, 1 residue, 1 model selected > select clear > select H 13 atoms, 1 residue, 1 model selected > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293@H & H) radius 10 > reveal true Atom specifier selects no atoms > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 10 18 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 3 18 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius1 Expected a keyword > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 1 18 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 0.5 18 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) radius 0.1 18 hydrogen bonds found > hbonds (#1.1/A:260,261,267,268,269,271,272,286,289,290,293) relax true 18 hydrogen bonds found > hbonds protein relax true 38 hydrogen bonds found > hbonds (protein & #1.2/A) relax true Atom specifier selects no atoms > hbonds #1.2/A relax true 2 hydrogen bonds found > hbonds (protein & #1.2/A) relax true Atom specifier selects no atoms > hbonds (protein & #1.2/A) relax true interSubmodel true Atom specifier selects no atoms > hbonds (protein & #1.2/A) relax true interSubmodel true Atom specifier selects no atoms > hbonds (protein #1.2/A) relax true interSubmodel true Expected a keyword > hbonds (protein,#1.2/A) relax true interSubmodel true Expected a keyword > hbonds relax true interSubmodel true 48 hydrogen bonds found > hbonds relax true interSubmodel true intraModel false 8 hydrogen bonds found > hbonds relax false interSubmodel true intraModel false 5 hydrogen bonds found > hbonds relax true interSubmodel true intraModel false 8 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 1 10 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 1 angleSlop 30 12 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30 33 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 20 22 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30 33 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 30 28 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 20 20 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 25 24 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 20 22 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30 33 hydrogen bonds found > close > runscript > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/viridis_colormaps.py New colormaps: `inferno`, `magma`, `plasma`, `viridis`, `cividis`, `turbo`, `sunset`, `burg`, `tealrose`, `tokyo`, `araucaria` Default colormap for `rainbow` set to 'turbo' To unpatch, run `runscript viridis_colormaps.py --reset_defaults` > open > /Users/APCamargo-M55/Downloads/hydrolases_anlysis/CW_7/cw_7_Structure2D_COMPOUND_CID_118984439_out_2.-5.0.complex.pdb Chain information for cw_7_Structure2D_COMPOUND_CID_118984439_out_2.-5.0.complex.pdb --- Chain | Description 1.1/A | No description available > set bgColor white > show surfaces > lighting soft intensity 0.1 > graphics silhouettes true width 2 color #363644 depthJump 0.05 > color bfactor protein palette tokyo 308 atoms, 40 residues, 1 surfaces, atom bfactor range 0.81 to 4.32 > surface smooth #1 factor 0.6 > transparency 80 target s > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30 33 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30 25 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3 angleSlop 25 22 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30 25 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 30 30 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30 25 hydrogen bonds found > hide surfaces > show surfaces > hide surfaces > show surfaces > hbonds interSubmodel true intraModel false distSlop 3.5 angleSlop 30 30 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 3 angleSlop 30 25 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 2 angleSlop 30 10 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 2.5 angleSlop 30 15 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 2.75 angleSlop 30 19 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 30 33 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 20 24 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 15 18 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 10 17 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 5 12 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4.5 angleSlop 5 13 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 5 angleSlop 5 13 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 7 angleSlop 5 23 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 6 angleSlop 5 19 hydrogen bonds found > hbonds interSubmodel true intraModel false distSlop 4 angleSlop 5 12 hydrogen bonds found ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle Could not find virtual screen for QCocoaScreen(0x600002e000b0, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 Could not find virtual screen for QCocoaScreen(0x600002e000b0, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 Could not find virtual screen for QCocoaScreen(0x600002e000b0, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 Could not find virtual screen for QCocoaScreen(0x600002e000b0, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Could not find virtual screen for QCocoaScreen(0x600002e000b0, ""ASUS VG289"", QRect(0,0 1920x1080), dpr=2, displayId=4128833, ) with displayId 4128833 [Repeated 3 time(s)] OpenGL version: 4.1 ATI-5.2.4 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0) OS Loader Version: 580~1053 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 49 days, 4 hours, 17 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX