id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15267 Scipy: Symbol not found, macOS 11 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-11.7.9-arm64-arm-64bit ChimeraX Version: 1.9.dev202405202355 (2024-05-20 23:55:30 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.9.dev202405202355 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/avabostjancic/Downloads/SP-15-Bostjancic-celotna-struktura- > cartoon.cxs Log from Mon May 20 19:42:07 2024UCSF ChimeraX version: 1.8rc202405102050 (2024-05-10) © 2016-2024 Regents of the University of California. All rights reserved. > open C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/SP-15-Bostjancic- > celotna-struktura.cxs Log from Mon May 20 19:32:43 2024 Startup Messages --- notes | available bundle cache has not been initialized yet Database-fetch provider 'redo' in bundle Map specified unknown data format 'MTZ' UCSF ChimeraX version: 1.8rc202405102050 (2024-05-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open C:/Users/janhv/Downloads/8qv2.cif 8qv2.cif title: Structure of the native y-Tubulin Ring Complex (yTuRC) capping microtubule minus ends at the spindle pole body [more info...] Chain information for 8qv2.cif #1 --- Chain | Description | UniProt Ab Ac Ad Ae Af Ag Ah Ai Aj Ak Al Am An Ao Ap Aq Ar | Tubulin alpha-1 chain | TBA1_YEAST 1-447 Bb Bc Bd Be Bf Bg Bh Bi Bj Bk Bl Bm Bn Bo Bp Bq Br | Tubulin beta chain | A0A6A5PXT5_YEASX 1-457 C E G I K M O | Spindle pole body component | A0A8H4C290_YEASX 1-823 D F H J L N P | Spindle pole body component | A0A8H4BVY6_YEASX 1-846 Sa Sb Sc Sd Se Sf Sg Sh Si Sj Sk Sl Sm Sn | Spindle pole body component 110 | A0A8H8UNQ3_YEASX 1-944 Ua Ub Uc Ud Ue Uf Ug Uh Ui Uj Uk Ul Um Un | Unkown protein | a b c d e f g h i j k l m n | Tubulin gamma chain | A0A8H4BZN3_YEASX 1-473 Non-standard residues in 8qv2.cif #1 --- GDP — guanosine-5'-diphosphate GTP — guanosine-5'-triphosphate > sequence chain > #1/Ab#1/Ac#1/Ad#1/Ae#1/Af#1/Ag#1/Ah#1/Ai#1/Aj#1/Ak#1/Al#1/Am#1/An#1/Ao#1/Ap#1/Aq#1/Ar Alignment identifier is 1 > select clear > select > #1/Ab#1/Ac#1/Ad#1/Ae#1/Af#1/Ag#1/Ah#1/Ai#1/Aj#1/Ak#1/Al#1/Am#1/An#1/Ao#1/Ap#1/Aq#1/Ar 58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected > select clear > select > #1/Ab#1/Ac#1/Ad#1/Ae#1/Af#1/Ag#1/Ah#1/Ai#1/Aj#1/Ak#1/Al#1/Am#1/An#1/Ao#1/Ap#1/Aq#1/Ar 58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected > color (#!1 & sel) #689ed9ff > color (#!1 & sel) #3bd995ff > color (#!1 & sel) #a78ef5ff > color (#!1 & sel) #3bd995ff > color (#!1 & sel) #a78ef5ff > select clear > select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br 56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected > color (#!1 & sel) #3bd9cbff > color (#!1 & sel) #eb8ef5ff > select clear > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > select /Sa/Sb/Sc/Sd/Se/Sf/Sg/Sh/Si/Sj/Sk/Sl/Sm/Sn 6933 atoms, 6978 bonds, 825 residues, 1 model selected > select /a/b/c/d/e/f/g/h/i/j/k/l/m/n 49343 atoms, 50397 bonds, 7 pseudobonds, 6265 residues, 2 models selected > color (#!1 & sel) #3bb4d9ff > color (#!1 & sel) #f58ecaff > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #3b83d9ff > color (#!1 & sel) #f58e8eff > select clear > select /a/b/c/d/e/f/g/h/i/j/k/l/m/n 49343 atoms, 50397 bonds, 7 pseudobonds, 6265 residues, 2 models selected > color (#!1 & sel) #a78ef5ff > color (#!1 & sel) #aa7df0ff > select clear > select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br 56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected > select /Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar 58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected > color (#!1 & sel) #eb8ef5ff > color (#!1 & sel) #f07da1ff > select clear > select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br 56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected > color (#!1 & sel) #f58ecaff > color (#!1 & sel) #cf7df0ff > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #3b83d9ff > color (#!1 & sel) #98554fff > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #3b83d9ff > color (#!1 & sel) #d2766dff > select clear [Repeated 1 time(s)] > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > color sel #ffffffff > color sel #9ef07dff > select clear [Repeated 1 time(s)] > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #d2766dff > color (#!1 & sel) #847df0ff > select clear > select /Ab/Ac/Ad/Ae/Af/Ag/Ah/Ai/Aj/Ak/Al/Am/An/Ao/Ap/Aq/Ar 58320 atoms, 59608 bonds, 1 pseudobond, 7463 residues, 2 models selected > color (#!1 & sel) #a78ef5ff > color (#!1 & sel) #ecc3f0ff > select clear > select /Bb/Bc/Bd/Be/Bf/Bg/Bh/Bi/Bj/Bk/Bl/Bm/Bn/Bo/Bp/Bq/Br 56735 atoms, 57974 bonds, 1 pseudobond, 7246 residues, 2 models selected > color (#!1 & sel) #f07da1ff > color (#!1 & sel) #e673f0ff > select clear > select /a/b/c/d/e/f/g/h/i/j/k/l/m/n 49343 atoms, 50397 bonds, 7 pseudobonds, 6265 residues, 2 models selected > color (#!1 & sel) #f58ecaff > color (#!1 & sel) #9473f0ff > select clear [Repeated 1 time(s)] > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > style sel ball Changed 4277 atom styles > cartoon sel > style sel sphere Changed 4277 atom styles > select clear > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > hide sel target a > cartoon hide sel > surface sel > surface hidePatches (#!1 & sel) > style (#!1 & sel) ringFill thick Changed 861 residue ring styles > show (#!1 & sel) target ab > select clear > undo [Repeated 9 time(s)] > select clear > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > cartoon hide (#!1 & sel) > style (#!1 & sel) ringFill thick Changed 861 residue ring styles > show (#!1 & sel) target ab > style (#!1 & sel) stick Changed 4277 atom styles > style (#!1 & sel) ringFill thick Changed 861 residue ring styles > style (#!1 & sel) ball Changed 4277 atom styles > style (#!1 & sel) ringFill thin Changed 861 residue ring styles > style (#!1 & sel) ringFill thick Changed 861 residue ring styles > show (#!1 & sel) target ab > hide (#!1 & sel) target a > style (#!1 & sel) sphere Changed 4277 atom styles > show (#!1 & sel) target ab > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #d2766dff > color (#!1 & sel) #f0ae73ff > select clear > select /Sa/Sb/Sc/Sd/Se/Sf/Sg/Sh/Si/Sj/Sk/Sl/Sm/Sn 6933 atoms, 6978 bonds, 825 residues, 1 model selected > color sel #3b51d9ff > color sel #f0d173ff > color sel #d2766dff > color sel #f0ae73ff > color sel #f0d173ff > select clear > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > color (#!1 & sel) #74c4dbff > color (#!1 & sel) #73f0d2ff > select clear > save test.png format png width 3840 height 2160 supersample 9 > transparentBackground true > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > color (#!1 & sel) #b29a05ff > color (#!1 & sel) #73bcf0ff > select clear > save test1.png format png width 3840 height 2160 supersample 9 > transparentBackground true > save C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/barvetest1.cxs > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #acb935ff > color (#!1 & sel) #f073b8ff > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #68d97fff > color (#!1 & sel) #bd73f0ff > color (#!1 & sel) #f073b8ff > select clear > select /Sa/Sb/Sc/Sd/Se/Sf/Sg/Sh/Si/Sj/Sk/Sl/Sm/Sn 6933 atoms, 6978 bonds, 825 residues, 1 model selected > color sel #bd73f0ff > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #689ed9ff > color (#!1 & sel) #ffbae0ff > select clear > color #fab6ddff > color #936b82ff > color #90697fff > color #664a5aff > undo [Repeated 3 time(s)] > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #ffbae0ff > color (#!1 & sel) #fdb9dfff > color (#!1 & sel) #cf97b7ff > color (#!1 & sel) #ce96b6ff > color (#!1 & sel) #c28eabff > color (#!1 & sel) #be8ba8ff > color (#!1 & sel) #846075ff > color (#!1 & sel) #866276ff > color (#!1 & sel) #ac7d98ff > color (#!1 & sel) #ad7e99ff > color (#!1 & sel) #c18daaff > select clear > lighting full > lighting soft > lighting full > lighting simple > lighting soft > lighting full > save test2.png format png width 3840 height 2160 supersample 9 > transparentBackground true > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > color (#!1 & sel) #ffffffff > color (#!1 & sel) #73bcf0ff > color (#!1 & sel) #74c4dbff > color (#!1 & sel) #73bcf0ff > color (#!1 & sel) #ffffffff > color (#!1 & sel) #c3f0e5ff > color (#!1 & sel) #73f07eff > color (#!1 & sel) #acf073ff > color (#!1 & sel) #ffffffff > color (#!1 & sel) #acf073ff > select clear > save test3.png format png width 3840 height 2160 supersample 9 > transparentBackground true > select clear > select /C/D/E/F/G/H/I/J/K/L/M/N/O/P 79592 atoms, 81219 bonds, 43 pseudobonds, 9582 residues, 2 models selected > color (#!1 & sel) #ffffffff > undo > color (#!1 & sel) #dee9adff > color (#!1 & sel) #bd8aa6ff > color (#!1 & sel) #e8a9ccff > color (#!1 & sel) #e2a5c6ff > color (#!1 & sel) #efafd2ff > color (#!1 & sel) #ffddffff > color (#!1 & sel) #ffffffff > color (#!1 & sel) #ddeeeeff > color (#!1 & sel) #dee9adff > color (#!1 & sel) #dee9afff > color (#!1 & sel) #ddeeeeff > color (#!1 & sel) #ffbae0ff > color (#!1 & sel) #fab6ddff > color (#!1 & sel) #cf97b7ff > select clear > select /Ua/Ub/Uc/Ud/Ue/Uf/Ug/Uh/Ui/Uj/Uk/Ul/Um/Un 4277 atoms, 4256 bonds, 861 residues, 1 model selected > cartoon style (#!1 & sel) modeHelix tube sides 20 > cartoon (#!1 & sel) > hide (#!1 & sel) target a > cartoon style (#!1 & sel & coil) xsection oval > cartoon style (#!1 & sel) xsection barbell modeHelix default > cartoon style (#!1 & sel) xsection rectangle modeHelix default > cartoon style (#!1 & sel) xsection oval modeHelix default > cartoon hide (#!1 & sel) > show (#!1 & sel) target ab > select clear > select /C 5778 atoms, 5890 bonds, 5 pseudobonds, 693 residues, 2 models selected > select /C/E 11625 atoms, 11851 bonds, 10 pseudobonds, 1394 residues, 2 models selected > select /C/E/G/I/K/M/O 40860 atoms, 41656 bonds, 35 pseudobonds, 4899 residues, 2 models selected > color (#!1 & sel) #d198b8ff > color (#!1 & sel) #c690afff > color (#!1 & sel) #d39abaff > color (#!1 & sel) #c892b1ff > color (#!1 & sel) #c690afff > color (#!1 & sel) #a37790ff > color (#!1 & sel) #a57892ff > color (#!1 & sel) #79586bff > color (#!1 & sel) #ffbae0ff > color (#!1 & sel) #fdb9dfff > color (#!1 & sel) #836074ff > color (#!1 & sel) #846075ff > color (#!1 & sel) #6b4e5eff > select clear > save SP-S15-Bostjancic-celotna-struktura.png format png width 3840 height > 2160 supersample 9 transparentBackground true [Repeated 1 time(s)] > select 255200 atoms, 260432 bonds, 52 pseudobonds, 32242 residues, 2 models selected > style (#!1 & sel) ringFill thick Changed 32242 residue ring styles > select clear > select 255200 atoms, 260432 bonds, 52 pseudobonds, 32242 residues, 2 models selected > hide (#!1 & sel) target a > show (#!1 & sel) target ab > select clear > save C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/SP-15-Bostjancic- > celotna-struktura.cxs ——— End of log from Mon May 20 19:32:43 2024 ——— opened ChimeraX session > select 255200 atoms, 260432 bonds, 52 pseudobonds, 32242 residues, 2 models selected > hide (#!1 & sel) target a > cartoon (#!1 & sel) > cartoon style (#!1 & sel) modeHelix tube sides 20 > select clear > save C:/Users/janhv/Documents/Šola/FKKT/Struktura/Ava/SP-15-Bostjancic- > celotna-struktura-cartoon.cxs ——— End of log from Mon May 20 19:42:07 2024 ——— opened ChimeraX session Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 1906, in _update_graphics_if_needed s[i].update_graphics_if_needed() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 357, in update_graphics_if_needed self._create_ribbon_graphics() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/structure.py"", line 667, in _create_ribbon_graphics ribbons_drawing.compute_ribbons(self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/ribbon.py"", line 630, in compute_ribbons _make_ribbon_graphics(structure, self) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/ribbon.py"", line 142, in _make_ribbon_graphics centers = _arc_helix_geometry(coords, xs_mgr, displays, start, end, geometry) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/ribbon.py"", line 1010, in _arc_helix_geometry hc = HelixCylinder(coords[start:end]) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py"", line 198, in __init__ self._try_curved() File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py"", line 403, in _try_curved self._curved_optimize(c_center, c_axis, c_radius) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py"", line 447, in _curved_optimize opt = OptArc(self.coords, center, axis, major_radius) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/sse.py"", line 96, in __init__ from scipy.optimize import minimize File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/__init__.py"", line 413, in from ._optimize import * File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_optimize.py"", line 40, in from ._numdiff import approx_derivative File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_numdiff.py"", line 8, in from ._group_columns import group_dense, group_sparse ImportError: dlopen(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not found: __ZTTNSt3__119basic_ostringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE Referenced from: /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built for Mac OS X 12.0) Expected in: /usr/lib/libc++.1.dylib in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_group_columns.cpython-311-darwin.so Error processing trigger ""graphics update"": ImportError: dlopen(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_group_columns.cpython-311-darwin.so, 2): Symbol not found: __ZTTNSt3__119basic_ostringstreamIcNS_11char_traitsIcEENS_9allocatorIcEEEE Referenced from: /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_group_columns.cpython-311-darwin.so (which was built for Mac OS X 12.0) Expected in: /usr/lib/libc++.1.dylib in /Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_group_columns.cpython-311-darwin.so File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/scipy/optimize/_numdiff.py"", line 8, in from ._group_columns import group_dense, group_sparse See log for complete Python traceback. OpenGL version: 4.1 Metal - 71.7.1 OpenGL renderer: Apple M1 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 Air Model Identifier: MacBookAir10,1 Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8422.141.2 OS Loader Version: 6723.140.2 Software: System Software Overview: System Version: macOS 11.7.9 (20G1426) Kernel Version: Darwin 20.6.0 Time since boot: 9:36 Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Resolution: 2880 x 1800 UI Looks like: 1440 x 900 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal 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: 1.6.3 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: 1.58 ChimeraX-AtomicLibrary: 14.0.5 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: 1.2.4 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: 1.0.4 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: 1.9.dev202405202355 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: 1.2.3 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: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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: 1.13.4 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: 3.0.4 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: 1.4.1 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: 4.51.0 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: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 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: 3.0.43 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: 2.32.0 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 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Core limitation Greg Couch all ChimeraX