id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8460 self._current_reference is None mille153@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Loading a PAE file Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33, shown at level 0.0974, step 1, values float32 Log from Tue Feb 7 14:18:19 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33, shown at level 0.0974, step 1, values float32 Log from Thu Feb 2 16:14:31 2023UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:user > open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold- > model-5-1.pdb Chain information for fnv-m-alphafold-model-5-1.pdb #1 --- Chain | Description A | No description available > open /Users/andrewmiller/Documents/FNV-modeling/FNV-M-model-5-chainD- > edit.pdb Chain information for FNV-M-model-5-chainD-edit.pdb #2 --- Chain | Description D | No description available > open /Users/andrewmiller/Documents/FNV-modeling/FNV-M-model-5-chainF- > edit.pdb Chain information for FNV-M-model-5-chainF-edit.pdb #3 --- Chain | Description F | No description available > open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold- > model-5-1.pdb Chain information for fnv-m-alphafold-model-5-1.pdb #4 --- Chain | Description A | No description available > hide #1 models > show #1 models > open /Users/andrewmiller/Documents/FNV-modeling/fnv-m-alphafold- > model-5-1.pdb Chain information for fnv-m-alphafold-model-5-1.pdb #5 --- Chain | Description A | No description available > hide #1 models > hide #4 models > hide #5 models > show #5 models > show #4 models > show #1 models > matchmaker #5 to #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 FNV-M-model-5-chainD-edit.pdb, chain D (#2) with fnv-m-alphafold- model-5-1.pdb, chain A (#5), sequence alignment score = 276.1 RMSD between 49 pruned atom pairs is 0.948 angstroms; (across all 58 pairs: 2.540) > matchmaker #4 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 FNV-M-model-5-chainF-edit.pdb, chain F (#3) with fnv-m-alphafold- model-5-1.pdb, chain A (#4), sequence alignment score = 276.1 RMSD between 49 pruned atom pairs is 0.948 angstroms; (across all 58 pairs: 2.540) > hide #4 models > show #4 models Populating font family aliases took 168 ms. Replace uses of missing font family "".AppleSystemUIFont"" with one that exists to avoid this cost. > save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainF- > edit.pdb models #4 > hide #5 models > show #5 models > save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainD- > edit.pdb models #5 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-M-alphafold-chainB- > edit.pdb models #1 > close session > open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4 Opened test-fnv-asu_box.ccp4 as #1, grid size 81,145,67, pixel 1.33, shown at level 0.168, step 1, values float32 > set bgColor white > set bgColor #ffffff00 > volume #1 level 0.107 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best- > model-edit.pdb Chain information for FNV-E-prediction-1-best-model-edit.pdb #2 --- Chain | Description A | No description available > transparency 50 > open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best- > model-edit.pdb Chain information for FNV-E-prediction-1-best-model-edit.pdb #3 --- Chain | Description A | No description available > open /Users/andrewmiller/Documents/FNV-modeling/FNV-E-prediction-1-best- > model-edit.pdb Chain information for FNV-E-prediction-1-best-model-edit.pdb #4 --- Chain | Description A | No description available > select add #4 7449 atoms, 7530 bonds, 493 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-20.268,0,1,0,-48.587,0,0,1,13.227 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.99857,0.049338,0.020729,772.69,-0.032585,-0.86781,0.49583,519.1,0.042452,0.49445,0.86817,-150.72 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.99857,0.049338,0.020729,789.19,-0.032585,-0.86781,0.49583,500.69,0.042452,0.49445,0.86817,-146.12 > view matrix models > #4,-0.99857,0.049338,0.020729,790.53,-0.032585,-0.86781,0.49583,500.53,0.042452,0.49445,0.86817,-145.92 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.99885,0.040425,0.025861,791.66,-0.022372,-0.86901,0.4943,497.76,0.042455,0.49315,0.86891,-145.77 > ui mousemode right ""translate selected models"" > ui tool show ""Fit in Map"" > fitmap #4 inMap #1 Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#4) to map test-fnv- asu_box.ccp4 (#1) using 7449 atoms average map value = 0.1097, steps = 128 shifted from previous position = 9.03 rotated from previous position = 15.1 degrees atoms outside contour = 3535, contour level = 0.107 Position of FNV-E-prediction-1-best-model-edit.pdb (#4) relative to test-fnv- asu_box.ccp4 (#1) coordinates: Matrix rotation and translation -0.97725858 0.02825152 0.21016072 679.12240517 0.04060965 -0.94780665 0.31624897 609.72599973 0.20812624 0.31759157 0.92510489 -174.14668121 Axis 0.10658756 0.16151476 0.98109738 Axis point 348.04241714 320.28749895 0.00000000 Rotation angle (degrees) 179.63914225 Shift along axis 0.01089425 > select subtract #4 Nothing selected > select add #3 7449 atoms, 7530 bonds, 493 residues, 1 model selected > view matrix models #3,1,0,0,32.528,0,1,0,-10.989,0,0,1,4.6657 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.9561,-0.073497,-0.28369,1044.2,0.075903,-0.99711,0.0025182,863.07,-0.28305,-0.019125,0.95891,154.94 > view matrix models > #3,-0.94178,-0.08722,-0.32471,1068.9,0.063398,-0.99451,0.083256,819.18,-0.33019,0.057824,0.94214,149.46 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.94178,-0.08722,-0.32471,1068,0.063398,-0.99451,0.083256,803.24,-0.33019,0.057824,0.94214,149.27 > fitmap #3 inMap #1 Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#3) to map test-fnv- asu_box.ccp4 (#1) using 7449 atoms average map value = 0.1057, steps = 224 shifted from previous position = 3.16 rotated from previous position = 55.2 degrees atoms outside contour = 3805, contour level = 0.107 Position of FNV-E-prediction-1-best-model-edit.pdb (#3) relative to test-fnv- asu_box.ccp4 (#1) coordinates: Matrix rotation and translation -0.91036793 0.12790971 0.39353442 524.69773237 0.14183002 -0.79696794 0.58713401 377.91727979 0.38873446 0.59032296 0.70739262 -250.71847076 Axis 0.21166597 0.31859580 0.92395575 Axis point 290.29657732 233.25421562 -0.00000000 Rotation angle (degrees) 179.56838716 Shift along axis -0.18925892 > view matrix models > #3,-0.91037,0.12791,0.39353,524.11,0.14183,-0.79697,0.58713,376.06,0.38873,0.59032,0.70739,-250.55 > view matrix models > #3,-0.91037,0.12791,0.39353,524.12,0.14183,-0.79697,0.58713,376.12,0.38873,0.59032,0.70739,-250.55 > fitmap #3 inMap #1 Fit molecule FNV-E-prediction-1-best-model-edit.pdb (#3) to map test-fnv- asu_box.ccp4 (#1) using 7449 atoms average map value = 0.1057, steps = 52 shifted from previous position = 1.91 rotated from previous position = 0.0252 degrees atoms outside contour = 3806, contour level = 0.107 Position of FNV-E-prediction-1-best-model-edit.pdb (#3) relative to test-fnv- asu_box.ccp4 (#1) coordinates: Matrix rotation and translation -0.91035553 0.12831748 0.39343034 524.59477571 0.14143086 -0.79699351 0.58719559 378.06830941 0.38890889 0.59019994 0.70739939 -250.74625657 Axis 0.21168422 0.31857800 0.92395771 Axis point 290.29507266 233.26980806 0.00000000 Rotation angle (degrees) 179.59340820 Shift along axis -0.18625781 > ui mousemode right select > select clear > view orient > save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainA- > edit.pdb models #4 relModel #1 > view orient > save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainC- > edit.pdb models #2 relModel #1 > save /Users/andrewmiller/Documents/FNV-modeling/FNV-E-alphafold-chainE- > edit.pdb models #3 relModel #1 > close session > set bgColor white > open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4 Opened test-fnv-asu_box.ccp4 as #1, grid size 81,145,67, pixel 1.33, shown at level 0.168, step 1, values float32 > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.pdb Chain information for 020223-FNV-alphafold-asu.pdb #2 --- Chain | Description A C E | No description available B D F | No description available > hide atoms > style stick Changed 25200 atom styles > style stick Changed 25200 atom styles > show atoms > show cartoons > hide atoms > volume #1 level 0.1108 > transparency 50 > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for 020223-FNV-alphafold-asu.pdb --- Chain | Description 2.2/A 2.2/C 2.2/E | No description available 2.2/B 2.2/D 2.2/F | No description available ISOLDE: created disulfide bonds between the following residues: E92-E116; A92-A116; A74-A105; C3-C30; E3-E30; C60-C121; A3-A30; A300-A330; C74-C105; C300-C330; A182-A283; C92-C116; E60-E121; E300-E330; E74-E105; C182-C283; A60-A121; E182-E283 > clipper associate #1 toModel #2 Opened test-fnv-asu_box.ccp4 as #2.1.1.1, grid size 81,145,67, pixel 1.33, shown at step 1, values float32 > volume #2.1.1.1 level 0.09739 > select add #2.2 25200 atoms, 25473 bonds, 1653 residues, 6 models selected > addh Summary of feedback from adding hydrogens to 020223-FNV-alphafold-asu.pdb #2.2 --- notes | No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain A; guessing termini instead No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain B; guessing termini instead No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain C; guessing termini instead No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain D; guessing termini instead No usable SEQRES records for 020223-FNV-alphafold-asu.pdb (#2.2) chain E; guessing termini instead 1 messages similar to the above omitted Chain-initial residues that are actual N termini: /A ALA 1, /C ALA 1, /E ALA 1 Chain-initial residues that are not actual N termini: /B LYS 18, /D LYS 18, /F LYS 18 Chain-final residues that are actual C termini: /A ALA 493, /C ALA 493, /E ALA 493 Chain-final residues that are not actual C termini: /B SER 75, /D SER 75, /F SER 75 1432 hydrogen bonds /B SER 75 is not terminus, removing H atom from 'C' /D SER 75 is not terminus, removing H atom from 'C' /F SER 75 is not terminus, removing H atom from 'C' 0 hydrogens added > ui tool show ""Ramachandran Plot"" Traceback (most recent call last): File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/cbook/__init__.py"", line 287, in process func(*args, **kwargs) File ""/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/validation/ramaplot/ramaplot.py"", line 292, in on_resize c.draw() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/backends/backend_agg.py"", line 436, in draw self.figure.draw(self.renderer) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/artist.py"", line 73, in draw_wrapper result = draw(artist, renderer, *args, **kwargs) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/artist.py"", line 50, in draw_wrapper return draw(artist, renderer) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/figure.py"", line 2796, in draw artists = self._get_draw_artists(renderer) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/figure.py"", line 238, in _get_draw_artists ax.apply_aspect() File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/axes/_base.py"", line 1890, in apply_aspect pb1 = pb.shrunk_to_aspect(box_aspect, pb, fig_aspect) File ""/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/matplotlib/transforms.py"", line 558, in shrunk_to_aspect raise ValueError(""'box_aspect' and 'fig_aspect' must be positive"") ValueError: 'box_aspect' and 'fig_aspect' must be positive > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs [Repeated 1 time(s)] ——— End of log from Thu Feb 2 16:14:31 2023 ——— opened ChimeraX session > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.cxs ——— End of log from Tue Feb 7 14:18:19 2023 ——— opened ChimeraX session > close session > open /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold-asu.pdb Chain information for 020223-FNV-alphafold-asu.pdb #1 --- Chain | Description A C E | No description available B D F | No description available > style stick Changed 25011 atom styles > show cartoons > hide atoms > open /Users/andrewmiller/Documents/FNV-modeling/test-fnv-asu_box.ccp4 Opened test-fnv-asu_box.ccp4 as #2, grid size 81,145,67, pixel 1.33, shown at level 0.168, step 1, values float32 > volume #2 level 0.1034 > transparency 50 > isolde start > set selectionWidth 4 Populating font family aliases took 156 ms. Replace uses of missing font family ""Carlito"" with one that exists to avoid this cost. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for 020223-FNV-alphafold-asu.pdb --- Chain | Description 1.2/A 1.2/C 1.2/E | No description available 1.2/B 1.2/D 1.2/F | No description available ISOLDE: created disulfide bonds between the following residues: A60-A121; A74-A105; C74-C105; C92-C116; A3-A30; C300-C330; C182-C283; E74-E105; E182-E283; E92-E116; A300-A330; C3-C30; E3-E30; E300-E330; A92-A116; C60-C121; A182-A283; E60-E121 > clipper associate #2 toModel #1 Opened test-fnv-asu_box.ccp4 as #1.1.1.1, grid size 81,145,67, pixel 1.33, shown at step 1, values float32 > volume #1.1.1.1 level 0.1058 > ui tool show ""Ramachandran Plot"" > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > volume #1.1.1.1 style surface > transparency 50 > select clear > show cartoons [Repeated 1 time(s)] > hide atoms > ui tool show ""Ramachandran Plot"" > volume #1.1.1.1 level 0.09391 > show sel atoms > select clear > select add #1.2 25011 atoms, 25278 bonds, 1644 residues, 11 models selected > show sel atoms > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > volume #1.1.1.1 level 0.08533 > select clear [Repeated 1 time(s)] > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > select clear [Repeated 3 time(s)] > isolde sim start sel ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > select #1.2/A:201 15 atoms, 14 bonds, 1 residue, 1 model selected > isolde sim start sel ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select clear > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > isolde sim start sel ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. [Repeated 1 time(s)] > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim Tugging of non-polar hydrogens is not enabled. Applying tug to the nearest bonded heavy atom. > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > isolde sim start sel ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > select clear [Repeated 1 time(s)] > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > select clear [Repeated 2 time(s)] > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > select clear > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > save /Users/andrewmiller/Documents/FNV-modeling/020223-FNV-alphafold- > asu-1.cxs Taking snapshot of stepper: 020223-FNV-alphafold-asu.pdb > isolde cisflip #1.2/A:329 Performing cis<\-->trans flip for 1 residues ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde cisflip #1.2/E:329 Performing cis<\-->trans flip for 1 residues ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde cisflip #1.2/C:329 Performing cis<\-->trans flip for 1 residues ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde cisflip #1.2/C:329 Performing cis<\-->trans flip for 1 residues ISOLDE: started sim > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view orient > select add #1.2 25011 atoms, 25278 bonds, 1644 residues, 11 models selected > isolde pepflip sel Flipping the peptide bond for 1 residues ISOLDE: started sim > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > ui mousemode right ""isolde tug residue"" > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select clear > volume #1.1.1.1 level 0.09105 > volume #1.1.1.1 level 0.09534 Traceback (most recent call last): File ""/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 343, in _load_pae_from_file run(self.session,f'alphafold pae #{self._current_reference.id_string} file ""{selected_file}"" plot false') AttributeError: 'NoneType' object has no attribute 'id_string' AttributeError: 'NoneType' object has no attribute 'id_string' File ""/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 343, in _load_pae_from_file run(self.session,f'alphafold pae #{self._current_reference.id_string} file ""{selected_file}"" plot false') See log for complete Python traceback. Traceback (most recent call last): File ""/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 343, in _load_pae_from_file run(self.session,f'alphafold pae #{self._current_reference.id_string} file ""{selected_file}"" plot false') AttributeError: 'NoneType' object has no attribute 'id_string' AttributeError: 'NoneType' object has no attribute 'id_string' File ""/Users/andrewmiller/Library/Application Support/ChimeraX/1.4/site- packages/chimerax/isolde/ui/restraints_tab/reference_model.py"", line 343, in _load_pae_from_file run(self.session,f'alphafold pae #{self._current_reference.id_string} file ""{selected_file}"" plot false') See log for complete Python traceback. OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Model Number: MK193LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 8419.60.44 OS Loader Version: 8419.60.44 Software: System Software Overview: System Version: macOS 13.1 (22C65) Kernel Version: Darwin 22.2.0 Time since boot: 4 hours, 25 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect assigned normal Third Party all ChimeraX