id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9839 Crash in garbage collection during new object allocation chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.4-arm64-arm-64bit ChimeraX Version: 1.7.dev202309190305 (2023-09-19 03:05:58 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00000002c21cb000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001f8b01e00 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 150 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 150 in __iter__ File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 945 in _atomspec_attr_filter File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 992 in _atomspec_filter_atom File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 910 in atomspec_filter File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 568 in _filter_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 550 in find_selected_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 561 in find_selected_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 561 in find_selected_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 626 in _add_model_parts File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 606 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 444 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 993 in find_matches File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 990 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1080 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1100 in evaluate File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 1298 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 890 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2488 in _parse_arg File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2629 in _process_positional_arguments File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2853 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 38 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/manager.py"", line 88 in execute File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/builtin.py"", line 49 in run_preset File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/__init__.py"", line 44 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py"", line 1291 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py"", line 386 in run_provider File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/manager.py"", line 60 in cb File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/cmd.py"", line 71 in run_preset File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/preset_mgr/cmd.py"", line 50 in preset_cmd File 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""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1063 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, charset_normalizer.md, PIL._imaging, 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ballscale 0.1; size > stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10 > position cofr; color ##~num_residues cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #10000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps UCSF ChimeraX version: 1.7.dev202309190305 (2023-09-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/alexandre/Documents/Novalix/TGR5-Krios- > Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb Summary of feedback from opening /Users/alexandre/Documents/Novalix/TGR5-Krios- Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb --- warnings | Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54 1 3 Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87 1 3 Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99 1 3 Start residue of secondary structure not found: HELIX 27 27 PRO N 111 ASP N 113 1 3 Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N 30 0 8 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (45 ) Cannot find LINK/SSBOND residue CYS (122 ) Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > windowsize 800 800 > set bgColor white > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > style stick Changed 8939 atom styles > hide atoms > show cartoons > color #1 #E7E6E6 > graphics silhouettes true > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color > #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127 > #FFC000 > dssp > select /A:328 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 172 atoms, 175 bonds, 20 residues, 1 model selected > select up 1092 atoms, 1118 bonds, 131 residues, 1 model selected > color #1/A:38-54,39-51,269-275,271-275,276-281 #FF0000 > color #1/A:101-108,168-176,229-239,233-239,238-251,240-245,345-352 #ED7D31 > slect /A Unknown command: slect /A > select /A 2756 atoms, 2812 bonds, 3 pseudobonds, 337 residues, 2 models selected > select /A:11 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:12 5 atoms, 4 bonds, 1 residue, 1 model selected > color #1/A:68-79,181-190 #FFC000 > color #1/G:29-37 FFC000 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/G:29-37 #FFC000 > color #1 #E7E6E6 > graphics silhouettes true > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color #1/A:358-370 #ED7D31 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color #1/A:19-25,202-216,358-372 #ED7D31 > color > #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127 > #FFC000 > color #1/A:11-36,19-30,191-197,252-258 #FFC000 > color #1/G: #FFC000 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/B:114-121 #FFC000 > color #1/N:109-125 #FF0000 > color #1/A:19-25,202-216,358-372 #ED7D31 > color #1/N:96-106,95-107,107-115,115-125 #ED7D31 > color #1/B:114-121 #FFC000 > color #1/N:22-34,51-65,109-115,109-134 #FFC000 > color #1/A:1-10 #00B050 > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color #1/A:1-10,159-160,319-321,340-344 #00B050 > select /B 2603 atoms, 2650 bonds, 340 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > close session > open /Users/alexandre/Documents/Novalix/TGR5-Krios- > Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb Summary of feedback from opening /Users/alexandre/Documents/Novalix/TGR5-Krios- Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb --- warnings | Start residue of secondary structure not found: HELIX 18 18 SER B 12 ALA B 34 1 23 Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42 1 3 End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1 3 Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B 140 1 3 Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54 1 3 Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87 1 3 Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99 1 3 1 messages similar to the above omitted Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62 0 Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73 0 Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B 93 0 Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B 104 0 Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B 115 0 18 messages similar to the above omitted End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B 319 0 Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B 330 0 Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B 341 0 Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B 350 0 Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N 30 0 Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N 48 0 7 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (45 ) Cannot find LINK/SSBOND residue CYS (122 ) Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > windowsize 800 800 > set bgColor white > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > style stick Changed 8939 atom styles > hide atoms > show cartoons > color #1 #E7E6E6 > graphics silhouettes true > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color #1/A:1-10,159-160,319-321,340-344 #00B050 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color #1/A:358-370 #FF0000 > color #1/N:109-125 #FF0000 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color #1/A:19-25,202-216,358-372 #ED7D31 > color #1/N:96-106,95-107,107-115,115-125 #ED7D31 > color > #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127 > #FFC000 > color #1/A:11-36,19-30,191-197,252-258 #FFC000 > color #1/B:114-121 #FFC000 > color #1/N:22-34,51-65,109-115,109-134 #FFC000 > dssp > color #1/B:114-121 #FFC000 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color #1/A:358-370 #FF0000 > color #1/N:109-125 #FF0000 > color #1/A:1-10,159-160,319-321,340-344 #00B050 > color #1/B:1-4,169-172,253-255 #00B050 > color #1/G:1-2,40, #00B050 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/G:1-2,40 #00B050 > ui tool show ""Show Sequence Viewer"" > sequence chain /N Alignment identifier is 1/N > color #1/N:66-67 #00B050 > open /Users/alexandre/Documents/Novalix/TGR5-Krios- > Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb Summary of feedback from opening /Users/alexandre/Documents/Novalix/TGR5-Krios- Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb --- warnings | Start residue of secondary structure not found: HELIX 18 18 SER B 12 ALA B 34 1 23 Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42 1 3 End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1 3 Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B 140 1 3 Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54 1 3 Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87 1 3 Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99 1 3 1 messages similar to the above omitted Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62 0 Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73 0 Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B 93 0 Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B 104 0 Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B 115 0 18 messages similar to the above omitted End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B 319 0 Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B 330 0 Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B 341 0 Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B 350 0 Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N 30 0 Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N 48 0 7 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (45 ) Cannot find LINK/SSBOND residue CYS (122 ) Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > windowsize 800 800 > set bgColor white > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > style stick Changed 17878 atom styles > hide atoms > show cartoons > color #1 #E7E6E6 > graphics silhouettes true > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color #1/A:1-10,159-160,319-321,340-344 #00B050 > color #1/B:1-4,169-172,253-255 #00B050 > color #1/G:1-2,40, #00B050 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/N:66-67 #00B050 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color #1/A:358-370 #FF0000 > color #1/N:109-125 #FF0000 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color #1/A:19-25,202-216,358-372 #ED7D31 > color #1/N:96-106,95-107,107-115,115-125 #ED7D31 > color > #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127 > #FFC000 > color #1/A:11-36,19-30,191-197,252-258 #FFC000 > color #1/B:114-121 #FFC000 > color #1/N:22-34,51-65,109-115,109-134 #FFC000 > close session > open /Users/alexandre/Documents/Novalix/TGR5-Krios- > Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb Summary of feedback from opening /Users/alexandre/Documents/Novalix/TGR5-Krios- Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb --- warnings | Start residue of secondary structure not found: HELIX 18 18 SER B 12 ALA B 34 1 23 Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42 1 3 End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1 3 Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B 140 1 3 Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54 1 3 Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87 1 3 Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99 1 3 1 messages similar to the above omitted Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62 0 Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73 0 Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B 93 0 Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B 104 0 Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B 115 0 18 messages similar to the above omitted End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B 319 0 Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B 330 0 Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B 341 0 Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B 350 0 Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N 30 0 Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N 48 0 7 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (45 ) Cannot find LINK/SSBOND residue CYS (122 ) Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #1 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > windowsize 800 800 > set bgColor white > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > style stick Changed 8939 atom styles > hide atoms > show cartoons > color #1 #E7E6E6 > graphics silhouettes true > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color #1/A:1-10,159-160,319-321,340-344 #00B050 > color #1/B:1-4,169-172,253-255 #00B050 > color #1/G:1-2,40, #00B050 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/N:66-67 #00B050 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color #1/A:358-370 #FF0000 > color #1/N:109-125 #FF0000 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color #1/A:19-25,202-216,358-372 #ED7D31 > color #1/N:96-106,95-107,107-115,115-125 #ED7D31 > color > #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127 > #FFC000 > color #1/A:11-36,19-30,191-197,252-258 #FFC000 > color #1/B:114-121 #FFC000 > color #1/N:22-34,51-65,109-115,109-134 #FFC000 > dssp > color #1/A:1-10,159-160,319-321,340-344,372-387 #00B050 > select /B 2603 atoms, 2650 bonds, 340 residues, 1 model selected > select /B:340 9 atoms, 8 bonds, 1 residue, 1 model selected > select /N:134 Nothing selected > show surfaces > color #1/R #177792 surfaces > color #1/A #c0cc0e surfaces > color #1/N #02abd1 surfaces > color #1/B #79ae2b surfaces > color #1/G #ebdf00 surfaces > transparency #1 85 surfaces > transparency #1 90 surfaces > graphics silhouettes false > graphics silhouettes true > lighting flat > color #1/R blue surfaces > color #1/A Crim s Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/A crimson surfaces > color #1/N plum surfaces > color #1/G violet surfaces > color #1/G purple surfaces > color #1/B brown surfaces > color #1/B sadlebrown s Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/B sadle s Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/B sandybrown surfaces > transparency #1 90 surfaces > transparency #1 95 surfaces > view matrix camera > -0.30054,0.20526,0.93142,199.65,-0.95274,-0.10985,-0.28321,92.179,0.044186,-0.97252,0.22857,128.79 > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > lighting full > lighting soft > lighting simple > windowsize 800 800 > set bgColor white > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > style stick Changed 8939 atom styles > hide atoms > show cartoons > color #1 #E7E6E6 > graphics silhouettes true > color > #1/R:41-57,75-86,97-99,106-111,128-130,138-141,199-214,233-235,246-249,287-302 > #00B050 > color #1/A:1-10,159-160,319-321,340-344,372-387 #00B050 > color #1/B:1-4,169-172,253-255 #00B050 > color #1/G:1-2,40, #00B050 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1/N:66-67 #00B050 > color > #1/R:266-286,277-286,267-286,269-286,237-245,266-273,274-286,272-286,224-231,66-74 > #FF0000 > color #1/A:358-370 #FF0000 > color #1/N:109-125 #FF0000 > color > #1/R:88-96,87-96,69-74,66-71,88-94,190-198,89-96,159-167,225-232,188-198,155-156,224-232,156-166,64-71,63-71,156-167,64-74, > 35-40,184-189,155-167,168-173,168-174,112-125,218-223,112-127,175-183,225-231 > #ED7D31 > color #1/A:19-25,202-216,358-372 #ED7D31 > color #1/N:96-106,95-107,107-115,115-125 #ED7D31 > color > #1/R:170-174,215-223,176-184,172-183,176-183,170-175,59-68,142-154,280-286,100-104,131-137,142-155,113-125,172-182,237-242,249-262,114-127 > #FFC000 > color #1/A:11-36,19-30,191-197,252-258 #FFC000 > color #1/B:114-121 #FFC000 > color #1/N:22-34,51-65,109-115,109-134 #FFC000 > save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.1.png > width 1600 supersample 3 transparentBackground true > view matrix camera > -0.30054,0.20526,0.93142,199.65,-0.95274,-0.10985,-0.28321,92.179,0.044186,-0.97252,0.22857,128.79 > save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-2.1.png > width 1600 supersample 3 transparentBackground true > hide surfaces > save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.2.png > width 1600 supersample 3 transparentBackground true > save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.3.png > width 1600 supersample 3 transparentBackground true > view matrix camera > -0.80318,0.34259,-0.48736,-15.845,0.50974,-0.028167,-0.85987,-104.25,-0.30831,-0.93906,-0.15201,73.245 > style stick Changed 8939 atom styles > save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.3.png > width 1600 supersample 3 transparentBackground true > turn y -1 90 > save /Users/alexandre/Documents/Novalix/TGR5-Krios-Mai/Figures/Image-1.3.png > width 1600 supersample 3 transparentBackground true > show atoms > hide cartoons > hide atoms > open /Users/alexandre/Documents/Novalix/TGR5-Krios- > Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb Summary of feedback from opening /Users/alexandre/Documents/Novalix/TGR5-Krios- Mai/pdb/TGR5-WithFlexDomaine-210623_refined-mod.pdb --- warnings | Start residue of secondary structure not found: HELIX 18 18 SER B 12 ALA B 34 1 23 Start residue of secondary structure not found: HELIX 19 19 LEU B 40 GLN B 42 1 3 End residue of secondary structure not found: HELIX 20 20 ILE B 43 ASN B 45 1 3 Start residue of secondary structure not found: HELIX 21 21 THR B 138 GLU B 140 1 3 Start residue of secondary structure not found: HELIX 24 24 PHE N 52 ASN N 54 1 3 Start residue of secondary structure not found: HELIX 25 25 GLY N 85 VAL N 87 1 3 Start residue of secondary structure not found: HELIX 26 26 ASN N 97 LYS N 99 1 3 1 messages similar to the above omitted Start residue of secondary structure not found: SHEET 7 7 7 ARG B 56 ARG B 62 0 Start residue of secondary structure not found: SHEET 8 8 8 ILE B 68 TRP B 73 0 Start residue of secondary structure not found: SHEET 10 1010 LYS B 88 ASP B 93 0 Start residue of secondary structure not found: SHEET 11 1111 ASN B 98 PRO B 104 0 Start residue of secondary structure not found: SHEET 12 1212 VAL B 110 TYR B 115 0 18 messages similar to the above omitted End residue of secondary structure not found: SHEET 31 3131 ARG B 314 ALA B 319 0 Start residue of secondary structure not found: SHEET 32 3232 VAL B 325 VAL B 330 0 Start residue of secondary structure not found: SHEET 33 3333 VAL B 337 SER B 341 0 Start residue of secondary structure not found: SHEET 34 3434 PHE B 345 ASN B 350 0 Start residue of secondary structure not found: SHEET 35 3535 GLN N 26 SER N 30 0 Start residue of secondary structure not found: SHEET 36 3636 LEU N 41 SER N 48 0 7 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (45 ) Cannot find LINK/SSBOND residue CYS (122 ) Chain information for TGR5-WithFlexDomaine-210623_refined-mod.pdb #2 --- Chain | Description A | No description available B | No description available G | No description available N | No description available R | No description available > hide atoms > select add #2 8939 atoms, 9136 bonds, 3 pseudobonds, 1140 residues, 2 models selected > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals ===== Log before crash end ===== Log: > camera ortho > cofr centerOfView > volume defaultvalues limitVoxelCount false voxelLimitForPlane > 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true Saved volume settings > mousemode rightMode clip > mousemode alt rightMode ""contour level"" > mousemode alt leftMode ""translate selected models"" > mousemode shift leftMode ""rotate selected models"" > alias cofron cofr centerofview showpivot true > alias cofroff cofr centerofview showpivot false > alias symclip cofr centerofview; clip near -$1 far $1 position cofr > alias cootmode surface cap false; surface style solid; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; transparency 70; cofr centerofview; clip near -10 far 10 > position cofr; color ##~num_residues cornflower blue > alias cootmode_mesh surface cap false; surface style mesh; lighting flat; > graphics silhouettes false; style stick; ~rib; color ##num_residues gold; > color byhet ; disp; ~disp @H*; style solvent ball; size ballscale 0.1; size > stickradius 0.07; cofr centerofview; clip near -10 far 10 position cofr; > color ##~num_residues #3d60ffff; transparency 50 > alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; > disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp > ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1 > alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp > @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius > 0.1 > alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000; > marker #10000 position cofr; sel ~sel; surface zone ##~num_residues > nearAtoms sel distance 15; close #10000 > alias map_unsphere surface unzone ##~num_residues > alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5; > lighting soft > alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker > #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel > distance 0; close #10000 > alias showmaps surface unzone ##~num_residues > alias caps_off surface cap false > alias caps_on surface cap true > alias selbetween ks ri > alias helix setattr $1 res is_helix true > alias strand setattr $1 res is_strand true > alias coil setattr $1 res is_strand false; setattr $1 res is_helix false > buttonpanel Shortcuts rows 3 columns 4 > buttonpanel Shortcuts add Vol_Viewer command ""tool show 'Volume Viewer'"" > buttonpanel Shortcuts add Model_Panel command ""tool show Models"" > buttonpanel Shortcuts add Log command ""tool show Log"" > buttonpanel Shortcuts add default_disp command default_mol_display > buttonpanel Shortcuts add map_sphere command map_sphere_15 > buttonpanel Shortcuts add map_unsphere command map_unsphere > buttonpanel Shortcuts add cofron command cofron > buttonpanel Shortcuts add cofroff command cofroff > buttonpanel Shortcuts add cootmode command cootmode > buttonpanel Shortcuts add mark_cofr command ""marker #10000 position cofr"" > buttonpanel Shortcuts add hidemaps command hidemaps > buttonpanel Shortcuts add showmaps command showmaps UCSF ChimeraX version: 1.7.dev202309190305 (2023-09-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple 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: MacBookPro18,1 Model Number: MK193FN/A Chip: Apple M1 Pro Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4 (22F66) Kernel Version: Darwin 22.5.0 Time since boot: 71 jours, 17 heures et 13 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.0 Babel: 2.12.1 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: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.47.2 ChimeraX-AtomicLibrary: 10.0.8 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: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309190305 ChimeraX-CoreFormats: 1.1 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: 1.1.2 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: 1.2.1 ChimeraX-Log: 1.1.5 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 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: 1.5.12 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: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 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: 1.31.5 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 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: 5.3.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.6 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 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: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 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: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 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: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core can't reproduce Tom Goddard all ChimeraX