id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15985 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.5.1-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 Current thread 0x0000000204460600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py"", line 353 in raw_decode File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/decoder.py"", line 337 in decode File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py"", line 346 in loads File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/json/__init__.py"", line 293 in load File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 990 in read_json_pae_matrix File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 977 in read_pae_matrix File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 847 in __init__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 1188 in alphafold_pae File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 209 in _open_pae_from_file File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 185 in _open_pae File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/alphafold/pae.py"", line 172 in _choose_pae_file 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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, chimerax.pdb_lib._load_libs, 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'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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 > open > /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/EPS_depoKP36_c3_trimer.pdb > format pdb Chain information for EPS_depoKP36_c3_trimer.pdb #1 --- Chain | Description A | No description available B C | No description available > close > open /Users/joe/Downloads/cryosparc_P4_J110_007_volume_map.mrc format mrc Opened cryosparc_P4_J110_007_volume_map.mrc as #1, grid size 336,336,336, pixel 1.05, shown at level 0.063, step 2, values float32 > volume #1 step 1 > volume #1 level 0.3609 > lighting soft > volume #1 level 0.3331 > volume #1 level 0.48 > close > open > /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/apo_depoKP36_c3_chainA_WIP.pdb > format pdb Chain information for apo_depoKP36_c3_chainA_WIP.pdb #1 --- Chain | Description A | No description available > select carboxylate 189 atoms, 126 bonds, 63 residues, 1 model selected > show sel atoms > select /A:622@OD2 1 atom, 1 residue, 1 model selected > select add /A:588@OE2 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance /A:622@OD2 /A:588@OE2 Distance between /A ASP 622 OD2 and GLU 588 OE2: 5.031Å > select clear > open > /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J114_005_volume_map_C3_apo.mrc > format mrc Opened cryosparc_P4_J114_005_volume_map_C3_apo.mrc as #3, grid size 336,336,336, pixel 1.05, shown at level 0.0535, step 2, values float32 > volume #3 step 1 > volume #3 level 0.6347 > close #3 > open > /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J162_006_volume_map_C3_EPS.mrc Opened cryosparc_P4_J162_006_volume_map_C3_EPS.mrc as #3, grid size 336,336,336, pixel 1.1, shown at level 0.0215, step 2, values float32 > view > volume #3 step 1 > volume #3 level 0.2975 > fitmap #1 inMap #3 Fit molecule apo_depoKP36_c3_chainA_WIP.pdb (#1) to map cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) using 10542 atoms average map value = 0.1534, steps = 148 shifted from previous position = 12.8 rotated from previous position = 8.73 degrees atoms outside contour = 8536, contour level = 0.29746 Position of apo_depoKP36_c3_chainA_WIP.pdb (#1) relative to cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) coordinates: Matrix rotation and translation 0.99643987 -0.04902652 0.06858560 2.18549632 0.03995467 0.99098216 0.12789829 -15.89245310 -0.07423752 -0.12470264 0.98941298 39.12785882 Axis -0.83224298 0.47055859 0.29316588 Axis point 0.00000000 295.66083173 153.10255089 Rotation angle (degrees) 8.72888423 Shift along axis 2.17375905 > close #2 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.8452,0.53228,0.048089,-79.751,-0.53439,0.84295,0.062189,117.4,-0.0074347,-0.078261,0.99691,16.612 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.8452,0.53228,0.048089,-80.344,-0.53439,0.84295,0.062189,122.31,-0.0074347,-0.078261,0.99691,16.946 > fitmap #1 inMap #3 Fit molecule apo_depoKP36_c3_chainA_WIP.pdb (#1) to map cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) using 10542 atoms average map value = 0.1789, steps = 76 shifted from previous position = 3.39 rotated from previous position = 3.97 degrees atoms outside contour = 8004, contour level = 0.29746 Position of apo_depoKP36_c3_chainA_WIP.pdb (#1) relative to cryosparc_P4_J162_006_volume_map_C3_EPS.mrc (#3) coordinates: Matrix rotation and translation 0.83496129 -0.55016356 -0.01263759 137.26469351 0.55023176 0.83500836 0.00245695 -59.16449587 0.00920077 -0.00900506 0.99991712 0.55666186 Axis -0.01041365 -0.01984094 0.99974891 Axis point 167.28392309 199.32164329 0.00000000 Rotation angle (degrees) 33.39005620 Shift along axis 0.30097429 > close #3 > close > open > /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/EPS_depoKP36_c3_chainA.pdb Chain information for EPS_depoKP36_c3_chainA.pdb #1 --- Chain | Description A | No description available > open > /Users/joe/projects/depoKP36/depoKP36_cryoEM_models/cryosparc_P4_J162_006_volume_map_C3_EPS.mrc Opened cryosparc_P4_J162_006_volume_map_C3_EPS.mrc as #2, grid size 336,336,336, pixel 1.1, shown at level 0.0215, step 2, values float32 > volume #2 step 1 > volume #2 level 0.3089 > select carboxylate 192 atoms, 128 bonds, 64 residues, 1 model selected > volume #2 level 0.5575 > volume #2 level 0.2496 > show sel atoms > hide #!2 models > close #2 > close > open /Users/joe/projects/depoKP36/tomo/capsid/run_class001.mrc Opened run_class001.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level 0.0149, step 1, values float32 > volume #1 level 0.01135 > volume #1 level 0.01111 > volume #1 level 0.01002 > volume #1 level 0.002496 > volume #1 level 0.00204 > volume #1 level 0.006986 > volume #1 style image region 0,0,49,99,99,49 step 1 showOutlineBox true > ui mousemode right ""tape measure"" > marker segment #2 position 745.8,293.3,558.6 toPosition 382.4,843,558.6 > color yellow radius 2.85 label 659 labelHeight 65.9 labelColor yellow > marker segment #2 position 875.1,608.6,558.6 toPosition 261.4,536.2,558.6 > color yellow radius 2.85 label 617.9 labelHeight 61.79 labelColor yellow > close #2 > close > open /Users/joe/projects/depoKP36/tomo/capsid/capsid_i2.mrc Opened capsid_i2.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level 0.0159, step 1, values float32 > volume #1 level 0.01131 > close #1 > open /Users/joe/projects/depoKP36/tomo/capsid/capsid_i4.mrc Opened capsid_i4.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level 0.015, step 1, values float32 > volume #1 level 0.01281 > volume #1 level 0.01093 > volume #1 style image region 0,0,49,99,99,49 step 1 showOutlineBox true > volume #1 level -0.000816,0 level 0.01606,0.8 level 0.01675,1 > volume #1 level -0.000816,0 level 0.01302,0.5206 level 0.01675,1 > volume #1 level -0.001256,0 level 0.01302,0.5206 level 0.01675,1 > volume #1 level -0.002116,0.01471 level 0.01302,0.5206 level 0.01675,1 > volume #1 region 0,0,0,99,99,99 step 1 > volume #1 style surface region 0,0,0,99,99,99 step 1 > volume #1 style image region 0,0,49,99,99,49 step 1 > ui mousemode right ""tape measure"" > marker segment #2 position 466.5,849.8,558.6 toPosition 667.2,289.3,558.6 > color yellow radius 2.85 label 595.3 labelHeight 59.53 labelColor yellow > volume #1 level -0.002116,0.01471 level 0.007361,0.9118 level 0.01675,1 > marker segment #2 position 252.3,619.4,558.6 toPosition 871,547.8,558.6 > color yellow radius 2.85 label 622.8 labelHeight 62.28 labelColor yellow > close #1 > close > open /Users/joe/projects/depoKP36/tomo/capsid/capsid_i4.mrc format mrc Opened capsid_i4.mrc as #1, grid size 100,100,100, pixel 11.4, shown at level 0.015, step 1, values float32 > volume #1 level 0.01072 > volume #1 level 0.009624 > lighting soft > lighting simple > lighting full > lighting simple > volume #1 color #73fdff > volume #1 color #fffb00 > volume #1 color #f0fe48 > volume #1 color #ffff66 > volume #1 color #ffff33 > volume #1 color #ffccff > volume #1 color #ff99ff > volume #1 color #ff99ffdc > volume #1 color #e4c099 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > ui mousemode right ""tape measure"" > volume #1 style image region 0,0,49,99,99,49 step 1 showOutlineBox true > volume #1 level -0.000816,0 level 0.01606,0.8 level 0.01675,1 > volume #1 level -0.000816,0 level 0.01474,0.8735 level 0.01675,1 > ui mousemode right ""tape measure"" > marker segment #2 position 869.5,714.7,558.6 toPosition 272.1,461.6,558.6 > color yellow radius 2.85 label 648.9 labelHeight 64.89 labelColor yellow > open > /Users/joe/Downloads/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif Chain information for fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif #3 --- Chain | Description A B C D E F | . > close #1 > close #2 > view > ui tool show ""AlphaFold Error Plot"" Must choose path to predicted aligned file > alphafold pae #3 file > /Users/joe/Downloads/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer/fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_full_data_0.json > color bfactor #3 palette alphafold 5214 atoms, 684 residues, atom bfactor range 28.8 to 97.4 > alphafold pae #3 colorDomains true > color bfactor #3 palette alphafold 5214 atoms, 684 residues, atom bfactor range 28.8 to 97.4 > save /Users/joe/projects/depoKP36/AF3_DIT_hexamer_K9L8K4.pdb relModel #3 > open 8xcg Summary of feedback from opening 8xcg fetched from pdb --- note | Fetching compressed mmCIF 8xcg from http://files.rcsb.org/download/8xcg.cif 8xcg title: Tail tip complex of bacteriophage λ in the open state [more info...] Chain information for 8xcg #1 --- Chain | Description | UniProt E K M Y e m | Tail tip protein M | TIPM_LAMBD 1-109 F J Z | Tip attachment protein J | TIPJ_LAMBD 1-1132 I P h | Tail tip assembly protein I | TIPI_LAMBD 1-223 L N f | Tail tip protein L | TIPL_LAMBD 1-232 Non-standard residues in 8xcg #1 --- SF4 — iron/sulfur cluster > view > select #1/E 884 atoms, 909 bonds, 109 residues, 1 model selected > select add #3 6098 atoms, 6243 bonds, 793 residues, 2 models selected > select add #1 31155 atoms, 31841 bonds, 11 pseudobonds, 3999 residues, 3 models selected > select subtract #1 5214 atoms, 5334 bonds, 684 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,172.62,0,1,0,37.915,0,0,1,-27.603 > view matrix models #3,1,0,0,192.6,0,1,0,62.955,0,0,1,295.35 > view matrix models #3,1,0,0,169.08,0,1,0,110.17,0,0,1,288.08 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.92049,-0.18797,0.34258,169.77,-0.24979,0.39115,0.88578,112.2,-0.3005,-0.90093,0.31309,289.12 > view matrix models > #3,0.90373,-0.23226,0.35963,169.88,-0.2376,0.42669,0.87263,112.12,-0.35612,-0.87407,0.33043,289.18 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.90373,-0.23226,0.35963,171,-0.2376,0.42669,0.87263,117.13,-0.35612,-0.87407,0.33043,288.31 > view matrix models > #3,0.90373,-0.23226,0.35963,171.51,-0.2376,0.42669,0.87263,116.65,-0.35612,-0.87407,0.33043,276.4 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.857,-0.12267,0.50051,171.55,-0.39798,0.45944,0.79406,116.76,-0.32736,-0.8797,0.34492,276.38 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.857,-0.12267,0.50051,175.26,-0.39798,0.45944,0.79406,113.44,-0.32736,-0.8797,0.34492,277.01 > hide #3 models > show #3 models > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.73207,-0.61992,-0.28244,175.4,-0.45463,-0.13583,-0.88026,112.79,0.50732,0.77282,-0.38127,272.84 > view matrix models > #3,0.78353,-0.50457,-0.36261,175.09,-0.51098,-0.19121,-0.83806,112.99,0.35352,0.84193,-0.40764,272.94 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.78353,-0.50457,-0.36261,170.72,-0.51098,-0.19121,-0.83806,112.74,0.35352,0.84193,-0.40764,272.52 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.86776,-0.43992,-0.23122,170.63,-0.36747,-0.25473,-0.89447,112.57,0.3346,0.86115,-0.38271,272.54 > align #3 toAtoms #1 Unequal number of atoms to pair, 5214 and 25941 > ui tool show Matchmaker > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8xcg, chain e (#1) with fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif, chain A (#3), sequence alignment score = 156.9 RMSD between 49 pruned atom pairs is 1.210 angstroms; (across all 104 pairs: 3.747) > matchmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8xcg, chain e (#1) with fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif, chain A (#3), sequence alignment score = 156.9 RMSD between 49 pruned atom pairs is 1.210 angstroms; (across all 104 pairs: 3.747) > select clear > color #3 #9bb7e5ff > select #1/I 412 atoms, 415 bonds, 56 residues, 1 model selected > view matrix models #1,1,0,0,0.67132,0,1,0,1.8325,0,0,1,0.90392 > undo > select #1/I#1/P#1/h 1276 atoms, 1285 bonds, 173 residues, 1 model selected > delete sel > select #1/L#1/N#1/f 5427 atoms, 5544 bonds, 11 pseudobonds, 699 residues, 2 models selected > delete sel > select #1/F#1/J#1/Z 13934 atoms, 14224 bonds, 1789 residues, 1 model selected > delete sel > show atoms > show cartoons > hide surfaces > style stick Changed 10518 atom styles > hide #!1 models > hide #3 models > open /Users/joe/projects/depoKP36/tomo/capsid/run_class001.mrc Opened run_class001.mrc as #2, grid size 512,512,512, pixel 1.9, shown at level 0.016, step 2, values float32 > volume #2 level 0.01137 > volume #2 step 1 > volume #2 step 2 > volume #2 step 4 > volume #2 level 0.01197 > volume #2 level 0.01077 > volume #2 step 1 > volume #2 level 0.00938 > volume #2 level 0.01 > close #2 > show #3 models > show #!1 models > hide #3 models > show #3 models > hide #!1 models > show #!1 models > open 8xcg 8xcg title: Tail tip complex of bacteriophage λ in the open state [more info...] Chain information for 8xcg #2 --- Chain | Description | UniProt E K M Y e m | Tail tip protein M | TIPM_LAMBD 1-109 F J Z | Tip attachment protein J | TIPJ_LAMBD 1-1132 I P h | Tail tip assembly protein I | TIPI_LAMBD 1-223 L N f | Tail tip protein L | TIPL_LAMBD 1-232 Non-standard residues in 8xcg #2 --- SF4 — iron/sulfur cluster > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > mlp #3#!1 Map values for surface ""fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_A SES surface"": minimum -25.79, mean -5.512, maximum 21.34 Map values for surface ""fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_B SES surface"": minimum -27.68, mean -5.51, maximum 22.43 Map values for surface ""fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_C SES surface"": minimum -25.85, mean -5.525, maximum 22.27 Map values for surface ""fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_D SES surface"": minimum -25.84, mean -5.476, maximum 22.31 Map values for surface ""fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_E SES surface"": minimum -27.47, mean -5.574, maximum 22.39 Map values for surface ""fold_2024_09_10_10_26_kp36_k9l8k4_putativedit_minortailprotein_hexamer_model_0.cif_F SES surface"": minimum -26.06, mean -5.532, maximum 22.14 Map values for surface ""8xcg_E SES surface"": minimum -25.76, mean -4.146, maximum 21.74 Map values for surface ""8xcg_K SES surface"": minimum -26.65, mean -3.956, maximum 24.64 Map values for surface ""8xcg_M SES surface"": minimum -24.19, mean -3.863, maximum 22.62 Map values for surface ""8xcg_Y SES surface"": minimum -25.45, mean -3.962, maximum 23.48 Map values for surface ""8xcg_e SES surface"": minimum -25.64, mean -4.067, maximum 23.15 Map values for surface ""8xcg_m SES surface"": minimum -24.43, mean -4.146, maximum 21.51 To also show corresponding color key, enter the above mlp command and add key true > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select add #1 5304 atoms, 5454 bonds, 654 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.75795,0.075882,-0.64788,473.4,-0.02055,-0.9955,-0.092553,250.76,-0.65199,-0.056837,0.7561,186.05 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.75795,0.075882,-0.64788,455.53,-0.02055,-0.9955,-0.092553,287.21,-0.65199,-0.056837,0.7561,178.52 > view matrix models > #1,-0.75795,0.075882,-0.64788,447.76,-0.02055,-0.9955,-0.092553,301.59,-0.65199,-0.056837,0.7561,177.86 > select subtract #1 6 models selected > select add #3 5214 atoms, 5334 bonds, 684 residues, 1 model selected > view matrix models > #3,-0.52059,0.62126,0.58568,191.68,0.82141,0.17726,0.54209,76.755,0.23297,0.76329,-0.60259,276.38 > ui mousemode right ""move picked models"" > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.63935,0.61509,0.46141,191.82,0.71483,0.25438,0.6514,76.989,0.2833,0.74629,-0.60232,276.29 > view matrix models > #3,-0.77615,-0.09986,0.6226,193.3,0.62934,-0.061352,0.77471,77.751,-0.039165,0.99311,0.11046,277.38 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.77615,-0.09986,0.6226,179.55,0.62934,-0.061352,0.77471,70.549,-0.039165,0.99311,0.11046,263.73 > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > color #!1,3 byhetero > style #!1,3 stick Changed 10518 atom styles > style #!1,3 stick Changed 10518 atom styles > hide #!1,3 surfaces > open > /Users/joe/Downloads/fold_2024_09_05_15_54_depokp36_timer_k9l8k6/fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif > format mmcif Chain information for fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif #4 --- Chain | Description A B C | . > select add #4 19830 atoms, 20169 bonds, 2649 residues, 1 model selected > view matrix models #4,1,0,0,40.808,0,1,0,-63.945,0,0,1,273.36 > view matrix models #4,1,0,0,29.037,0,1,0,-109.82,0,0,1,268.85 > view matrix models #4,1,0,0,21.452,0,1,0,-129.81,0,0,1,254.06 > show #!2 models > select #1/E#1/K#1/M#1/Y#1/e#1/m#2/E#2/K#2/M#2/Y#2/e#2/m 10608 atoms, 10908 bonds, 1308 residues, 2 models selected > hide #!2 models > show #!2 models > hide #!1 models > hide #!3 models > select add #4 30438 atoms, 31077 bonds, 3957 residues, 9 models selected > select subtract #1 25134 atoms, 25623 bonds, 3303 residues, 8 models selected > select add #2 45771 atoms, 46676 bonds, 11 pseudobonds, 5964 residues, 3 models selected > select subtract #2 19830 atoms, 20169 bonds, 2649 residues, 1 model selected > view matrix models #4,1,0,0,30.157,0,1,0,-76.398,0,0,1,183.37 > view matrix models #4,1,0,0,20.936,0,1,0,-92.156,0,0,1,179.05 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.76952,-0.28861,-0.56968,39.566,-0.50702,0.26626,-0.81978,-48.455,0.38828,0.91968,0.05856,135.75 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.76952,-0.28861,-0.56968,95.996,-0.50702,0.26626,-0.81978,84.257,0.38828,0.91968,0.05856,3.0853 > view matrix models > #4,0.76952,-0.28861,-0.56968,94.028,-0.50702,0.26626,-0.81978,78.69,0.38828,0.91968,0.05856,-12.449 > view matrix models > #4,0.76952,-0.28861,-0.56968,110.59,-0.50702,0.26626,-0.81978,100.36,0.38828,0.91968,0.05856,-37.238 > view matrix models > #4,0.76952,-0.28861,-0.56968,110.35,-0.50702,0.26626,-0.81978,98.024,0.38828,0.91968,0.05856,-35.298 > view matrix models > #4,0.76952,-0.28861,-0.56968,138.64,-0.50702,0.26626,-0.81978,91.507,0.38828,0.91968,0.05856,63.353 > view matrix models > #4,0.76952,-0.28861,-0.56968,154.03,-0.50702,0.26626,-0.81978,26.604,0.38828,0.91968,0.05856,78.909 > color sel byhetero > show sel atoms > hide sel surfaces > select subtract #4 Nothing selected > select add #1 5304 atoms, 5454 bonds, 654 residues, 1 model selected > select subtract #1 6 models selected > select add #2 25941 atoms, 26507 bonds, 11 pseudobonds, 3315 residues, 2 models selected > hide sel surfaces > show sel cartoons > show sel atoms > hide sel surfaces > color sel byhetero > style sel stick Changed 25941 atom styles > hide sel cartoons > show sel cartoons > hide sel atoms > select clear > select add #4 19830 atoms, 20169 bonds, 2649 residues, 1 model selected > hide sel cartoons > show sel cartoons > hide sel atoms > view matrix models > #4,0.76952,-0.28861,-0.56968,140.8,-0.50702,0.26626,-0.81978,107.28,0.38828,0.91968,0.05856,69.66 > view matrix models > #4,0.76952,-0.28861,-0.56968,85.031,-0.50702,0.26626,-0.81978,106.51,0.38828,0.91968,0.05856,60.857 > view matrix models > #4,0.76952,-0.28861,-0.56968,67.457,-0.50702,0.26626,-0.81978,83.42,0.38828,0.91968,0.05856,70.268 > view matrix models > #4,0.76952,-0.28861,-0.56968,67.645,-0.50702,0.26626,-0.81978,83.001,0.38828,0.91968,0.05856,68.577 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.65719,-0.52346,-0.54231,79.503,-0.38198,0.38896,-0.83833,74.652,0.64977,0.75809,0.055673,65.741 > view matrix models > #4,-0.53735,-0.62149,-0.57009,121.89,0.47385,0.3367,-0.81369,48.574,0.69765,-0.70738,0.11357,115.54 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.53735,-0.62149,-0.57009,96.446,0.47385,0.3367,-0.81369,66.635,0.69765,-0.70738,0.11357,255.27 > view matrix models > #4,-0.53735,-0.62149,-0.57009,218.73,0.47385,0.3367,-0.81369,-3.4628,0.69765,-0.70738,0.11357,258.64 > view matrix models > #4,-0.53735,-0.62149,-0.57009,290.5,0.47385,0.3367,-0.81369,-45.878,0.69765,-0.70738,0.11357,260.74 > view matrix models > #4,-0.53735,-0.62149,-0.57009,293.1,0.47385,0.3367,-0.81369,-41.329,0.69765,-0.70738,0.11357,260.22 > view matrix models > #4,-0.53735,-0.62149,-0.57009,294.18,0.47385,0.3367,-0.81369,-37.074,0.69765,-0.70738,0.11357,274.14 > view matrix models > #4,-0.53735,-0.62149,-0.57009,294.11,0.47385,0.3367,-0.81369,-38.282,0.69765,-0.70738,0.11357,273.69 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.30586,-0.7008,-0.64446,289.48,0.33699,0.5534,-0.7617,-41.525,0.89044,-0.45015,0.066904,258.46 > view matrix models > #4,-0.10574,-0.70948,-0.69675,283.36,0.18705,0.67398,-0.71468,-40.958,0.97664,-0.2059,0.061438,247.09 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.10574,-0.70948,-0.69675,302.55,0.18705,0.67398,-0.71468,-71.648,0.97664,-0.2059,0.061438,216.03 > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A #4/B #4/C Alignment identifier is 1 > select #4/A-C:83 21 atoms, 18 bonds, 3 residues, 1 model selected > select #4/A-C:83-883 18054 atoms, 18372 bonds, 2403 residues, 1 model selected > hide sel > delete sel > select add #4 1776 atoms, 1794 bonds, 246 residues, 1 model selected > view matrix models > #4,-0.10574,-0.70948,-0.69675,307.19,0.18705,0.67398,-0.71468,-74.228,0.97664,-0.2059,0.061438,149.96 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.43661,-0.68043,-0.58854,346.12,-0.25088,0.72033,-0.64667,-23.694,0.86396,-0.13469,-0.48521,155.47 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.43661,-0.68043,-0.58854,312.84,-0.25088,0.72033,-0.64667,20.614,0.86396,-0.13469,-0.48521,165.67 > view matrix models > #4,-0.43661,-0.68043,-0.58854,298.2,-0.25088,0.72033,-0.64667,5.8736,0.86396,-0.13469,-0.48521,151.88 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.25513,-0.74018,-0.62213,283.24,-0.051475,0.65291,-0.75568,-10.154,0.96554,-0.16077,-0.20468,141.77 > view matrix models > #4,-0.45333,-0.72507,-0.51843,306.81,-0.031048,0.59412,-0.80378,-4.0825,0.8908,-0.34828,-0.29184,179.36 > view matrix models > #4,-0.62166,-0.62306,-0.4747,313.81,-0.31454,0.7536,-0.57719,9.1874,0.71736,-0.20951,-0.66446,182.53 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.62166,-0.62306,-0.4747,314.34,-0.31454,0.7536,-0.57719,10.839,0.71736,-0.20951,-0.66446,180.99 > view matrix models > #4,-0.62166,-0.62306,-0.4747,314.31,-0.31454,0.7536,-0.57719,10.608,0.71736,-0.20951,-0.66446,181.44 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.50152,-0.69513,-0.51505,309.22,-0.11804,0.64475,-0.75523,1.2077,0.85705,-0.31797,-0.40541,178.48 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.50152,-0.69513,-0.51505,309.29,-0.11804,0.64475,-0.75523,0.9308,0.85705,-0.31797,-0.40541,179.64 > view matrix models > #4,-0.50152,-0.69513,-0.51505,336.89,-0.11804,0.64475,-0.75523,-53.466,0.85705,-0.31797,-0.40541,189.54 > view matrix models > #4,-0.50152,-0.69513,-0.51505,337.71,-0.11804,0.64475,-0.75523,-52.535,0.85705,-0.31797,-0.40541,190.84 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.081959,-0.94989,-0.30165,298.11,-0.78748,-0.24724,0.56458,163.69,-0.61086,0.19128,-0.76828,309.47 > view matrix models > #4,0.017377,-0.8854,-0.46451,297.46,-0.80951,-0.28514,0.51322,172.27,-0.58685,0.36711,-0.72169,280.35 > view matrix models > #4,-0.52609,-0.83545,-0.1589,360.8,-0.23508,-0.036701,0.97128,59.303,-0.81729,0.54834,-0.17709,282.76 > view matrix models > #4,-0.083086,-0.87271,0.48111,306.72,0.090771,0.47415,0.87575,-58.418,-0.9924,0.11643,0.039822,368.81 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.083086,-0.87271,0.48111,276.56,0.090771,0.47415,0.87575,-6.0315,-0.9924,0.11643,0.039822,366.92 > view matrix models > #4,-0.083086,-0.87271,0.48111,280.69,0.090771,0.47415,0.87575,1.4425,-0.9924,0.11643,0.039822,359.44 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.43527,-0.82742,0.35486,320.54,-0.55889,0.55734,0.61401,75.078,-0.70582,0.068935,-0.70503,330.42 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.43527,-0.82742,0.35486,317.48,-0.55889,0.55734,0.61401,69.216,-0.70582,0.068935,-0.70503,326.81 > view matrix models > #4,-0.43527,-0.82742,0.35486,316.76,-0.55889,0.55734,0.61401,70.486,-0.70582,0.068935,-0.70503,326.38 > view matrix models > #4,-0.43527,-0.82742,0.35486,318.06,-0.55889,0.55734,0.61401,69.067,-0.70582,0.068935,-0.70503,327.34 > select #2/Z 4650 atoms, 4747 bonds, 597 residues, 1 model selected > ui tool show Matchmaker > matchmaker #4 to #2 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8xcg, chain Z (#2) with fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif, chain A (#4), sequence alignment score = 71.7 RMSD between 11 pruned atom pairs is 1.051 angstroms; (across all 80 pairs: 10.961) > matchmaker #4 to #2 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 8xcg, chain Z (#2) with fold_2024_09_05_15_54_depokp36_timer_k9l8k6_model_0.cif, chain A (#4), sequence alignment score = 71.7 RMSD between 11 pruned atom pairs is 1.051 angstroms; (across all 80 pairs: 10.961) > select clear > select #4/A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select #4/A-C 1776 atoms, 1794 bonds, 246 residues, 1 model selected > save /Users/joe/projects/depoKP36/depoKP36_nterm_AF3.pdb models #4 > selectedOnly true > lighting simple > lighting soft > lighting simple > select #2/N 1809 atoms, 1848 bonds, 4 pseudobonds, 233 residues, 2 models selected > select #2/Z 4650 atoms, 4747 bonds, 597 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/F #2/J #2/Z Alignment identifier is 1 > select clear > select #2/F,J,Z 13934 atoms, 14224 bonds, 1789 residues, 1 model selected > select #2/F,Z:11-12/J:10-12 61 atoms, 61 bonds, 7 residues, 1 model selected > select #2/F,J,Z 13934 atoms, 14224 bonds, 1789 residues, 1 model selected > select clear > select #2/J:10 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/F,Z:11-28/J:10-28 430 atoms, 430 bonds, 55 residues, 1 model selected > select > #2/F,J,Z:21-30,35-38,45-46,64-69,84-94,111-118,135-143,146-155,163-170,179-183,197-206,216-223,235-236,238-241,243-246,249-250,255-256,264-267,311-313,319-321,327-329,348-353,356-361,368-372,386-389,398-405,411-418,430-434,460-463,478-482,492-499,504-507,520-524,530-539,543-546,558-562,570-578,584-590 5298 atoms, 5289 bonds, 663 residues, 1 model selected > select #2/F,J,Z:594-595 54 atoms, 51 bonds, 6 residues, 1 model selected > select #2/F,J,Z:594-603 216 atoms, 213 bonds, 30 residues, 1 model selected > select #2/F,J,Z:557-558 39 atoms, 36 bonds, 6 residues, 1 model selected > select #2/F,J,Z:557-573 450 atoms, 459 bonds, 51 residues, 1 model selected > select #2/F,J,Z:225 27 atoms, 24 bonds, 3 residues, 1 model selected > select #2/F,J,Z:225-488 6321 atoms, 6495 bonds, 792 residues, 1 model selected > select > #2/F,J,Z:21-30,35-38,45-46,64-69,84-94,111-118,135-143,146-155,163-170,179-183,197-206,216-223,235-236,238-241,243-246,249-250,255-256,264-267,311-313,319-321,327-329,348-353,356-361,368-372,386-389,398-405,411-418,430-434,460-463,478-482,492-499,504-507,520-524,530-539,543-546,558-562,570-578,584-590 5298 atoms, 5289 bonds, 663 residues, 1 model selected > select #2/F,J,Z:11-12 54 atoms, 54 bonds, 6 residues, 1 model selected > select #2/F,J,Z:11-223 4917 atoms, 4992 bonds, 639 residues, 1 model selected > select #2/F,J,Z:492 12 atoms, 9 bonds, 3 residues, 1 model selected > select #2/F,J,Z:492-591 2274 atoms, 2301 bonds, 300 residues, 1 model selected > select clear > select #2/F,J,Z:21 21 atoms, 18 bonds, 3 residues, 1 model selected > select #2/F,J,Z:21-224 4695 atoms, 4767 bonds, 612 residues, 1 model selected > select #2/F,J,Z:492 12 atoms, 9 bonds, 3 residues, 1 model selected > select #2/F:492-604/J,Z:492-606 2600 atoms, 2635 bonds, 343 residues, 1 model selected > select #2/F,J,Z:477-478 45 atoms, 42 bonds, 6 residues, 1 model selected > select #2/F,J,Z:477-603 2868 atoms, 2901 bonds, 381 residues, 1 model selected > open /Users/joe/Downloads/txtfile/12082/12082.xml Opened 12082.xml > close > set bgColor black > open > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_0.cif Chain information for fold_2024_09_20_myadm_trail_trimer_model_0.cif #1 --- Chain | Description A B C | . D | . > open > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_1.cif Chain information for fold_2024_09_20_myadm_trail_trimer_model_1.cif #2 --- Chain | Description A B C | . D | . > open > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_2.cif Chain information for fold_2024_09_20_myadm_trail_trimer_model_2.cif #3 --- Chain | Description A B C | . D | . > open > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_3.cif Chain information for fold_2024_09_20_myadm_trail_trimer_model_3.cif #4 --- Chain | Description A B C | . D | . > open > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_model_4.cif Chain information for fold_2024_09_20_myadm_trail_trimer_model_4.cif #5 --- Chain | Description A B C | . D | . > hide #2 models > hide #3 models > hide #4 models > hide #5 models > select #1/A 2442 atoms, 2500 bonds, 304 residues, 1 model selected > select clear > select #1/D 2484 atoms, 2553 bonds, 322 residues, 1 model selected > color sel cornflower blue > select clear > ui tool show Contacts > contacts resSeparation 5 intraMol false ignoreHiddenModels true color > #ff9300 1038 contacts > close #6 > ui tool show Distances > ui tool show Contacts > contacts distanceOnly 4.0 resSeparation 5 intraMol false ignoreHiddenModels > true color #ff9300 1387 distances > close #6 > select #1/A 2442 atoms, 2500 bonds, 304 residues, 1 model selected > color sel mauve Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel violet > select #1/B 2442 atoms, 2500 bonds, 304 residues, 1 model selected > color sel palegreen pink Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel pink > select #1/C 2442 atoms, 2500 bonds, 304 residues, 1 model selected > color sel fushia Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > ui tool show ""Color Actions"" > color sel plum > select clear Drag select of 17 residues > show sel atoms Drag select of 3 atoms, 15 residues, 2 bonds > show sel atoms Drag select of 5 residues > show sel atoms Drag select of 24 atoms, 16 residues, 23 bonds > show sel atoms > select clear Drag select of 2 atoms, 6 residues, 1 bonds > show sel atoms > select #1/B:150 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #1/B:151 12 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > select clear > color #1 byhetero > select #1/B:272 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/B:271 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #1/B:270 21 atoms, 18 bonds, 3 residues, 1 model selected > select add #1/B:153 31 atoms, 28 bonds, 4 residues, 1 model selected > select add #1/B:152 35 atoms, 31 bonds, 5 residues, 1 model selected > show sel atoms > select #1/B:151@CA 1 atom, 1 residue, 1 model selected > select clear > select #1/D:266 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #1/D:267 21 atoms, 20 bonds, 2 residues, 1 model selected > select #1/C:201 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/D:266 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #1 models > show #1 models > show #2 models > hide #2 models > hide #1 models > show #2 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_1.json > color bfactor #2 palette alphafold 9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6 > hide #2 models > show #1 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json > color bfactor #2 palette alphafold 9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6 > show #2 models > hide #2 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #2 file > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json > color bfactor #2 palette alphafold 9810 atoms, 1234 residues, atom bfactor range 13.5 to 92.6 > show #2 models > hide #2 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #1 file > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_0.json > color bfactor #1 palette alphafold 9810 atoms, 1234 residues, atom bfactor range 14.7 to 92.7 > hide #1 models > show #3 models > ui tool show ""AlphaFold Error Plot"" > alphafold pae #3 file > /Users/joe/Downloads/fold_2024_09_20_myadm_trail_trimer/fold_2024_09_20_myadm_trail_trimer_full_data_2.json ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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 OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M2 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: Mac Model Identifier: Mac14,7 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 8 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 7 days 19:04 Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes 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-Clipper: 0.22.4 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-ISOLDE: 1.7.1 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