id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19882 ChimeraX bug report submission tomas.pelletier1@… "{{{ The following bug report has been submitted: Platform: macOS-26.3-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x000000020af43080 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/whole.grains/Desktop/16-33a_modelling/head/RealSpaceRefine_2/head_fit_real_space_refined_002.pdb Chain information for head_fit_real_space_refined_002.pdb #1 --- Chain | Description A | No description available > open /Users/whole.grains/Desktop/16-33a_modelling/head/head_sharpened.ccp4 Opened head_sharpened.ccp4 as #2, grid size 600,600,600, pixel 0.59, shown at level 0.00073, step 4, values float32 > volume #2 level 0.01325 > open > /Users/whole.grains/Downloads/cryosparc_P1_J1786_006_volume_mask_refine.mrc Opened cryosparc_P1_J1786_006_volume_mask_refine.mrc as #3, grid size 600,600,600, pixel 0.59, shown at level 5e-05, step 4, values float32 > volume flip #3 Opened cryosparc_P1_J1786_006_volume_mask_refine.mrc z flip as #4, grid size 600,600,600, pixel 0.59, shown at step 1, values float32 > close #3 > volume #4 level 0.632 > volume #4 color #ffffb20d > volume #4 color #bbbbbb > volume #4 color #bbbbbb03 > open > /Users/whole.grains/Desktop/16-33a_modelling/body/RealSpaceRefine_12/body_refined_update_real_space_refined_012_01.pdb Chain information for body_refined_update_real_space_refined_012_01.pdb #3 --- Chain | Description A | No description available B | No description available > dssp > open ""/Users/whole.grains/Desktop/16-33a_modelling/body/Sharpened > maps/full_map_sharpened.ccp4"" Opened full_map_sharpened.ccp4 as #5, grid size 600,600,600, pixel 0.59, shown at level 0.00263, step 4, values float32 > open /Users/whole.grains/Desktop/16-33a_modelling/body/mask.mrc Opened mask.mrc as #6, grid size 600,600,600, pixel 0.59, shown at level 0.0956, step 4, values float32 > volume #6 level 0.5118 > volume #6 color #bbbbbb > volume #6 color #bbbbbb03 > volume #5 color #c3c3c3 > color #5 #c3c3c3ff models > color #6 #cacacaff models > volume #6 color #cacaca0d > volume #4 color #bbbbbb0d > volume #5 level 0.01148 > select add #3 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 2 models selected > select add #5 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 4 models selected > select add #6 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 6 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,1,0,0,-47.09,0,1,0,-98.577,0,0,1,5.131,#5,1,0,0,-47.09,0,1,0,-98.577,0,0,1,5.131,#6,1,0,0,-47.09,0,1,0,-98.577,0,0,1,5.131 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.67233,-0.42216,-0.60808,193.31,-0.73887,-0.43289,-0.51641,385.6,-0.045223,0.79649,-0.60296,141.22,#5,0.67233,-0.42216,-0.60808,193.31,-0.73887,-0.43289,-0.51641,385.6,-0.045223,0.79649,-0.60296,141.22,#6,0.67233,-0.42216,-0.60808,193.31,-0.73887,-0.43289,-0.51641,385.6,-0.045223,0.79649,-0.60296,141.22 > view matrix models > #3,0.55947,-0.54199,-0.62708,238.62,-0.82862,-0.34808,-0.43844,372.25,0.019357,0.76491,-0.64385,142.75,#5,0.55947,-0.54199,-0.62708,238.62,-0.82862,-0.34808,-0.43844,372.25,0.019357,0.76491,-0.64385,142.75,#6,0.55947,-0.54199,-0.62708,238.62,-0.82862,-0.34808,-0.43844,372.25,0.019357,0.76491,-0.64385,142.75 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.55947,-0.54199,-0.62708,232.7,-0.82862,-0.34808,-0.43844,373.81,0.019357,0.76491,-0.64385,187.19,#5,0.55947,-0.54199,-0.62708,232.7,-0.82862,-0.34808,-0.43844,373.81,0.019357,0.76491,-0.64385,187.19,#6,0.55947,-0.54199,-0.62708,232.7,-0.82862,-0.34808,-0.43844,373.81,0.019357,0.76491,-0.64385,187.19 > view matrix models > #3,0.55947,-0.54199,-0.62708,228.08,-0.82862,-0.34808,-0.43844,387.78,0.019357,0.76491,-0.64385,185.4,#5,0.55947,-0.54199,-0.62708,228.08,-0.82862,-0.34808,-0.43844,387.78,0.019357,0.76491,-0.64385,185.4,#6,0.55947,-0.54199,-0.62708,228.08,-0.82862,-0.34808,-0.43844,387.78,0.019357,0.76491,-0.64385,185.4 > view matrix models > #3,0.55947,-0.54199,-0.62708,229.43,-0.82862,-0.34808,-0.43844,389.14,0.019357,0.76491,-0.64385,184.99,#5,0.55947,-0.54199,-0.62708,229.43,-0.82862,-0.34808,-0.43844,389.14,0.019357,0.76491,-0.64385,184.99,#6,0.55947,-0.54199,-0.62708,229.43,-0.82862,-0.34808,-0.43844,389.14,0.019357,0.76491,-0.64385,184.99 > open ""/Users/whole.grains/Desktop/PDB and > MRC/fold_vps33a_vps16/fold_vps33a_vps16_model_0.cif"" Chain information for fold_vps33a_vps16_model_0.cif #7 --- Chain | Description A | . B | . Computing secondary structure > select subtract #3 4 models selected > select subtract #5 2 models selected > select subtract #6 Nothing selected > select add #7 11424 atoms, 11657 bonds, 1435 residues, 1 model selected > view matrix models #7,1,0,0,111.09,0,1,0,0.97154,0,0,1,1.9178 > view matrix models #7,1,0,0,128,0,1,0,146.37,0,0,1,98.093 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.095869,0.9635,0.24995,128.21,-0.90859,0.017854,-0.41732,142.78,-0.40655,-0.26711,0.87371,96.849 > view matrix models > #7,-0.43931,0.89781,0.030766,128.34,-0.87019,-0.4168,-0.26277,140.41,-0.22309,-0.14221,0.96437,97.26 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.43931,0.89781,0.030766,117.59,-0.87019,-0.4168,-0.26277,154.81,-0.22309,-0.14221,0.96437,191.09 > view matrix models > #7,-0.43931,0.89781,0.030766,141.81,-0.87019,-0.4168,-0.26277,124.28,-0.22309,-0.14221,0.96437,196.1 > view matrix models > #7,-0.43931,0.89781,0.030766,136.37,-0.87019,-0.4168,-0.26277,128.21,-0.22309,-0.14221,0.96437,203.2 > matchmaker #7 to #4 No 'to' model specified > view matrix models > #7,-0.43931,0.89781,0.030766,135.82,-0.87019,-0.4168,-0.26277,125.98,-0.22309,-0.14221,0.96437,209.09 > matchmaker #7 to #3 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 body_refined_update_real_space_refined_012_01.pdb, chain B (#3) with fold_vps33a_vps16_model_0.cif, chain B (#7), sequence alignment score = 2750 RMSD between 462 pruned atom pairs is 1.114 angstroms; (across all 566 pairs: 1.625) > select subtract #7 Nothing selected > select add #1 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected > select add #2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #4 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected > view matrix models > #1,1,0,0,-1.0779,0,1,0,3.1558,0,0,1,13.734,#2,1,0,0,-1.0779,0,1,0,3.1558,0,0,1,13.734,#4,1,0,0,-1.0779,0,1,0,3.1558,0,0,1,13.734 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.54767,0.043536,-0.83556,216.12,0.12617,0.98293,0.13391,-39.307,0.82712,-0.17876,0.53283,-17.32,#2,0.54767,0.043536,-0.83556,216.12,0.12617,0.98293,0.13391,-39.307,0.82712,-0.17876,0.53283,-17.32,#4,0.54767,0.043536,-0.83556,216.12,0.12617,0.98293,0.13391,-39.307,0.82712,-0.17876,0.53283,-17.32 > view matrix models > #1,0.37601,0.37658,-0.84665,190.11,-0.21291,0.92436,0.31658,-2.1319,0.90182,0.061224,0.42775,-53.576,#2,0.37601,0.37658,-0.84665,190.11,-0.21291,0.92436,0.31658,-2.1319,0.90182,0.061224,0.42775,-53.576,#4,0.37601,0.37658,-0.84665,190.11,-0.21291,0.92436,0.31658,-2.1319,0.90182,0.061224,0.42775,-53.576 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.37601,0.37658,-0.84665,206.09,-0.21291,0.92436,0.31658,-33.67,0.90182,0.061224,0.42775,-1.5982,#2,0.37601,0.37658,-0.84665,206.09,-0.21291,0.92436,0.31658,-33.67,0.90182,0.061224,0.42775,-1.5982,#4,0.37601,0.37658,-0.84665,206.09,-0.21291,0.92436,0.31658,-33.67,0.90182,0.061224,0.42775,-1.5982 > hide #!2 models > view matrix models > #1,0.37601,0.37658,-0.84665,206.11,-0.21291,0.92436,0.31658,-34.084,0.90182,0.061224,0.42775,-3.949,#2,0.37601,0.37658,-0.84665,206.11,-0.21291,0.92436,0.31658,-34.084,0.90182,0.061224,0.42775,-3.949,#4,0.37601,0.37658,-0.84665,206.11,-0.21291,0.92436,0.31658,-34.084,0.90182,0.061224,0.42775,-3.949 > view matrix models > #1,0.37601,0.37658,-0.84665,213.05,-0.21291,0.92436,0.31658,-37.733,0.90182,0.061224,0.42775,-21.783,#2,0.37601,0.37658,-0.84665,213.05,-0.21291,0.92436,0.31658,-37.733,0.90182,0.061224,0.42775,-21.783,#4,0.37601,0.37658,-0.84665,213.05,-0.21291,0.92436,0.31658,-37.733,0.90182,0.061224,0.42775,-21.783 > view matrix models > #1,0.37601,0.37658,-0.84665,211.14,-0.21291,0.92436,0.31658,-39.986,0.90182,0.061224,0.42775,-24.759,#2,0.37601,0.37658,-0.84665,211.14,-0.21291,0.92436,0.31658,-39.986,0.90182,0.061224,0.42775,-24.759,#4,0.37601,0.37658,-0.84665,211.14,-0.21291,0.92436,0.31658,-39.986,0.90182,0.061224,0.42775,-24.759 > view matrix models > #1,0.37601,0.37658,-0.84665,208.95,-0.21291,0.92436,0.31658,-33.133,0.90182,0.061224,0.42775,-28.911,#2,0.37601,0.37658,-0.84665,208.95,-0.21291,0.92436,0.31658,-33.133,0.90182,0.061224,0.42775,-28.911,#4,0.37601,0.37658,-0.84665,208.95,-0.21291,0.92436,0.31658,-33.133,0.90182,0.061224,0.42775,-28.911 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.38108,0.48007,-0.79014,180.25,-0.35375,0.8653,0.35513,-5.1499,0.85419,0.14418,0.49957,-47.568,#2,0.38108,0.48007,-0.79014,180.25,-0.35375,0.8653,0.35513,-5.1499,0.85419,0.14418,0.49957,-47.568,#4,0.38108,0.48007,-0.79014,180.25,-0.35375,0.8653,0.35513,-5.1499,0.85419,0.14418,0.49957,-47.568 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.38108,0.48007,-0.79014,183.44,-0.35375,0.8653,0.35513,-9.5357,0.85419,0.14418,0.49957,-48.134,#2,0.38108,0.48007,-0.79014,183.44,-0.35375,0.8653,0.35513,-9.5357,0.85419,0.14418,0.49957,-48.134,#4,0.38108,0.48007,-0.79014,183.44,-0.35375,0.8653,0.35513,-9.5357,0.85419,0.14418,0.49957,-48.134 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.38776,0.44456,-0.80747,191.47,-0.28052,0.89137,0.35604,-26.942,0.87804,0.088449,0.47035,-37.508,#2,0.38776,0.44456,-0.80747,191.47,-0.28052,0.89137,0.35604,-26.942,0.87804,0.088449,0.47035,-37.508,#4,0.38776,0.44456,-0.80747,191.47,-0.28052,0.89137,0.35604,-26.942,0.87804,0.088449,0.47035,-37.508 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.92544,0.058135,-0.3744,89.441,-0.27634,0.7796,-0.56202,152.05,0.2592,0.62358,0.73754,-69.468,#2,0.92544,0.058135,-0.3744,89.441,-0.27634,0.7796,-0.56202,152.05,0.2592,0.62358,0.73754,-69.468,#4,0.92544,0.058135,-0.3744,89.441,-0.27634,0.7796,-0.56202,152.05,0.2592,0.62358,0.73754,-69.468 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.92544,0.058135,-0.3744,82.868,-0.27634,0.7796,-0.56202,161.75,0.2592,0.62358,0.73754,-67.862,#2,0.92544,0.058135,-0.3744,82.868,-0.27634,0.7796,-0.56202,161.75,0.2592,0.62358,0.73754,-67.862,#4,0.92544,0.058135,-0.3744,82.868,-0.27634,0.7796,-0.56202,161.75,0.2592,0.62358,0.73754,-67.862 > view matrix models > #1,0.92544,0.058135,-0.3744,78.773,-0.27634,0.7796,-0.56202,159.49,0.2592,0.62358,0.73754,-63.308,#2,0.92544,0.058135,-0.3744,78.773,-0.27634,0.7796,-0.56202,159.49,0.2592,0.62358,0.73754,-63.308,#4,0.92544,0.058135,-0.3744,78.773,-0.27634,0.7796,-0.56202,159.49,0.2592,0.62358,0.73754,-63.308 > view matrix models > #1,0.92544,0.058135,-0.3744,79.296,-0.27634,0.7796,-0.56202,159.12,0.2592,0.62358,0.73754,-63.465,#2,0.92544,0.058135,-0.3744,79.296,-0.27634,0.7796,-0.56202,159.12,0.2592,0.62358,0.73754,-63.465,#4,0.92544,0.058135,-0.3744,79.296,-0.27634,0.7796,-0.56202,159.12,0.2592,0.62358,0.73754,-63.465 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.92181,0.0056881,-0.3876,91.331,-0.23883,0.7959,-0.55633,148.78,0.30533,0.6054,0.73503,-67.887,#2,0.92181,0.0056881,-0.3876,91.331,-0.23883,0.7959,-0.55633,148.78,0.30533,0.6054,0.73503,-67.887,#4,0.92181,0.0056881,-0.3876,91.331,-0.23883,0.7959,-0.55633,148.78,0.30533,0.6054,0.73503,-67.887 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.92181,0.0056881,-0.3876,89.025,-0.23883,0.7959,-0.55633,150.6,0.30533,0.6054,0.73503,-67.625,#2,0.92181,0.0056881,-0.3876,89.025,-0.23883,0.7959,-0.55633,150.6,0.30533,0.6054,0.73503,-67.625,#4,0.92181,0.0056881,-0.3876,89.025,-0.23883,0.7959,-0.55633,150.6,0.30533,0.6054,0.73503,-67.625 > view matrix models > #1,0.92181,0.0056881,-0.3876,88.21,-0.23883,0.7959,-0.55633,150.43,0.30533,0.6054,0.73503,-67.116,#2,0.92181,0.0056881,-0.3876,88.21,-0.23883,0.7959,-0.55633,150.43,0.30533,0.6054,0.73503,-67.116,#4,0.92181,0.0056881,-0.3876,88.21,-0.23883,0.7959,-0.55633,150.43,0.30533,0.6054,0.73503,-67.116 > view matrix models > #1,0.92181,0.0056881,-0.3876,88.666,-0.23883,0.7959,-0.55633,150.28,0.30533,0.6054,0.73503,-67.117,#2,0.92181,0.0056881,-0.3876,88.666,-0.23883,0.7959,-0.55633,150.28,0.30533,0.6054,0.73503,-67.117,#4,0.92181,0.0056881,-0.3876,88.666,-0.23883,0.7959,-0.55633,150.28,0.30533,0.6054,0.73503,-67.117 > view matrix models > #1,0.92181,0.0056881,-0.3876,88.196,-0.23883,0.7959,-0.55633,150.08,0.30533,0.6054,0.73503,-66.71,#2,0.92181,0.0056881,-0.3876,88.196,-0.23883,0.7959,-0.55633,150.08,0.30533,0.6054,0.73503,-66.71,#4,0.92181,0.0056881,-0.3876,88.196,-0.23883,0.7959,-0.55633,150.08,0.30533,0.6054,0.73503,-66.71 > hide #7 models > show #!2 models > color #4 #bbbbbbff models > color #6 #bbbbbbff models > color #5 #bbbbbbff models > color #6 #bbbbbb0d models > color #4 #bbbbbb0d models > select subtract #1 4 models selected > select subtract #2 2 models selected > select subtract #4 Nothing selected > ui tool show Distances > hide #!5 models > hide #!2 models > ui mousemode right ""rotate selected models"" > show #7 models > hide #7 models > hide #!4 models > hide #!6 models > select clear > select #3/A:642 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:624 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & ((protein&@ca)|(nucleic&@p))) target ab > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > color sel #d3be99ff > view matrix models > #1,0.92032,0.0079164,-0.39108,88.692,-0.24283,0.79538,-0.55535,150.68,0.30666,0.60607,0.73392,-66.855 > view matrix models > #1,0.92759,0.013038,-0.37338,83.431,-0.24139,0.7837,-0.57231,155.43,0.28516,0.621,0.7301,-65.024 > view matrix models > #1,0.92437,0.006702,-0.38145,86.492,-0.23591,0.79581,-0.5577,149.84,0.29982,0.60551,0.7372,-66.171 > select #3/A:642 9 atoms, 8 bonds, 1 residue, 1 model selected > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > color sel #daabe0ff > view matrix models > #3,0.5519,-0.55109,-0.62587,232.16,-0.83336,-0.33728,-0.43789,387.96,0.030225,0.76325,-0.6454,183.65 > select #3/A:643 11 atoms, 10 bonds, 1 residue, 1 model selected Exactly two atoms must be selected! > select #3/A:642@N 1 atom, 1 residue, 1 model selected > select #1/A:624@O 1 atom, 1 residue, 1 model selected > select add #3/A:642@N 2 atoms, 2 residues, 2 models selected > distance #1/A:624@O #3/A:642@N Distance between head_fit_real_space_refined_002.pdb #1/A ASP 624 O and body_refined_update_real_space_refined_012_01.pdb #3/A GLU 642 N: 30.894Å > close #8.1 > view matrix models > #1,0.97854,-0.040619,-0.20203,50.147,-0.12705,0.653,-0.74663,194.45,0.16225,0.75627,0.63382,-49.149,#3,0.67063,-0.39856,-0.62562,187.2,-0.71611,-0.56786,-0.40587,401.25,-0.1935,0.7202,-0.66623,231.53 > close #8.1 > hide #8 models > show #8 models > select add #3 5751 atoms, 5857 bonds, 3 pseudobonds, 717 residues, 3 models selected > show sel cartoons > select add #1 10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 4 models selected > show sel atoms > hide sel atoms > select subtract #1 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 2 models selected > select subtract #3 Nothing selected > split chains Did not split head_fit_real_space_refined_002.pdb, has only one piece Split body_refined_update_real_space_refined_012_01.pdb (#3) into 2 models Split fold_vps33a_vps16_model_0.cif (#7) into 2 models Chain information for body_refined_update_real_space_refined_012_01.pdb A #3.1 --- Chain | Description A | No description available Chain information for body_refined_update_real_space_refined_012_01.pdb B #3.2 --- Chain | Description B | No description available Chain information for fold_vps33a_vps16_model_0.cif A #7.1 --- Chain | Description A | No description available Chain information for fold_vps33a_vps16_model_0.cif B #7.2 --- Chain | Description B | No description available > color #1 #edbd7bff > color #3.1 #72411cff > color #3.1 #edbd7bff > color #3.2 #72411cff > color #7.1 #72411cff > color #7.1 #c3c3c3ff > color #7.2 #c3c3c3ff > color #8 #e9c78aff models > select subtract #8 Nothing selected > hide #8 models > show #8 models Exactly two atoms must be selected! > show #7.1 models > show #7.2 models > select subtract #8 Nothing selected > select add #7.1 6663 atoms, 6804 bonds, 839 residues, 1 model selected > select add #7.2 11424 atoms, 11657 bonds, 1435 residues, 2 models selected > view matrix models > #7.1,-0.39814,0.85895,-0.32202,144.42,-0.80417,-0.49571,-0.328,121.65,-0.44137,0.12836,0.8881,226.16,#7.2,-0.39814,0.85895,-0.32202,144.42,-0.80417,-0.49571,-0.328,121.65,-0.44137,0.12836,0.8881,226.16 > ui mousemode right ""translate selected models"" > view matrix models > #7.1,-0.39814,0.85895,-0.32202,145.12,-0.80417,-0.49571,-0.328,121.46,-0.44137,0.12836,0.8881,222.35,#7.2,-0.39814,0.85895,-0.32202,145.12,-0.80417,-0.49571,-0.328,121.46,-0.44137,0.12836,0.8881,222.35 > view matrix models > #7.1,-0.39814,0.85895,-0.32202,145.38,-0.80417,-0.49571,-0.328,119.99,-0.44137,0.12836,0.8881,221.56,#7.2,-0.39814,0.85895,-0.32202,145.38,-0.80417,-0.49571,-0.328,119.99,-0.44137,0.12836,0.8881,221.56 > hide #7.1 models > show #7.1 models > matchmaker #7.1 to #3.1 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 body_refined_update_real_space_refined_012_01.pdb A, chain A (#3.1) with fold_vps33a_vps16_model_0.cif A, chain A (#7.1), sequence alignment score = 775.8 RMSD between 138 pruned atom pairs is 0.940 angstroms; (across all 150 pairs: 1.104) > matchmaker #7.2 to #3.2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker body_refined_update_real_space_refined_012_01.pdb B, chain B (#3.2) with fold_vps33a_vps16_model_0.cif B, chain B (#7.2), sequence alignment score = 2750 RMSD between 462 pruned atom pairs is 1.114 angstroms; (across all 566 pairs: 1.625) > select subtract #7.1 4761 atoms, 4853 bonds, 596 residues, 1 model selected > select add #7 11424 atoms, 11657 bonds, 1435 residues, 3 models selected > select subtract #7 Nothing selected > select add #1 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected > select add #2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #3.2 9057 atoms, 9245 bonds, 4 pseudobonds, 1137 residues, 6 models selected > select subtract #3.2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #4 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected > view matrix models > #1,0.97854,-0.040619,-0.20203,49.793,-0.12705,0.653,-0.74663,194.52,0.16225,0.75627,0.63382,-50.066,#2,0.92181,0.0056881,-0.3876,87.843,-0.23883,0.7959,-0.55633,150.16,0.30533,0.6054,0.73503,-67.627,#4,0.92181,0.0056881,-0.3876,87.843,-0.23883,0.7959,-0.55633,150.16,0.30533,0.6054,0.73503,-67.627 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98676,-0.046354,-0.1554,41.059,-0.094565,0.61401,-0.78361,202.1,0.13174,0.78793,0.6015,-44.425,#2,0.93833,-0.0097655,-0.34561,80.356,-0.21527,0.76571,-0.60609,160.21,0.27055,0.64311,0.71639,-65.056,#4,0.93833,-0.0097655,-0.34561,80.356,-0.21527,0.76571,-0.60609,160.21,0.27055,0.64311,0.71639,-65.056 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.98676,-0.046354,-0.1554,40.712,-0.094565,0.61401,-0.78361,201.87,0.13174,0.78793,0.6015,-44.454,#2,0.93833,-0.0097655,-0.34561,80.009,-0.21527,0.76571,-0.60609,159.98,0.27055,0.64311,0.71639,-65.085,#4,0.93833,-0.0097655,-0.34561,80.009,-0.21527,0.76571,-0.60609,159.98,0.27055,0.64311,0.71639,-65.085 > view matrix models > #1,0.98676,-0.046354,-0.1554,40.612,-0.094565,0.61401,-0.78361,201.95,0.13174,0.78793,0.6015,-44.386,#2,0.93833,-0.0097655,-0.34561,79.909,-0.21527,0.76571,-0.60609,160.07,0.27055,0.64311,0.71639,-65.017,#4,0.93833,-0.0097655,-0.34561,79.909,-0.21527,0.76571,-0.60609,160.07,0.27055,0.64311,0.71639,-65.017 > view matrix models > #1,0.98676,-0.046354,-0.1554,40.168,-0.094565,0.61401,-0.78361,201.81,0.13174,0.78793,0.6015,-44.712,#2,0.93833,-0.0097655,-0.34561,79.465,-0.21527,0.76571,-0.60609,159.92,0.27055,0.64311,0.71639,-65.343,#4,0.93833,-0.0097655,-0.34561,79.465,-0.21527,0.76571,-0.60609,159.92,0.27055,0.64311,0.71639,-65.343 > view matrix models > #1,0.98676,-0.046354,-0.1554,39.683,-0.094565,0.61401,-0.78361,201.86,0.13174,0.78793,0.6015,-44.664,#2,0.93833,-0.0097655,-0.34561,78.98,-0.21527,0.76571,-0.60609,159.97,0.27055,0.64311,0.71639,-65.294,#4,0.93833,-0.0097655,-0.34561,78.98,-0.21527,0.76571,-0.60609,159.97,0.27055,0.64311,0.71639,-65.294 > view matrix models > #1,0.98676,-0.046354,-0.1554,39.558,-0.094565,0.61401,-0.78361,201.77,0.13174,0.78793,0.6015,-44.689,#2,0.93833,-0.0097655,-0.34561,78.855,-0.21527,0.76571,-0.60609,159.89,0.27055,0.64311,0.71639,-65.32,#4,0.93833,-0.0097655,-0.34561,78.855,-0.21527,0.76571,-0.60609,159.89,0.27055,0.64311,0.71639,-65.32 > select subtract #1 4 models selected > select subtract #2 2 models selected > select subtract #4 Nothing selected > select subtract #8 Nothing selected > color #7.1 #c3c3c357 > color #7.2 #c3c3c34e > color #7.2 #c3c3c366 > color #7.1 #c3c3c366 > show #!2 models > hide #!2 models > show #!4 models > show #!6 models > volume #6 level 0.8145 > hide #!6 models > show #!6 models > show #!5 models > ui tool show ""Fit in Map"" > select add #7.1 6663 atoms, 6804 bonds, 839 residues, 1 model selected > select add #7.2 11424 atoms, 11657 bonds, 1435 residues, 2 models selected > select add #3.1 12648 atoms, 12903 bonds, 1585 residues, 3 models selected > select add #3.2 17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 5 models selected > select subtract #8 17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 5 models selected > fitmap sel inMap #2 Fit molecules body_refined_update_real_space_refined_012_01.pdb A (#3.1), body_refined_update_real_space_refined_012_01.pdb B (#3.2), fold_vps33a_vps16_model_0.cif A (#7.1), fold_vps33a_vps16_model_0.cif B (#7.2) to map head_sharpened.ccp4 (#2) using 17174 atoms average map value = 0.004934, steps = 292 shifted from previous position = 20.9 rotated from previous position = 14.7 degrees atoms outside contour = 13987, contour level = 0.013253 Position of body_refined_update_real_space_refined_012_01.pdb A (#3.1) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation 0.65438901 0.16115234 -0.73878612 118.71316057 -0.75599779 0.11931857 -0.64360734 360.65900877 -0.01556793 0.97969025 0.19991158 -7.33060995 Axis 0.81171942 -0.36164056 -0.45861496 Axis point 0.00000000 219.79103216 242.36652220 Rotation angle (degrees) 90.75577740 Shift along axis -30.70522149 Position of body_refined_update_real_space_refined_012_01.pdb B (#3.2) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation 0.65438901 0.16115234 -0.73878612 118.71316057 -0.75599779 0.11931857 -0.64360734 360.65900877 -0.01556793 0.97969025 0.19991158 -7.33060995 Axis 0.81171942 -0.36164056 -0.45861496 Axis point 0.00000000 219.79103216 242.36652220 Rotation angle (degrees) 90.75577740 Shift along axis -30.70522149 Position of fold_vps33a_vps16_model_0.cif A (#7.1) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation -0.36346722 0.87256139 0.32638658 153.95428804 -0.86226239 -0.44772861 0.23673335 154.49065449 0.35269699 -0.19538606 0.91511154 185.69585179 Axis -0.24167416 -0.01471479 -0.97024588 Axis point 101.97504290 43.74390158 0.00000000 Rotation angle (degrees) 116.61813922 Shift along axis -219.65070602 Position of fold_vps33a_vps16_model_0.cif B (#7.2) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation -0.34238012 0.88837568 0.30588318 154.54217613 -0.86630367 -0.42451693 0.26325528 155.83617513 0.36372218 -0.17485435 0.91494926 186.05433877 Axis -0.24212029 -0.03196459 -0.96971956 Axis point 102.69426755 41.94363569 0.00000000 Rotation angle (degrees) 115.21232322 Shift along axis -222.81956819 > view matrix models > #3.1,0.62679,-0.18854,-0.75603,176.92,-0.71031,-0.53711,-0.45495,406.55,-0.32029,0.82217,-0.47058,198.71,#3.2,0.62679,-0.18854,-0.75603,176.92,-0.71031,-0.53711,-0.45495,406.55,-0.32029,0.82217,-0.47058,198.71,#7.1,-0.45453,0.89065,-0.012323,145.29,-0.79577,-0.41224,-0.44363,124.11,-0.4002,-0.19184,0.89612,213.94,#7.2,-0.43851,0.89816,-0.031765,145.7,-0.81008,-0.41032,-0.41881,124.79,-0.38919,-0.15792,0.90752,215.22 > ui mousemode right ""rotate selected models"" > view matrix models > #3.1,0.5808,-0.59687,-0.55355,226.56,-0.81398,-0.43399,-0.38611,397.4,-0.0097745,0.67483,-0.7379,208.83,#3.2,0.5808,-0.59687,-0.55355,226.56,-0.81398,-0.43399,-0.38611,397.4,-0.0097745,0.67483,-0.7379,208.83,#7.1,-0.36746,0.81115,-0.45498,146.76,-0.7576,-0.54482,-0.35945,124.26,-0.53945,0.21261,0.81473,214.78,#7.2,-0.35999,0.80407,-0.47316,146.7,-0.77298,-0.54104,-0.33133,124.99,-0.52241,0.24647,0.8163,216.1 > ui mousemode right ""translate selected models"" > view matrix models > #3.1,0.5808,-0.59687,-0.55355,224.48,-0.81398,-0.43399,-0.38611,395.87,-0.0097745,0.67483,-0.7379,219.21,#3.2,0.5808,-0.59687,-0.55355,224.48,-0.81398,-0.43399,-0.38611,395.87,-0.0097745,0.67483,-0.7379,219.21,#7.1,-0.36746,0.81115,-0.45498,144.67,-0.7576,-0.54482,-0.35945,122.74,-0.53945,0.21261,0.81473,225.16,#7.2,-0.35999,0.80407,-0.47316,144.62,-0.77298,-0.54104,-0.33133,123.47,-0.52241,0.24647,0.8163,226.48 > fitmap sel inMap #2 Fit molecules body_refined_update_real_space_refined_012_01.pdb A (#3.1), body_refined_update_real_space_refined_012_01.pdb B (#3.2), fold_vps33a_vps16_model_0.cif A (#7.1), fold_vps33a_vps16_model_0.cif B (#7.2) to map head_sharpened.ccp4 (#2) using 17174 atoms average map value = 0.005148, steps = 448 shifted from previous position = 29.6 rotated from previous position = 22.5 degrees atoms outside contour = 13872, contour level = 0.013253 Position of body_refined_update_real_space_refined_012_01.pdb A (#3.1) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation 0.74954332 0.09587242 -0.65497579 105.66387981 -0.65968709 0.02634601 -0.75107844 374.15695982 -0.05475171 0.99504490 0.08299327 7.33549087 Axis 0.87524311 -0.30086190 -0.37872368 Axis point -0.00000000 205.94427166 222.02601512 Rotation angle (degrees) 94.04607789 Shift along axis -22.86611528 Position of body_refined_update_real_space_refined_012_01.pdb B (#3.2) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation 0.74954332 0.09587242 -0.65497579 105.66387981 -0.65968709 0.02634601 -0.75107844 374.15695982 -0.05475171 0.99504490 0.08299327 7.33549087 Axis 0.87524311 -0.30086190 -0.37872368 Axis point -0.00000000 205.94427166 222.02601512 Rotation angle (degrees) 94.04607789 Shift along axis -22.86611528 Position of fold_vps33a_vps16_model_0.cif A (#7.1) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation -0.26168474 0.93304532 0.24687555 158.70772508 -0.93610895 -0.30764474 0.17045455 153.49937761 0.23499178 -0.18649706 0.95393801 179.10022594 Axis -0.18757609 0.00624486 -0.98223022 Axis point 119.57971818 32.75984254 0.00000000 Rotation angle (degrees) 107.92041958 Shift along axis -204.72884837 Position of fold_vps33a_vps16_model_0.cif B (#7.2) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation -0.24080862 0.94459665 0.22304348 159.09233189 -0.93866097 -0.28510173 0.19399124 154.85910068 0.24683355 -0.16264744 0.95531095 179.63667900 Axis -0.18605197 -0.01241085 -0.98246152 Axis point 120.32662883 30.60585760 0.00000000 Rotation angle (degrees) 106.57676371 Shift along axis -208.00749947 > view matrix models > #3.1,0.72868,-0.25419,-0.63593,143.77,-0.6333,-0.60355,-0.48442,409.25,-0.26068,0.75572,-0.60078,222.69,#3.2,0.72868,-0.25419,-0.63593,143.77,-0.6333,-0.60355,-0.48442,409.25,-0.26068,0.75572,-0.60078,222.69,#7.1,-0.31762,0.94296,-0.099702,136.33,-0.80288,-0.32339,-0.5008,124.77,-0.50448,-0.079014,0.8598,218.18,#7.2,-0.3021,0.94534,-0.12277,136.49,-0.81651,-0.32307,-0.47848,125.4,-0.49199,-0.044306,0.86948,219.54 > fitmap sel inMap #5 Fit molecules body_refined_update_real_space_refined_012_01.pdb A (#3.1), body_refined_update_real_space_refined_012_01.pdb B (#3.2), fold_vps33a_vps16_model_0.cif A (#7.1), fold_vps33a_vps16_model_0.cif B (#7.2) to map full_map_sharpened.ccp4 (#5) using 17174 atoms average map value = 0.01875, steps = 340 shifted from previous position = 10.9 rotated from previous position = 22.2 degrees atoms outside contour = 7489, contour level = 0.011478 Position of body_refined_update_real_space_refined_012_01.pdb A (#3.1) relative to full_map_sharpened.ccp4 (#5) coordinates: Matrix rotation and translation 0.99999900 0.00070524 0.00122795 -0.33946076 -0.00070328 0.99999848 -0.00159662 0.43461266 -0.00122907 0.00159575 0.99999797 -0.06563660 Axis 0.74805382 0.57574274 -0.33005420 Axis point -0.00000000 37.75641627 265.69839846 Rotation angle (degrees) 0.12225680 Shift along axis 0.01795380 Position of body_refined_update_real_space_refined_012_01.pdb B (#3.2) relative to full_map_sharpened.ccp4 (#5) coordinates: Matrix rotation and translation 0.99999900 0.00070524 0.00122795 -0.33946076 -0.00070328 0.99999848 -0.00159662 0.43461266 -0.00122907 0.00159575 0.99999797 -0.06563660 Axis 0.74805382 0.57574274 -0.33005420 Axis point -0.00000000 37.75641627 265.69839846 Rotation angle (degrees) 0.12225680 Shift along axis 0.01795380 Position of fold_vps33a_vps16_model_0.cif A (#7.1) relative to full_map_sharpened.ccp4 (#5) coordinates: Matrix rotation and translation 0.40975593 0.91195808 0.02079824 175.87794379 0.18236134 -0.10423493 0.97769087 170.26435524 0.89378098 -0.39682183 -0.20901678 145.23346250 Axis -0.77034098 -0.48926021 -0.40890001 Axis point 0.00000000 41.83965371 12.31132467 Rotation angle (degrees) 116.85588197 Shift along axis -278.17552684 Position of fold_vps33a_vps16_model_0.cif B (#7.2) relative to full_map_sharpened.ccp4 (#5) coordinates: Matrix rotation and translation 0.42643508 0.90442945 -0.01266954 175.23877942 0.19608409 -0.07876091 0.97741893 170.87325609 0.88300859 -0.41929002 -0.21093064 144.00657220 Axis -0.77418462 -0.49646724 -0.39263017 Axis point 0.00000000 43.58535411 14.00313805 Rotation angle (degrees) 115.57093635 Shift along axis -277.04146713 > hide #!5 models > hide #!6 models > hide #!4 models > select add #7 17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 6 models selected > select subtract #7.1 10511 atoms, 10710 bonds, 3 pseudobonds, 1312 residues, 5 models selected > select add #7 17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 6 models selected > select add #3 17174 atoms, 17514 bonds, 3 pseudobonds, 2151 residues, 7 models selected > select subtract #3 11424 atoms, 11657 bonds, 1435 residues, 3 models selected > select subtract #7 Nothing selected > select subtract #8 Nothing selected > select add #1 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected > select add #2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #4 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.96266,-0.051478,-0.26578,64.178,-0.15294,0.70665,-0.69083,179.67,0.22337,0.70568,0.67239,-59.143,#2,0.89398,0.008526,-0.44802,101.16,-0.25189,0.83646,-0.48671,132.72,0.3706,0.54796,0.74993,-71.49,#4,0.89398,0.008526,-0.44802,101.16,-0.25189,0.83646,-0.48671,132.72,0.3706,0.54796,0.74993,-71.49 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.96266,-0.051478,-0.26578,67.137,-0.15294,0.70665,-0.69083,177.49,0.22337,0.70568,0.67239,-60.425,#2,0.89398,0.008526,-0.44802,104.11,-0.25189,0.83646,-0.48671,130.53,0.3706,0.54796,0.74993,-72.772,#4,0.89398,0.008526,-0.44802,104.11,-0.25189,0.83646,-0.48671,130.53,0.3706,0.54796,0.74993,-72.772 > view matrix models > #1,0.96266,-0.051478,-0.26578,65.253,-0.15294,0.70665,-0.69083,175.68,0.22337,0.70568,0.67239,-57.724,#2,0.89398,0.008526,-0.44802,102.23,-0.25189,0.83646,-0.48671,128.72,0.3706,0.54796,0.74993,-70.071,#4,0.89398,0.008526,-0.44802,102.23,-0.25189,0.83646,-0.48671,128.72,0.3706,0.54796,0.74993,-70.071 > view matrix models > #1,0.96266,-0.051478,-0.26578,65.54,-0.15294,0.70665,-0.69083,175.85,0.22337,0.70568,0.67239,-57.636,#2,0.89398,0.008526,-0.44802,102.52,-0.25189,0.83646,-0.48671,128.9,0.3706,0.54796,0.74993,-69.983,#4,0.89398,0.008526,-0.44802,102.52,-0.25189,0.83646,-0.48671,128.9,0.3706,0.54796,0.74993,-69.983 > view matrix models > #1,0.96266,-0.051478,-0.26578,66.114,-0.15294,0.70665,-0.69083,174.48,0.22337,0.70568,0.67239,-58.504,#2,0.89398,0.008526,-0.44802,103.09,-0.25189,0.83646,-0.48671,127.52,0.3706,0.54796,0.74993,-70.851,#4,0.89398,0.008526,-0.44802,103.09,-0.25189,0.83646,-0.48671,127.52,0.3706,0.54796,0.74993,-70.851 > view matrix models > #1,0.96266,-0.051478,-0.26578,66.015,-0.15294,0.70665,-0.69083,174.43,0.22337,0.70568,0.67239,-58.213,#2,0.89398,0.008526,-0.44802,102.99,-0.25189,0.83646,-0.48671,127.47,0.3706,0.54796,0.74993,-70.56,#4,0.89398,0.008526,-0.44802,102.99,-0.25189,0.83646,-0.48671,127.47,0.3706,0.54796,0.74993,-70.56 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.95395,-0.052695,-0.29531,72.963,-0.16243,0.73689,-0.6562,164.8,0.25219,0.67395,0.6944,-61.718,#2,0.8799,0.013564,-0.47496,109.22,-0.25365,0.85866,-0.44539,116.64,0.40179,0.51237,0.75898,-71.207,#4,0.8799,0.013564,-0.47496,109.22,-0.25365,0.85866,-0.44539,116.64,0.40179,0.51237,0.75898,-71.207 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.95395,-0.052695,-0.29531,72.682,-0.16243,0.73689,-0.6562,164.74,0.25219,0.67395,0.6944,-61.918,#2,0.8799,0.013564,-0.47496,108.94,-0.25365,0.85866,-0.44539,116.58,0.40179,0.51237,0.75898,-71.407,#4,0.8799,0.013564,-0.47496,108.94,-0.25365,0.85866,-0.44539,116.58,0.40179,0.51237,0.75898,-71.407 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.94692,-0.066282,-0.31456,79.6,-0.15582,0.76124,-0.62947,154.75,0.28118,0.64508,0.7105,-64.885,#2,0.86892,0.0043422,-0.49494,115.9,-0.24129,0.87681,-0.41591,106.17,0.43216,0.48082,0.76292,-71.719,#4,0.86892,0.0043422,-0.49494,115.9,-0.24129,0.87681,-0.41591,106.17,0.43216,0.48082,0.76292,-71.719 > view matrix models > #1,0.95774,-0.078122,-0.27683,73.032,-0.12247,0.76006,-0.6382,150.78,0.26027,0.64514,0.71837,-62.709,#2,0.8861,-0.015188,-0.46325,110.82,-0.2102,0.8776,-0.43085,103.46,0.41309,0.47915,0.77445,-70.271,#4,0.8861,-0.015188,-0.46325,110.82,-0.2102,0.8776,-0.43085,103.46,0.41309,0.47915,0.77445,-70.271 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.95774,-0.078122,-0.27683,71.867,-0.12247,0.76006,-0.6382,152.07,0.26027,0.64514,0.71837,-62.89,#2,0.8861,-0.015188,-0.46325,109.66,-0.2102,0.8776,-0.43085,104.75,0.41309,0.47915,0.77445,-70.451,#4,0.8861,-0.015188,-0.46325,109.66,-0.2102,0.8776,-0.43085,104.75,0.41309,0.47915,0.77445,-70.451 > view matrix models > #1,0.95774,-0.078122,-0.27683,72.415,-0.12247,0.76006,-0.6382,152.45,0.26027,0.64514,0.71837,-63.615,#2,0.8861,-0.015188,-0.46325,110.2,-0.2102,0.8776,-0.43085,105.13,0.41309,0.47915,0.77445,-71.176,#4,0.8861,-0.015188,-0.46325,110.2,-0.2102,0.8776,-0.43085,105.13,0.41309,0.47915,0.77445,-71.176 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.92245,-0.1597,-0.35154,105.49,-0.14221,0.70593,-0.69386,174.85,0.35897,0.69004,0.62848,-72.118,#2,0.83453,-0.079195,-0.54525,144.37,-0.24194,0.83642,-0.4918,128.31,0.495,0.54234,0.67885,-78.983,#4,0.83453,-0.079195,-0.54525,144.37,-0.24194,0.83642,-0.4918,128.31,0.495,0.54234,0.67885,-78.983 > view matrix models > #1,0.90637,-0.14066,-0.39837,113.37,-0.18263,0.71984,-0.66968,175.14,0.38097,0.67974,0.62676,-73.847,#2,0.81076,-0.050723,-0.58318,150.1,-0.27662,0.84479,-0.45805,126.72,0.5159,0.53268,0.67089,-79.404,#4,0.81076,-0.050723,-0.58318,150.1,-0.27662,0.84479,-0.45805,126.72,0.5159,0.53268,0.67089,-79.404 > view matrix models > #1,0.91164,-0.11051,-0.39586,106.94,-0.20392,0.71465,-0.6691,179.56,0.35685,0.6907,0.62896,-71.952,#2,0.81752,-0.021769,-0.57548,142.6,-0.29761,0.83954,-0.45454,130.52,0.49303,0.54287,0.67986,-78.923,#4,0.81752,-0.021769,-0.57548,142.6,-0.29761,0.83954,-0.45454,130.52,0.49303,0.54287,0.67986,-78.923 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.91164,-0.11051,-0.39586,104.4,-0.20392,0.71465,-0.6691,176.78,0.35685,0.6907,0.62896,-68.683,#2,0.81752,-0.021769,-0.57548,140.06,-0.29761,0.83954,-0.45454,127.75,0.49303,0.54287,0.67986,-75.654,#4,0.81752,-0.021769,-0.57548,140.06,-0.29761,0.83954,-0.45454,127.75,0.49303,0.54287,0.67986,-75.654 > view matrix models > #1,0.91164,-0.11051,-0.39586,104.75,-0.20392,0.71465,-0.6691,176.36,0.35685,0.6907,0.62896,-68.737,#2,0.81752,-0.021769,-0.57548,140.41,-0.29761,0.83954,-0.45454,127.32,0.49303,0.54287,0.67986,-75.708,#4,0.81752,-0.021769,-0.57548,140.41,-0.29761,0.83954,-0.45454,127.32,0.49303,0.54287,0.67986,-75.708 > view matrix models > #1,0.91164,-0.11051,-0.39586,105.67,-0.20392,0.71465,-0.6691,177.18,0.35685,0.6907,0.62896,-67.128,#2,0.81752,-0.021769,-0.57548,141.33,-0.29761,0.83954,-0.45454,128.15,0.49303,0.54287,0.67986,-74.099,#4,0.81752,-0.021769,-0.57548,141.33,-0.29761,0.83954,-0.45454,128.15,0.49303,0.54287,0.67986,-74.099 > color #7.1 #c3c3c393 > color #7.1 #c3c3c394 > view matrix models > #1,0.91164,-0.11051,-0.39586,106.01,-0.20392,0.71465,-0.6691,176.32,0.35685,0.6907,0.62896,-67.326,#2,0.81752,-0.021769,-0.57548,141.67,-0.29761,0.83954,-0.45454,127.28,0.49303,0.54287,0.67986,-74.297,#4,0.81752,-0.021769,-0.57548,141.67,-0.29761,0.83954,-0.45454,127.28,0.49303,0.54287,0.67986,-74.297 > select subtract #1 4 models selected > select subtract #2 2 models selected > select subtract #4 Nothing selected > select subtract #8 Nothing selected > hide #8 models > close #8 > show #!2 models > show #!4 models > show #!5 models > show #!6 models > hide #!1 models > hide #3.1 models > hide #!3.2 models > hide #7.1 models > hide #7.2 models > volume #2 step 1 > volume #2 level 0.01971 > volume #2 level 0.021 > volume #2 level 0.018 > volume #5 step 1 > volume #5 level 0.014 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > lighting soft > show #!1 models > show #7.1 models > hide #!2 models > hide #!4 models > select add #1 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected > select add #2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #3.2 9057 atoms, 9245 bonds, 4 pseudobonds, 1137 residues, 6 models selected > select subtract #3.2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #4 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.92192,-0.072166,-0.3806,95.072,-0.20676,0.73918,-0.64099,167.67,0.32759,0.66963,0.66654,-65.443,#2,0.83189,0.012503,-0.5548,129.68,-0.29427,0.85755,-0.42192,117.85,0.47049,0.51425,0.71707,-72.124,#4,0.83189,0.012503,-0.5548,129.68,-0.29427,0.85755,-0.42192,117.85,0.47049,0.51425,0.71707,-72.124 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.92192,-0.072166,-0.3806,96.404,-0.20676,0.73918,-0.64099,168.4,0.32759,0.66963,0.66654,-66.573,#2,0.83189,0.012503,-0.5548,131.01,-0.29427,0.85755,-0.42192,118.58,0.47049,0.51425,0.71707,-73.254,#4,0.83189,0.012503,-0.5548,131.01,-0.29427,0.85755,-0.42192,118.58,0.47049,0.51425,0.71707,-73.254 > view matrix models > #1,0.92192,-0.072166,-0.3806,96.674,-0.20676,0.73918,-0.64099,168.55,0.32759,0.66963,0.66654,-67.253,#2,0.83189,0.012503,-0.5548,131.28,-0.29427,0.85755,-0.42192,118.73,0.47049,0.51425,0.71707,-73.934,#4,0.83189,0.012503,-0.5548,131.28,-0.29427,0.85755,-0.42192,118.73,0.47049,0.51425,0.71707,-73.934 > show #!2 models > show #!4 models > hide #!1 models > hide #7.1 models > select subtract #4 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select subtract #1 2 models selected > select subtract #2 Nothing selected > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > set bgColor white > set bgColor #ffffff00 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > volume #2 level 0.019 > volume #2 level 0.02 > volume #2 level 0.019 > volume #5 step 4 > volume #5 step 2 > volume #5 step 1 > ui tool show ""Surface Color"" > ui tool show ""Surface Zone"" > select add #3.1 1224 atoms, 1246 bonds, 150 residues, 1 model selected > select add #3.2 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 3 models selected > surface zone #5 nearAtoms sel distance 196.86 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > ui tool show ""Color Zone"" > color zone #5 near sel distance 85.05 > color zone #2 near #1 distance 119.06 > lighting flat > lighting soft > select add #1 10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 5 models selected > select add #3 10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 6 models selected > select subtract #3 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 2 models selected > select add #2 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 4 models selected > select add #4 4531 atoms, 4634 bonds, 1 pseudobond, 571 residues, 6 models selected > show #!1 models > show #7.1 models > view matrix models > #1,0.92192,-0.072166,-0.3806,97.322,-0.20676,0.73918,-0.64099,169.13,0.32759,0.66963,0.66654,-67.618,#2,0.83189,0.012503,-0.5548,131.93,-0.29427,0.85755,-0.42192,119.31,0.47049,0.51425,0.71707,-74.299,#4,0.83189,0.012503,-0.5548,131.93,-0.29427,0.85755,-0.42192,119.31,0.47049,0.51425,0.71707,-74.299 > view matrix models > #1,0.92192,-0.072166,-0.3806,96.289,-0.20676,0.73918,-0.64099,170.45,0.32759,0.66963,0.66654,-68.119,#2,0.83189,0.012503,-0.5548,130.9,-0.29427,0.85755,-0.42192,120.63,0.47049,0.51425,0.71707,-74.801,#4,0.83189,0.012503,-0.5548,130.9,-0.29427,0.85755,-0.42192,120.63,0.47049,0.51425,0.71707,-74.801 > view matrix models > #1,0.92192,-0.072166,-0.3806,96.805,-0.20676,0.73918,-0.64099,169.81,0.32759,0.66963,0.66654,-68.029,#2,0.83189,0.012503,-0.5548,131.42,-0.29427,0.85755,-0.42192,119.99,0.47049,0.51425,0.71707,-74.711,#4,0.83189,0.012503,-0.5548,131.42,-0.29427,0.85755,-0.42192,119.99,0.47049,0.51425,0.71707,-74.711 > view matrix models > #1,0.92192,-0.072166,-0.3806,95.941,-0.20676,0.73918,-0.64099,169.67,0.32759,0.66963,0.66654,-68.929,#2,0.83189,0.012503,-0.5548,130.55,-0.29427,0.85755,-0.42192,119.85,0.47049,0.51425,0.71707,-75.61,#4,0.83189,0.012503,-0.5548,130.55,-0.29427,0.85755,-0.42192,119.85,0.47049,0.51425,0.71707,-75.61 > fitmap #1 inMap #2 Fit molecule head_fit_real_space_refined_002.pdb (#1) to map head_sharpened.ccp4 (#2) using 4531 atoms average map value = 0.01843, steps = 160 shifted from previous position = 6.68 rotated from previous position = 16.4 degrees atoms outside contour = 2427, contour level = 0.019 Position of head_fit_real_space_refined_002.pdb (#1) relative to head_sharpened.ccp4 (#2) coordinates: Matrix rotation and translation 0.99999251 -0.00227889 -0.00312948 1.09767996 0.00226897 0.99999241 -0.00316874 0.21223268 0.00313667 0.00316162 0.99999008 -1.11174684 Axis 0.63296916 -0.62654906 0.45473763 Axis point 0.00000000 359.97435545 77.24041076 Rotation angle (degrees) 0.28651028 Shift along axis 0.05627026 > view matrix models > #1,0.83017,0.0088531,-0.55744,132.04,-0.29364,0.85688,-0.42371,126.52,0.4739,0.51544,0.71396,-75.68,#2,0.83189,0.012503,-0.5548,130.51,-0.29427,0.85755,-0.42192,126.19,0.47049,0.51425,0.71707,-75.508,#4,0.83189,0.012503,-0.5548,130.51,-0.29427,0.85755,-0.42192,126.19,0.47049,0.51425,0.71707,-75.508 > view matrix models > #1,0.83017,0.0088531,-0.55744,133.84,-0.29364,0.85688,-0.42371,124.06,0.4739,0.51544,0.71396,-75.85,#2,0.83189,0.012503,-0.5548,132.31,-0.29427,0.85755,-0.42192,123.73,0.47049,0.51425,0.71707,-75.678,#4,0.83189,0.012503,-0.5548,132.31,-0.29427,0.85755,-0.42192,123.73,0.47049,0.51425,0.71707,-75.678 > view matrix models > #1,0.83017,0.0088531,-0.55744,133.83,-0.29364,0.85688,-0.42371,124.58,0.4739,0.51544,0.71396,-79.263,#2,0.83189,0.012503,-0.5548,132.3,-0.29427,0.85755,-0.42192,124.25,0.47049,0.51425,0.71707,-79.092,#4,0.83189,0.012503,-0.5548,132.3,-0.29427,0.85755,-0.42192,124.25,0.47049,0.51425,0.71707,-79.092 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.89976,-0.03417,-0.43505,107.83,-0.22288,0.82112,-0.52544,136.27,0.37518,0.56973,0.73119,-74.55,#2,0.90119,-0.030749,-0.43233,106.37,-0.2231,0.82227,-0.52354,135.75,0.37159,0.56826,0.73416,-74.262,#4,0.90119,-0.030749,-0.43233,106.37,-0.2231,0.82227,-0.52354,135.75,0.37159,0.56826,0.73416,-74.262 > view matrix models > #1,0.90249,0.018977,-0.43028,97.309,-0.24361,0.84636,-0.47363,126.44,0.35519,0.53228,0.76846,-71.092,#2,0.90379,0.022388,-0.42739,95.838,-0.24406,0.8473,-0.47172,126,0.35156,0.53064,0.77125,-70.733,#4,0.90379,0.022388,-0.42739,95.838,-0.24406,0.8473,-0.47172,126,0.35156,0.53064,0.77125,-70.733 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.90249,0.018977,-0.43028,96.179,-0.24361,0.84636,-0.47363,127.61,0.35519,0.53228,0.76846,-71.153,#2,0.90379,0.022388,-0.42739,94.707,-0.24406,0.8473,-0.47172,127.17,0.35156,0.53064,0.77125,-70.794,#4,0.90379,0.022388,-0.42739,94.707,-0.24406,0.8473,-0.47172,127.17,0.35156,0.53064,0.77125,-70.794 > hide #!4 models > hide #!1 models > show #!1 models > hide #!2 models > view matrix models > #1,0.90249,0.018977,-0.43028,96.848,-0.24361,0.84636,-0.47363,128.08,0.35519,0.53228,0.76846,-70.908,#2,0.90379,0.022388,-0.42739,95.376,-0.24406,0.8473,-0.47172,127.65,0.35156,0.53064,0.77125,-70.549,#4,0.90379,0.022388,-0.42739,95.376,-0.24406,0.8473,-0.47172,127.65,0.35156,0.53064,0.77125,-70.549 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.94648,0.080547,-0.31254,57.997,-0.25881,0.76798,-0.58585,163.85,0.19283,0.63539,0.74773,-56.766,#2,0.94727,0.083684,-0.30931,56.596,-0.25872,0.76925,-0.58423,163.32,0.18904,0.63345,0.75034,-56.274,#4,0.94727,0.083684,-0.30931,56.596,-0.25872,0.76925,-0.58423,163.32,0.18904,0.63345,0.75034,-56.274 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.94648,0.080547,-0.31254,60.607,-0.25881,0.76798,-0.58585,162.41,0.19283,0.63539,0.74773,-57.485,#2,0.94727,0.083684,-0.30931,59.205,-0.25872,0.76925,-0.58423,161.88,0.18904,0.63345,0.75034,-56.993,#4,0.94727,0.083684,-0.30931,59.205,-0.25872,0.76925,-0.58423,161.88,0.18904,0.63345,0.75034,-56.993 > view matrix models > #1,0.94648,0.080547,-0.31254,60.872,-0.25881,0.76798,-0.58585,162.3,0.19283,0.63539,0.74773,-57.439,#2,0.94727,0.083684,-0.30931,59.47,-0.25872,0.76925,-0.58423,161.77,0.18904,0.63345,0.75034,-56.946,#4,0.94727,0.083684,-0.30931,59.47,-0.25872,0.76925,-0.58423,161.77,0.18904,0.63345,0.75034,-56.946 > show #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.90737,0.042199,-0.4182,92.867,-0.31902,0.71697,-0.61982,187.51,0.27368,0.69582,0.66402,-67.134,#2,0.90858,0.045582,-0.41522,91.399,-0.31871,0.71821,-0.61855,187.02,0.27002,0.69434,0.66708,-66.836,#4,0.90858,0.045582,-0.41522,91.399,-0.31871,0.71821,-0.61855,187.02,0.27002,0.69434,0.66708,-66.836 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.90737,0.042199,-0.4182,91.309,-0.31902,0.71697,-0.61982,184.17,0.27368,0.69582,0.66402,-62.062,#2,0.90858,0.045582,-0.41522,89.84,-0.31871,0.71821,-0.61855,183.68,0.27002,0.69434,0.66708,-61.764,#4,0.90858,0.045582,-0.41522,89.84,-0.31871,0.71821,-0.61855,183.68,0.27002,0.69434,0.66708,-61.764 > hide #!2 models > show #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.8837,-0.0094113,-0.46796,113.08,-0.33247,0.6911,-0.64175,194.83,0.32945,0.72269,0.6076,-66.432,#2,0.88518,-0.0059233,-0.46521,111.59,-0.33204,0.69238,-0.6406,194.34,0.3259,0.72151,0.61091,-66.264,#4,0.88518,-0.0059233,-0.46521,111.59,-0.33204,0.69238,-0.6406,194.34,0.3259,0.72151,0.61091,-66.264 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.8837,-0.0094113,-0.46796,111.09,-0.33247,0.6911,-0.64175,192.84,0.32945,0.72269,0.6076,-63.394,#2,0.88518,-0.0059233,-0.46521,109.6,-0.33204,0.69238,-0.6406,192.34,0.3259,0.72151,0.61091,-63.226,#4,0.88518,-0.0059233,-0.46521,109.6,-0.33204,0.69238,-0.6406,192.34,0.3259,0.72151,0.61091,-63.226 > view matrix models > #1,0.8837,-0.0094113,-0.46796,110.8,-0.33247,0.6911,-0.64175,193.22,0.32945,0.72269,0.6076,-63.551,#2,0.88518,-0.0059233,-0.46521,109.31,-0.33204,0.69238,-0.6406,192.72,0.3259,0.72151,0.61091,-63.382,#4,0.88518,-0.0059233,-0.46521,109.31,-0.33204,0.69238,-0.6406,192.72,0.3259,0.72151,0.61091,-63.382 > hide #!2 models > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.89303,-0.032896,-0.44878,109.75,-0.29696,0.70624,-0.64269,184.75,0.33809,0.70721,0.62093,-64.792,#2,0.89451,-0.029448,-0.44608,108.28,-0.29655,0.70759,-0.64138,184.21,0.33453,0.706,0.62422,-64.615,#4,0.89451,-0.029448,-0.44608,108.28,-0.29655,0.70759,-0.64138,184.21,0.33453,0.706,0.62422,-64.615 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.89303,-0.032896,-0.44878,109.1,-0.29696,0.70624,-0.64269,184.64,0.33809,0.70721,0.62093,-64.785,#2,0.89451,-0.029448,-0.44608,107.63,-0.29655,0.70759,-0.64138,184.1,0.33453,0.706,0.62422,-64.609,#4,0.89451,-0.029448,-0.44608,107.63,-0.29655,0.70759,-0.64138,184.1,0.33453,0.706,0.62422,-64.609 > view matrix models > #1,0.89303,-0.032896,-0.44878,108.79,-0.29696,0.70624,-0.64269,186.02,0.33809,0.70721,0.62093,-64.669,#2,0.89451,-0.029448,-0.44608,107.32,-0.29655,0.70759,-0.64138,185.49,0.33453,0.706,0.62422,-64.492,#4,0.89451,-0.029448,-0.44608,107.32,-0.29655,0.70759,-0.64138,185.49,0.33453,0.706,0.62422,-64.492 > show #!2 models > hide #!2 models > view matrix models > #1,0.89303,-0.032896,-0.44878,108.52,-0.29696,0.70624,-0.64269,186.53,0.33809,0.70721,0.62093,-64.659,#2,0.89451,-0.029448,-0.44608,107.05,-0.29655,0.70759,-0.64138,185.99,0.33453,0.706,0.62422,-64.483,#4,0.89451,-0.029448,-0.44608,107.05,-0.29655,0.70759,-0.64138,185.99,0.33453,0.706,0.62422,-64.483 > show #!2 models > hide #7.1 models > hide #!7 models > hide #!1 models > show #!4 models > select subtract #1 4 models selected > select subtract #2 2 models selected > select subtract #4 Nothing selected > color #6 #bbbbbb03 models > volume #6 level 0.5714 > volume #6 level 0.6 > volume #6 level 0.55 > volume #6 level 0.65 > volume #6 level 0.7 > volume #4 level 0.7 > color #4 #bbbbbb03 models > turn y 180 > volume #5 step 2 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > turn y 180 > show #7.1 models > hide #7.1 models > show #7.1 models > hide #7.1 models > color #7.1 #c3c3c3ff > show #7.1 models > hide #!2 models > show #!1 models > hide #!5 models > show #3.1 models > show #!3.2 models > color #7.1 #c3c3c3ff > hide #7.1 models > hide #!6 models > hide #!4 models > select #1/A:624 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show Distances > select add #3.1/A:642 17 atoms, 15 bonds, 2 residues, 2 models selected Exactly two atoms must be selected! > select subtract #3.1/A:642 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3.1/A:642 17 atoms, 15 bonds, 2 residues, 2 models selected > select subtract #3.1/A:642 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #3.1/A:642 17 atoms, 15 bonds, 2 residues, 2 models selected > select subtract #3.1/A:642 8 atoms, 7 bonds, 1 residue, 1 model selected > select subtract #1/A:624 Nothing selected > select #3.1/A:642 9 atoms, 8 bonds, 1 residue, 1 model selected > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > select #1/A:624 8 atoms, 7 bonds, 1 residue, 1 model selected > hide (sel-residues & (protein|nucleic)) target a > cartoon hide sel-residues > show (sel-residues & backbone) target ab > select #1/A:624@O 1 atom, 1 residue, 1 model selected > select add #3.1/A:642@N 2 atoms, 2 residues, 2 models selected > distance #1/A:624@O #3.1/A:642@N Distance between head_fit_real_space_refined_002.pdb #1/A ASP 624 O and body_refined_update_real_space_refined_012_01.pdb A #3.1/A GLU 642 N: 29.694Å > hide #8.1 models > color #8 #f9de49ff models > color #8 #e9c78aff models > select add #1 4532 atoms, 4634 bonds, 1 pseudobond, 572 residues, 3 models selected > select add #3 10281 atoms, 10491 bonds, 4 pseudobonds, 1287 residues, 6 models selected > show sel cartoons > show #8.1 models > hide #8.1 models > select subtract #1 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 4 models selected > select subtract #3 Nothing selected > show #!4 models > show #!6 models > show #7.1 models > transparency #7.1 50 > hide #7.1 models > show #!2 models > show #!5 models > hide #!1 models > hide #3.1 models > hide #!3.2 models > turn y 180 > turn y 90 > turn y 180 > show #!1 models > hide #!2 models > hide #!3 models > show #3.1 models > show #!3.2 models > hide #!3 models > hide #3.1 models > hide #!3.2 models > show #3.1 models > show #!3.2 models > hide #!5 models > turn y 180 > show #!5 models > show #!2 models > hide #!1 models > hide #!3 models > hide #3.1 models > hide #!3.2 models > turn y 180 > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > turn y 180 > volume #2 level 0.01589 > turn y 180 > select add #3.1 1224 atoms, 1246 bonds, 150 residues, 1 model selected > select add #3.2 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 3 models selected > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > surface dust #2 size 5.9 > surface dust #4 size 5.9 > surface dust #5 size 5.9 > surface dust #6 size 5.9 > select add #3 5750 atoms, 5857 bonds, 3 pseudobonds, 716 residues, 4 models selected > select subtract #3 Nothing selected > volume #5 level 0.015 > turn y 180 > turn x 90 > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > turn x 90 > show #!1 models > hide #!2 models > show #3.1 models > show #!3.2 models > hide #!5 models > turn x 90 > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > lighting shadows false > turn x 90 > show #!2 models > hide #!1 models > hide #!3 models > hide #3.1 models > hide #!3.2 models > show #!5 models > lighting soft > hide #!6 models > hide #!4 models > hide #!2 models > show #!1 models > show #3.1 models > show #!3.2 models > hide #!5 models > show #7.1 models > color #7.1 #c3c3c365 > color #7.1 #c3c3c366 > hide #7.1 models > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes false > graphics silhouettes true > lighting soft > graphics silhouettes width0.5 Expected true or false or a keyword > graphics silhouettes width 0.5 > graphics silhouettes width 0.75 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting shadows true > graphics silhouettes true > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes width 1 > graphics silhouettes true > show #!6 models > show #7.1 models > hide #7.1 models > show #!4 models > lighting soft > lighting full > lighting flat > graphics silhouettes width 0.8 > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > lighting soft > graphics silhouettes true > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > graphics silhouettes width 1 > graphics silhouettes true > lighting soft > turn Y 1801 > turn Y 180 > hide #!1 models > show #!2 models > hide #!3 models > hide #3.1 models > hide #!3.2 models > show #!5 models > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting soft > graphics silhouettes false > graphics silhouettes true > turn Y 180 > hide #!2 models > show #!1 models > turn Y 180 > hide #!1 models > show #!2 models > turn Y 180 > volume #5 level 0.016 > turn Y 180 > lighting soft > lighting flat > lighting soft > volume #5 step 1 > volume #5 step 2 > volume #2 step 2 > volume #2 step 4 > volume #2 step 2 > turn Y 180 > show #!1 models > hide #!2 models > show #3.1 models > show #!3.2 models > hide #!5 models > show #!2 models > hide #!1 models > hide #!3 models > hide #3.1 models > hide #!3.2 models > show #!5 models > turn Y 180 > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/map1.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > turn Y 180 > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/map2.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > undo > turn Y 180 > show #!1 models > hide #!2 models > undo > show #!1 models > hide #!2 models > hide #!4 models > show #7.1 models > hide #7.1 models > show #3.1 models > show #!3.2 models > hide #!5 models > hide #!6 models > turn Y 180 > show #7.1 models > hide #7.1 models > show #!6 models > show #7.1 models > hide #7.1 models > show #!2 models > hide #!1 models > show #!4 models > show #!5 models > hide #3.1 models > hide #!3.2 models > turn Y 180 > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/map1.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > turn Y 180 > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/map2.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > turn Y 180 > show #7.1 models > hide #!4 models > show #!1 models > hide #!2 models > turn Y 180 > color #7.1 #c3c3c34d > show #3.1 models > show #!3.2 models > hide #!5 models > hide #!6 models > show #7.2 models > color #7.2 #c3c3c34d > color #7.2 #c3c3c340 > color #7.1 #c3c3c340 > turn Y 180 > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/model1.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > turn Y 180 > hide #!7 models > hide #7.1 models > hide #7.2 models > hide #!1 models > show #!6 models > show #!4 models > open /Users/whole.grains/Desktop/16-33a_modelling/body/4bx9.pdb 4bx9.pdb title: Human VPS33A In complex with A fragment of human VPS16 [more info...] Chain information for 4bx9.pdb #9 --- Chain | Description A | No description available C | No description available Non-standard residues in 4bx9.pdb #9 --- FMT — formic acid LMR — (2S)-2-hydroxybutanedioic acid (L-malate) MLA — malonic acid (dicarboxylic acid C3; propanediolic acid;methanedicarboxylic acid) 5336 atoms have anisotropic B-factors. Depict anisotropic information with Thermal Ellipsoids [start tool...] or the aniso command. > hide #3.1#!9#!3.2 atoms > select add #9 5466 atoms, 5450 bonds, 2 pseudobonds, 783 residues, 3 models selected > view matrix models #9,1,0,0,-44.008,0,1,0,-63.605,0,0,1,31.229 > ui mousemode right ""rotate selected models"" > view matrix models > #9,0.38169,-0.21859,-0.89807,254.4,-0.75115,-0.63954,-0.16359,390.97,-0.53859,0.73703,-0.4083,229.02 > ui mousemode right ""translate selected models"" > view matrix models > #9,0.38169,-0.21859,-0.89807,248.3,-0.75115,-0.63954,-0.16359,381.93,-0.53859,0.73703,-0.4083,239.03 > matchmaker #9 to #3.2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker body_refined_update_real_space_refined_012_01.pdb B, chain B (#3.2) with 4bx9.pdb, chain A (#9), sequence alignment score = 2748.2 RMSD between 473 pruned atom pairs is 1.021 angstroms; (across all 563 pairs: 1.608) > select subtract #9 Nothing selected > split chains Did not split head_fit_real_space_refined_002.pdb, has only one piece Did not split body_refined_update_real_space_refined_012_01.pdb A, has only one piece Did not split body_refined_update_real_space_refined_012_01.pdb B, has only one piece Did not split fold_vps33a_vps16_model_0.cif A, has only one piece Did not split fold_vps33a_vps16_model_0.cif B, has only one piece Split 4bx9.pdb (#9) into 2 models Chain information for 4bx9.pdb A #9.1 --- Chain | Description A | No description available Chain information for 4bx9.pdb C #9.2 --- Chain | Description C | No description available > color #9.2 dodgerblue > hide #!6 models > show #!6 models > color #9.2 #1e90fffc > color #9.2 dodgerblue > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!9.1 models > show #!9.1 models > hide #9.2 models > show #9.2 models > color #9.2 #0081fffc > color #9.2 #0081ffff > color #9.2 #5dafffff > color #9.2 #5dff8bff > color #9.2 #5dff79ff > color #9.2 #5dfffeff > color #9.2 #6dff5dff > color #9.2 #5dff9cff > matchmaker #9.2 to #3.1 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 body_refined_update_real_space_refined_012_01.pdb A, chain A (#3.1) with 4bx9.pdb C, chain C (#9.2), sequence alignment score = 478.3 RMSD between 85 pruned atom pairs is 0.907 angstroms; (across all 95 pairs: 1.580) > matchmaker #9.1 to #3.2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker body_refined_update_real_space_refined_012_01.pdb B, chain B (#3.2) with 4bx9.pdb A, chain A (#9.1), sequence alignment score = 2751.7 RMSD between 473 pruned atom pairs is 1.021 angstroms; (across all 563 pairs: 1.608) > show #!1 models > cartoon style #1,3-4,6,9#!8 modeHelix tube sides 20 > cartoon style #1,3-4,6,9#!8 xsection oval modeHelix default > show #!2 models > hide #!1 models > show #7.1 models > hide #7.1 models > show #7.2 models > hide #7.2 models > show #7.2 models > hide #7.2 models > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/model2_4bx9_overlay.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > hide #!9.1 models > hide #9.2 models > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/model2.tif"" width 1346 height 903 supersample 3 > save ""/Users/whole.grains/Documents/HOPS-SNARE paper/fourth draft/cryoEM > figure images/model2.tif"" width 2000 height 1342 supersample 3 > transparentBackground true > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > hide #!6 models > show #!6 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Registration OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac14,2 Model Number: Z16000944LL/A Chip: Apple M2 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 16 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3 (25D125) Kernel Version: Darwin 25.3.0 Time since boot: 3 days, 9 hours, 32 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 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: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect new normal Unassigned