id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19299 Crash on Mac waking from sleep oswanson@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.0.1-arm64-arm-64bit ChimeraX Version: 1.10 (2025-06-26 08:57:52 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x000000030704f000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000306043000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File 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File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000017f2e3000 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 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Current thread 0x0000000209ac8800 (most recent call first): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1220 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, 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""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"" } }, ""logWritingSignature"" : ""03711014d73769830ab0acccb9a43391354ed4ce"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""652eff3d1bce5442b8d753c9"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000009 }, { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000008 } ], ""experiments"" : [ { ""treatmentId"" : ""f18344bb-554f-48ae-8449-e108a8813a55"", ""experimentId"" : ""6685b5584477001000e8c6c9"", ""deploymentId"" : 400000009 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs Log from Fri Oct 31 13:49:15 2025UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/oswanson/Desktop/Primocalins/231023_poly310-DH270UCA3_refine_001.pdb Chain information for 231023_poly310-DH270UCA3_refine_001.pdb #1 --- Chain | Description E | No description available H | No description available L | No description available Computing secondary structure > open /Users/oswanson/Desktop/Primocalins/Y513apo_refine_31.pdb Summary of feedback from opening /Users/oswanson/Desktop/Primocalins/Y513apo_refine_31.pdb --- warnings | Ignored bad PDB record found on line 1 REMARK Date 2022-07-08 Time 12:55:39 CDT -0500 (1657302939.20 s) Ignored bad PDB record found on line 2 REMARK PHENIX refinement Ignored bad PDB record found on line 4 REMARK ****************** INPUT FILES AND LABELS ****************************** Ignored bad PDB record found on line 5 REMARK Reflections: Ignored bad PDB record found on line 6 REMARK file name : /Users/danielwrapp/Desktop/PEDVnumber/Y513apo/Refine_4/Y513apo_refine_4.mtz 40 messages similar to the above omitted Chain information for Y513apo_refine_31.pdb #2 --- Chain | Description A B | No description available Computing secondary structure > hide #!1 models > set bgColor white > hide #2 models > show #!1 models > select #1/E:108 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 61 atoms, 60 bonds, 8 residues, 1 model selected > select up 604 atoms, 618 bonds, 74 residues, 1 model selected > select up 616 atoms, 629 bonds, 76 residues, 1 model selected > select up 1313 atoms, 1346 bonds, 164 residues, 1 model selected > select up 4851 atoms, 4757 bonds, 812 residues, 1 model selected > select down 1313 atoms, 1346 bonds, 164 residues, 1 model selected > color sel byhetero > color sel bychain > ui tool show H-Bonds > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8 > intraMol false intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.8 angstroms and 20 degrees Models used: 1 231023_poly310-DH270UCA3_refine_001.pdb 25 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O no hydrogen 2.874 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 71 N 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 86 O no hydrogen 2.780 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O no hydrogen 2.993 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1 no hydrogen 3.440 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 N 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O no hydrogen 2.550 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASN 164 N 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 242 O no hydrogen 2.990 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 2.679 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.050 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.339 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 44 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O no hydrogen 3.746 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 49 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 O no hydrogen 2.651 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 49 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 OD2 no hydrogen 2.434 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.428 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD2 no hydrogen 2.642 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 75 O no hydrogen 3.183 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 66 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O no hydrogen 3.912 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 86 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 51 O no hydrogen 2.817 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 242 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E GLU 163 OE1 no hydrogen 2.752 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 409 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E VAL 34 O no hydrogen 2.557 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 409 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 169 O no hydrogen 3.211 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O no hydrogen 4.003 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 416 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.243 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 38 O no hydrogen 2.357 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E VAL 41 O no hydrogen 2.400 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/S HOH 431 O 231023_poly310-DH270UCA3_refine_001.pdb #1/E HIS 165 O no hydrogen 3.686 N/A 25 hydrogen bonds found > select ::name=""HOH""::name=""SO4"" 234 atoms, 24 bonds, 210 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/E:109 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 61 atoms, 60 bonds, 8 residues, 1 model selected > select up 604 atoms, 618 bonds, 74 residues, 1 model selected > select up 616 atoms, 629 bonds, 76 residues, 1 model selected > select up 1313 atoms, 1346 bonds, 164 residues, 1 model selected > select up 4647 atoms, 4757 bonds, 608 residues, 1 model selected > select down 1313 atoms, 1346 bonds, 164 residues, 1 model selected > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8 > intraMol false intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.8 angstroms and 20 degrees Models used: 1 231023_poly310-DH270UCA3_refine_001.pdb 6 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O no hydrogen 2.874 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O no hydrogen 2.993 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1 no hydrogen 3.440 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 2.679 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.050 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.339 N/A 6 hydrogen bonds found > select up 93 atoms, 88 bonds, 10 residues, 1 model selected > color sel byhetero > select clear > select #1/E:128 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > open /Users/oswanson/Downloads/9NPI-sf.cif Summary of feedback from opening /Users/oswanson/Downloads/9NPI-sf.cif --- warning | No mmCIF models found. > open /Users/oswanson/Downloads/9NPI-sf.cif Summary of feedback from opening /Users/oswanson/Downloads/9NPI-sf.cif --- warning | No mmCIF models found. > open /Users/oswanson/coot_sessions/3FW4.mtz > /Users/oswanson/coot_sessions/3FW4.pdb Install the Clipper bundle to open ""MTZ"" format files. Opener for format 'MTZ' is not installed; see log for more info > open /Users/oswanson/coot_sessions/3FW4.pdb 3FW4.pdb title: Crystal structure of siderocalin (ngal, lipocalin 2) complexed with ferric catechol [more info...] Chain information for 3FW4.pdb #3 --- Chain | Description | UniProt A B C | neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-178 Non-standard residues in 3FW4.pdb #3 --- CAQ — catechol (1,2-dihydroxybenzene) CL — chloride ion FE — Fe (III) ion GOL — glycerol (glycerin; propane-1,2,3-triol) NA — sodium ion 31 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > open /Users/oswanson/coot_sessions/3FW4-sf.cif Summary of feedback from opening /Users/oswanson/coot_sessions/3FW4-sf.cif --- warning | No mmCIF models found. > open /Users/oswanson/Desktop/Primocalins/Structures/Cluster2c_lib1.pdb > /Users/oswanson/Desktop/Primocalins/Structures/design_start.pdb > /Users/oswanson/Desktop/Primocalins/Structures/RMSD4_NNK1.pdb > /Users/oswanson/Desktop/Primocalins/Structures/RMSD6_NNK1.pdb Chain information for Cluster2c_lib1.pdb #4 --- Chain | Description A | No description available G | No description available H | No description available Chain information for design_start.pdb #5 --- Chain | Description A | No description available G | No description available H | No description available Chain information for RMSD4_NNK1.pdb #6 --- Chain | Description A | No description available G | No description available H | No description available Chain information for RMSD6_NNK1.pdb #7 --- Chain | Description A | No description available G | No description available H | No description available Computing secondary structure [Repeated 3 time(s)] > select #1/E:68 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 53 atoms, 53 bonds, 7 residues, 1 model selected > select up 709 atoms, 728 bonds, 90 residues, 1 model selected > select up 727 atoms, 746 bonds, 92 residues, 1 model selected > select up 1313 atoms, 1346 bonds, 164 residues, 1 model selected > select up 4647 atoms, 4757 bonds, 608 residues, 1 model selected > select down 1313 atoms, 1346 bonds, 164 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2,4-7#!3 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with Y513apo_refine_31.pdb, chain B (#2), sequence alignment score = 692 RMSD between 154 pruned atom pairs is 0.689 angstroms; (across all 164 pairs: 1.591) Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with Cluster2c_lib1.pdb, chain A (#4), sequence alignment score = 692 RMSD between 151 pruned atom pairs is 0.676 angstroms; (across all 164 pairs: 1.416) Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with design_start.pdb, chain A (#5), sequence alignment score = 709.7 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs: 1.402) Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with RMSD4_NNK1.pdb, chain A (#6), sequence alignment score = 692.2 RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs: 1.442) Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with RMSD6_NNK1.pdb, chain A (#7), sequence alignment score = 683.1 RMSD between 152 pruned atom pairs is 0.697 angstroms; (across all 164 pairs: 1.421) Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with 3FW4.pdb, chain A (#3), sequence alignment score = 709.7 RMSD between 150 pruned atom pairs is 0.624 angstroms; (across all 164 pairs: 1.389) > matchmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with Cluster2c_lib1.pdb, chain A (#4), sequence alignment score = 692 RMSD between 151 pruned atom pairs is 0.676 angstroms; (across all 164 pairs: 1.416) > matchmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with design_start.pdb, chain A (#5), sequence alignment score = 709.7 RMSD between 150 pruned atom pairs is 0.630 angstroms; (across all 164 pairs: 1.402) > matchmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with RMSD4_NNK1.pdb, chain A (#6), sequence alignment score = 692.2 RMSD between 150 pruned atom pairs is 0.641 angstroms; (across all 164 pairs: 1.442) > matchmaker #7 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with RMSD6_NNK1.pdb, chain A (#7), sequence alignment score = 683.1 RMSD between 152 pruned atom pairs is 0.697 angstroms; (across all 164 pairs: 1.421) > show #2 models > hide #!3 models > show #!3 models > hide #!3 models > hide #4 models > hide #!1 models > hide #5 models > hide #6 models > hide #7 models > show #!1 models > show #!3 models > hide #!3 models > select #2/A:126 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 76 atoms, 78 bonds, 9 residues, 1 model selected > select up 1459 atoms, 1497 bonds, 181 residues, 1 model selected > ui tool show Matchmaker > matchmaker #2 & sel to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain E (#1) with Y513apo_refine_31.pdb, chain A (#2), sequence alignment score = 689 RMSD between 154 pruned atom pairs is 0.695 angstroms; (across all 164 pairs: 1.580) > hide #!1 models > show #5 models > show #6 models > hide #5 models > select add #6 7768 atoms, 7887 bonds, 591 residues, 2 models selected > color sel bychain > color sel byhetero > hide #6 models > show #7 models > color sel & #2 bychain > select add #7 14068 atoms, 14269 bonds, 1001 residues, 3 models selected > select subtract #6 7759 atoms, 7879 bonds, 591 residues, 2 models selected > color sel bychain > color sel byhetero > show #6 models > hide #6 models > show #6 models > select add #6 14068 atoms, 14269 bonds, 1001 residues, 3 models selected > color sel bychain > select subtract #6 7759 atoms, 7879 bonds, 591 residues, 2 models selected > select add #2 9248 atoms, 9400 bonds, 778 residues, 2 models selected > select subtract #2 6300 atoms, 6382 bonds, 410 residues, 1 model selected > hide #6 models > hide #2 models > show #2 models > hide #7 models > select #2/A:80 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 79 atoms, 81 bonds, 9 residues, 1 model selected [deleted to fit within ticket limits] > select up 1590 atoms, 1630 bonds, 197 residues, 1 model selected > contacts sel restrict cross interModel false intraMol false > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513 > reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 97 contacts atom1 atom2 overlap distance fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CB 0.972 2.788 fold_poly28_uca3_model_0.cif #11/A ASN 131 CB fold_poly28_uca3_model_0.cif #11/C TYR 51 OH 0.818 2.522 fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1 fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2 0.767 2.633 fold_poly28_uca3_model_0.cif #11/A SER 70 CB fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1 0.592 3.168 fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1 fold_poly28_uca3_model_0.cif #11/B ARG 72 NH2 0.548 2.972 fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2 fold_poly28_uca3_model_0.cif #11/B ARG 72 NH1 0.481 3.039 fold_poly28_uca3_model_0.cif #11/A MET 79 CE fold_poly28_uca3_model_0.cif #11/B LEU 104 CD2 0.440 3.320 fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CG 0.367 3.123 fold_poly28_uca3_model_0.cif #11/A GLU 81 CB fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1 0.341 3.419 fold_poly28_uca3_model_0.cif #11/A GLU 134 OE1 fold_poly28_uca3_model_0.cif #11/B TYR 106 CE1 0.329 2.851 fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1 fold_poly28_uca3_model_0.cif #11/B TYR 111 CE2 0.304 3.096 fold_poly28_uca3_model_0.cif #11/A LEU 9 CB fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ 0.273 3.247 fold_poly28_uca3_model_0.cif #11/A ASN 131 O fold_poly28_uca3_model_0.cif #11/C TYR 51 OH 0.230 2.250 fold_poly28_uca3_model_0.cif #11/A LEU 44 CD1 fold_poly28_uca3_model_0.cif #11/C TYR 32 CD1 0.219 3.421 fold_poly28_uca3_model_0.cif #11/A MET 79 SD fold_poly28_uca3_model_0.cif #11/B ILE 102 CG2 0.197 3.453 fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2 0.197 3.203 fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1 fold_poly28_uca3_model_0.cif #11/C TYR 93 CE1 0.186 2.994 fold_poly28_uca3_model_0.cif #11/A ASN 131 CA fold_poly28_uca3_model_0.cif #11/C TYR 51 OH 0.181 3.159 fold_poly28_uca3_model_0.cif #11/A ARG 132 CZ fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1 0.177 2.853 fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CD1 0.170 3.470 fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ 0.124 3.126 fold_poly28_uca3_model_0.cif #11/A GLU 134 OE1 fold_poly28_uca3_model_0.cif #11/B TYR 106 CD1 0.120 3.060 fold_poly28_uca3_model_0.cif #11/A ASN 131 C fold_poly28_uca3_model_0.cif #11/C TYR 51 OH 0.117 2.953 fold_poly28_uca3_model_0.cif #11/A ASN 131 CB fold_poly28_uca3_model_0.cif #11/C TYR 51 CZ 0.113 3.377 fold_poly28_uca3_model_0.cif #11/A ARG 132 CD fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1 0.108 3.192 fold_poly28_uca3_model_0.cif #11/A LEU 44 CD1 fold_poly28_uca3_model_0.cif #11/C LEU 34 CD1 0.106 3.654 fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1 fold_poly28_uca3_model_0.cif #11/C TYR 32 CE1 0.102 3.078 fold_poly28_uca3_model_0.cif #11/A ASP 75 CG fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2 0.098 3.542 fold_poly28_uca3_model_0.cif #11/A ARG 83 CZ fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2 0.062 3.308 fold_poly28_uca3_model_0.cif #11/A MET 79 CE fold_poly28_uca3_model_0.cif #11/B LEU 104 CG 0.045 3.715 fold_poly28_uca3_model_0.cif #11/A GLU 46 CD fold_poly28_uca3_model_0.cif #11/C TYR 93 OH 0.032 3.308 fold_poly28_uca3_model_0.cif #11/A GLU 134 CD fold_poly28_uca3_model_0.cif #11/B TYR 106 CE1 -0.011 3.651 fold_poly28_uca3_model_0.cif #11/A PHE 54 CZ fold_poly28_uca3_model_0.cif #11/B LEU 104 O -0.023 3.203 fold_poly28_uca3_model_0.cif #11/A SER 70 C fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1 -0.039 3.529 fold_poly28_uca3_model_0.cif #11/A SER 70 O fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1 -0.043 3.343 fold_poly28_uca3_model_0.cif #11/A ASP 75 OD2 fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2 -0.062 3.242 fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1 fold_poly28_uca3_model_0.cif #11/B TYR 105 CD2 -0.064 3.464 fold_poly28_uca3_model_0.cif #11/A GLU 46 CD fold_poly28_uca3_model_0.cif #11/C TYR 32 OH -0.077 3.417 fold_poly28_uca3_model_0.cif #11/A LEU 9 CD2 fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ -0.080 3.600 fold_poly28_uca3_model_0.cif #11/A LEU 9 CD1 fold_poly28_uca3_model_0.cif #11/C GLU 52 OE2 -0.089 3.389 fold_poly28_uca3_model_0.cif #11/A MET 79 CG fold_poly28_uca3_model_0.cif #11/B ASN 54 ND2 -0.098 3.618 fold_poly28_uca3_model_0.cif #11/A TYR 108 OH fold_poly28_uca3_model_0.cif #11/B TYR 105 CE2 -0.101 3.321 fold_poly28_uca3_model_0.cif #11/A SER 7 CB fold_poly28_uca3_model_0.cif #11/C ASN 33 OD1 -0.104 3.404 fold_poly28_uca3_model_0.cif #11/A ARG 83 NH2 fold_poly28_uca3_model_0.cif #11/B TYR 105 OH -0.121 2.821 fold_poly28_uca3_model_0.cif #11/A LEU 9 CB fold_poly28_uca3_model_0.cif #11/C LYS 55 CE -0.127 3.887 fold_poly28_uca3_model_0.cif #11/A PHE 125 CE1 fold_poly28_uca3_model_0.cif #11/B TYR 105 OH -0.143 3.363 fold_poly28_uca3_model_0.cif #11/A PHE 54 CE1 fold_poly28_uca3_model_0.cif #11/B LEU 104 O -0.144 3.324 fold_poly28_uca3_model_0.cif #11/A ALA 42 CB fold_poly28_uca3_model_0.cif #11/B TYR 111 OH -0.148 3.488 fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1 fold_poly28_uca3_model_0.cif #11/C SER 54 OG -0.156 2.636 fold_poly28_uca3_model_0.cif #11/A SER 70 CA fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1 -0.170 3.930 fold_poly28_uca3_model_0.cif #11/A ARG 132 NE fold_poly28_uca3_model_0.cif #11/C GLU 52 CD -0.177 3.697 fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1 fold_poly28_uca3_model_0.cif #11/C TYR 32 CZ -0.182 3.212 fold_poly28_uca3_model_0.cif #11/A MET 79 SD fold_poly28_uca3_model_0.cif #11/B ASN 52 ND2 -0.184 3.194 fold_poly28_uca3_model_0.cif #11/A ARG 132 CZ fold_poly28_uca3_model_0.cif #11/C GLU 52 CD -0.186 3.676 fold_poly28_uca3_model_0.cif #11/A ALA 42 O fold_poly28_uca3_model_0.cif #11/B TYR 111 OH -0.188 2.668 fold_poly28_uca3_model_0.cif #11/A LEU 9 CD1 fold_poly28_uca3_model_0.cif #11/C GLU 52 CD -0.198 3.958 fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CA -0.200 3.960 fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2 fold_poly28_uca3_model_0.cif #11/B ARG 72 NH2 -0.206 3.726 fold_poly28_uca3_model_0.cif #11/A GLU 46 OE2 fold_poly28_uca3_model_0.cif #11/C GLY 95 CA -0.224 3.524 fold_poly28_uca3_model_0.cif #11/A ARG 83 NH1 fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ -0.226 3.476 fold_poly28_uca3_model_0.cif #11/A PHE 125 CZ fold_poly28_uca3_model_0.cif #11/B TYR 105 OH -0.235 3.455 fold_poly28_uca3_model_0.cif #11/A SER 7 OG fold_poly28_uca3_model_0.cif #11/C VAL 53 CG1 -0.238 3.578 fold_poly28_uca3_model_0.cif #11/A LEU 38 CD2 fold_poly28_uca3_model_0.cif #11/B TYR 105 O -0.243 3.543 fold_poly28_uca3_model_0.cif #11/A PRO 103 O fold_poly28_uca3_model_0.cif #11/B TYR 32 OH -0.244 2.724 fold_poly28_uca3_model_0.cif #11/A SER 7 CB fold_poly28_uca3_model_0.cif #11/C ASN 33 ND2 -0.246 3.766 fold_poly28_uca3_model_0.cif #11/A GLU 46 CD fold_poly28_uca3_model_0.cif #11/C TYR 93 CE1 -0.250 3.890 fold_poly28_uca3_model_0.cif #11/A ASP 75 CB fold_poly28_uca3_model_0.cif #11/B GLY 57 CA -0.259 4.019 fold_poly28_uca3_model_0.cif #11/A SER 7 CB fold_poly28_uca3_model_0.cif #11/C ASN 33 CG -0.259 3.749 fold_poly28_uca3_model_0.cif #11/A LEU 196 CD2 fold_poly28_uca3_model_0.cif #11/B ARG 72 CZ -0.259 3.749 fold_poly28_uca3_model_0.cif #11/A LEU 136 CD2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CD2 -0.263 3.903 fold_poly28_uca3_model_0.cif #11/A ARG 132 CD fold_poly28_uca3_model_0.cif #11/C GLU 52 CD -0.269 4.029 fold_poly28_uca3_model_0.cif #11/A GLU 81 N fold_poly28_uca3_model_0.cif #11/B LEU 104 CD1 -0.276 3.796 fold_poly28_uca3_model_0.cif #11/A ALA 77 CB fold_poly28_uca3_model_0.cif #11/B SER 55 O -0.282 3.582 fold_poly28_uca3_model_0.cif #11/A ASP 75 OD1 fold_poly28_uca3_model_0.cif #11/B TRP 50 CH2 -0.283 3.463 fold_poly28_uca3_model_0.cif #11/A THR 138 CG2 fold_poly28_uca3_model_0.cif #11/B TYR 105 CD1 -0.286 3.926 fold_poly28_uca3_model_0.cif #11/A GLU 46 CD fold_poly28_uca3_model_0.cif #11/C GLY 95 CA -0.289 4.049 fold_poly28_uca3_model_0.cif #11/A PHE 54 CZ fold_poly28_uca3_model_0.cif #11/B TYR 105 CA -0.291 3.931 fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1 fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1 -0.302 2.962 fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1 fold_poly28_uca3_model_0.cif #11/B ARG 72 CZ -0.303 3.793 fold_poly28_uca3_model_0.cif #11/A SER 7 OG fold_poly28_uca3_model_0.cif #11/C VAL 53 CG2 -0.304 3.644 fold_poly28_uca3_model_0.cif #11/A LEU 9 CG fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ -0.320 3.840 fold_poly28_uca3_model_0.cif #11/A ARG 132 NE fold_poly28_uca3_model_0.cif #11/C GLU 52 OE1 -0.324 2.984 fold_poly28_uca3_model_0.cif #11/A ASN 131 CB fold_poly28_uca3_model_0.cif #11/C TYR 51 CE1 -0.333 3.973 fold_poly28_uca3_model_0.cif #11/A PRO 103 CB fold_poly28_uca3_model_0.cif #11/B TYR 32 OH -0.338 3.678 fold_poly28_uca3_model_0.cif #11/A ARG 132 CG fold_poly28_uca3_model_0.cif #11/C LYS 55 NZ -0.338 3.858 fold_poly28_uca3_model_0.cif #11/A ARG 132 NH1 fold_poly28_uca3_model_0.cif #11/B TYR 111 CD2 -0.350 3.750 fold_poly28_uca3_model_0.cif #11/A ASP 8 OD1 fold_poly28_uca3_model_0.cif #11/C SER 54 CB -0.363 3.663 fold_poly28_uca3_model_0.cif #11/A MET 79 CE fold_poly28_uca3_model_0.cif #11/B ILE 102 CG2 -0.367 4.127 fold_poly28_uca3_model_0.cif #11/A ARG 130 CZ fold_poly28_uca3_model_0.cif #11/C SER 58 OG -0.368 3.438 fold_poly28_uca3_model_0.cif #11/A ARG 83 CZ fold_poly28_uca3_model_0.cif #11/B TYR 105 OH -0.369 3.439 fold_poly28_uca3_model_0.cif #11/A ASN 131 ND2 fold_poly28_uca3_model_0.cif #11/C PRO 57 CA -0.373 3.893 fold_poly28_uca3_model_0.cif #11/A ASP 49 CB fold_poly28_uca3_model_0.cif #11/C SER 96 CA -0.379 4.139 fold_poly28_uca3_model_0.cif #11/A GLU 134 CD fold_poly28_uca3_model_0.cif #11/B TYR 106 CZ -0.382 3.872 fold_poly28_uca3_model_0.cif #11/A GLU 46 CG fold_poly28_uca3_model_0.cif #11/C TYR 93 OH -0.382 3.722 fold_poly28_uca3_model_0.cif #11/A LEU 196 CD1 fold_poly28_uca3_model_0.cif #11/B ARG 72 NH1 -0.386 3.906 fold_poly28_uca3_model_0.cif #11/A PHE 125 CE1 fold_poly28_uca3_model_0.cif #11/B TYR 105 CZ -0.387 3.757 fold_poly28_uca3_model_0.cif #11/A GLU 46 OE1 fold_poly28_uca3_model_0.cif #11/C TYR 32 OH -0.392 2.872 97 contacts > select clear > select #11/A:194 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 133 atoms, 136 bonds, 15 residues, 1 model selected > hide sel atoms > hide sel cartoons > select clear > select #11/A:197 10 atoms, 9 bonds, 1 residue, 1 model selected > hide sel cartoons > select #11/A:4 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 104 atoms, 107 bonds, 14 residues, 1 model selected > show #!1 models > hide #10.1 models > hide #!11 models > show #1.2 models > show #1.3 models > select #1/E:126 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 63 atoms, 63 bonds, 8 residues, 1 model selected > select up 604 atoms, 618 bonds, 74 residues, 1 model selected > select up 616 atoms, 629 bonds, 76 residues, 1 model selected > select up 1313 atoms, 1346 bonds, 164 residues, 1 model selected > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8 > intraMol false intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.8 angstroms and 20 degrees Models used: 1 231023_poly310-DH270UCA3_refine_001.pdb 6 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O no hydrogen 2.874 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O no hydrogen 2.993 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 66 OD1 no hydrogen 3.440 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 2.679 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 no hydrogen 3.050 N/A 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2 231023_poly310-DH270UCA3_refine_001.pdb #1/E TYR 78 O no hydrogen 3.339 N/A 6 hydrogen bonds found > hide #1.3 models > select #1/E:79 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 78 atoms, 80 bonds, 9 residues, 1 model selected > select up 709 atoms, 728 bonds, 90 residues, 1 model selected > select up 727 atoms, 746 bonds, 92 residues, 1 model selected > select up 1313 atoms, 1346 bonds, 164 residues, 1 model selected > contacts sel restrict cross interModel false intraMol false > ignoreHiddenModels true select true color #ff2600 name contacts_AF3_Y513 > reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 64 contacts atom1 atom2 overlap distance 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 68 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD1 0.171 3.589 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CD1 0.157 3.483 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 111 O 0.142 3.158 231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O 0.137 3.163 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE 231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2 0.135 3.625 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CZ2 0.103 3.537 231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CE2 0.101 3.539 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 O 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CB 0.095 3.205 231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD2 0.080 3.560 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 CE 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O 0.077 3.223 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 ND2 0.069 3.451 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 O 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CA 0.058 3.242 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CH2 0.052 3.588 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 CE1 0.052 3.128 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 NE1 0.046 3.474 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 37 OH 0.028 3.312 231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 70 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 0.025 3.735 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CH2 0.022 3.618 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 SD 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 CB -0.019 3.669 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 128 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 37 OH -0.052 3.392 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CG -0.060 3.360 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CD 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 -0.118 3.878 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 -0.120 3.880 231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB -0.127 3.887 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2 -0.129 3.619 231023_poly310-DH270UCA3_refine_001.pdb #1/E CYS 76 O 231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 62 CB -0.147 3.447 231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD1 -0.154 3.794 231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O -0.159 3.459 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CH2 -0.166 3.806 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CA -0.172 3.472 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH -0.172 3.512 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 O 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CB -0.184 3.484 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH -0.199 2.679 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2 -0.212 3.972 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B O -0.214 2.874 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2 -0.251 3.741 231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB -0.252 3.742 231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CD1 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CB -0.254 3.894 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D CG -0.259 4.019 231023_poly310-DH270UCA3_refine_001.pdb #1/E PHE 52 CE1 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CB -0.259 3.899 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CD2 -0.263 3.753 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 59 CG -0.267 3.757 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 OH -0.268 3.608 231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CZ -0.280 3.770 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 38 CZ -0.289 3.319 231023_poly310-DH270UCA3_refine_001.pdb #1/E ALA 49 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD1 -0.291 3.931 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CE2 -0.307 3.797 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CE 231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CB -0.315 4.075 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CA 231023_poly310-DH270UCA3_refine_001.pdb #1/H SER 111 O -0.318 3.618 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111C CA -0.322 3.842 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 74 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H THR 65 O -0.333 2.993 231023_poly310-DH270UCA3_refine_001.pdb #1/E ARG 127 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 109 CG -0.334 3.824 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111C C -0.335 3.585 231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CG -0.339 3.829 231023_poly310-DH270UCA3_refine_001.pdb #1/E LYS 50 NZ 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASP 112D N -0.340 3.620 231023_poly310-DH270UCA3_refine_001.pdb #1/E GLY 70 N 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 -0.342 3.862 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 -0.361 4.121 231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CE1 -0.370 4.010 231023_poly310-DH270UCA3_refine_001.pdb #1/E MET 77 SD 231023_poly310-DH270UCA3_refine_001.pdb #1/H ILE 110 CG2 -0.372 4.022 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H TRP 55 CZ2 -0.386 4.026 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CB 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 -0.388 4.148 231023_poly310-DH270UCA3_refine_001.pdb #1/E LEU 36 CD2 231023_poly310-DH270UCA3_refine_001.pdb #1/H TYR 111B CD1 -0.388 4.028 231023_poly310-DH270UCA3_refine_001.pdb #1/E ASP 73 OD1 231023_poly310-DH270UCA3_refine_001.pdb #1/H ASN 57 ND2 -0.390 3.050 231023_poly310-DH270UCA3_refine_001.pdb #1/E PRO 72 CG 231023_poly310-DH270UCA3_refine_001.pdb #1/H LEU 111A CD2 -0.396 4.156 64 contacts > select clear > hide #1.4 models > show #1.4 models > hide #1.4 models > show #1.3 models > hide #1.3 models > show #1.4 models > show #1.3 models > hide #1.3 models > open > /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #12 --- Chain | Description A B | . C D | . E F | . > hide #!1 models > hide #12 atoms > show #12 cartoons Computing secondary structure > color #12 bychain > open pdb:6QWL Summary of feedback from opening 6QWL fetched from pdb --- note | Fetching compressed mmCIF 6qwl from http://files.rcsb.org/download/6qwl.cif 6qwl title: Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter [more info...] Chain information for 6qwl #13 --- Chain | Description | UniProt E | Polymerase acidic protein | PA_INBP9 1-726 K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752 Q | Polymerase basic protein 2 | PB2_INBP9 1-770 T | 3' cRNA | W | 5' cRNA | > ui tool show Matchmaker > matchmaker #!13 to #12 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 fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#12) with 6qwl, chain K (#13), sequence alignment score = 3220.4 RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs: 3.053) > select add #13 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected > hide sel atoms > show sel cartoons > select clear > hide #12 models > nucleotides #!13 atoms > style nucleic & #!13 stick Changed 553 atom styles > nucleotides #!13 fill > style nucleic & #!13 stick Changed 553 atom styles > nucleotides #!13 fill > style nucleic & #!13 stick Changed 553 atom styles > nucleotides #!13 tube/slab shape box > nucleotides #!13 ladder > select #13/T:6 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 249 atoms, 275 bonds, 12 residues, 1 model selected > nucleotides sel ladder > nucleotides sel tube/slab shape box > nucleotides sel fill > style nucleic & sel stick Changed 249 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 249 atom styles > select add #13 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected > color sel bychain > select clear > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > hide #12 models > close #12#13 > show #!1 models > save /Users/oswanson/Desktop/Primocalins/Structures/initial_models.cxs > hide #1.4 models > show #1.3 models > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.3 models > show #1.3 models > hide #1.4 models > close #1.4 > color #1.3 #0433ffff models > color #1.3 #7a81ffff models > color #1.3 #0433ffff models > color #1.3 #f3f3f3ff models > color #1.3 #0433ffff models > color #1.3 #0b1e97ff models > color #1.2 #ea99faff models > hide #1.3 models > select add #1 4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected > size stickRadius 0.25 Changed 41190 bond radii > size stickRadius 0. Bond radius must be greater than 0. > size stickRadius 0.3 Changed 41190 bond radii > size stickRadius 0.275 Changed 41190 bond radii > size stickRadius 0.25 Changed 41190 bond radii > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/H Alignment identifier is 1/H > select #1/H:190 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/H:190 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/H:111A 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/H:111A 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/H:112D 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/H:112D 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/H:111A,112D 16 atoms, 14 bonds, 2 residues, 1 model selected > select #1/H:111A,112B,112D 22 atoms, 19 bonds, 3 residues, 1 model selected > show sel cartoons > show sel atoms > select #1/H:112B 6 atoms, 5 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/H:111B 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/H:111B-111C,112A,112B,112C,112D 48 atoms, 49 bonds, 6 residues, 1 model selected > open pdb:8sax Summary of feedback from opening 8sax fetched from pdb --- notes | Fetching compressed mmCIF 8sax from http://files.rcsb.org/download/8sax.cif Fetching CCD BMA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/BMA/BMA.cif Fetching CCD MAN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/MAN/MAN.cif 8sax title: CryoEM structure of DH270.UCA-CH848.10.17DT [more info...] Chain information for 8sax #12 --- Chain | Description | UniProt A E I | CH848.10.17.SOSIP gp120 | A0A1W6IPB2_9HIV1 34-511 B F J | CH848.10.17.SOSIP gp41 | C G K | DH270.UCA heavy chain | D H L | DH270.UCA light chain | Non-standard residues in 8sax #12 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > select clear > select #1/H:66 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/L:109 12 atoms, 10 bonds, 2 residues, 1 model selected > select up 55 atoms, 54 bonds, 8 residues, 1 model selected > select up 3334 atoms, 3411 bonds, 444 residues, 1 model selected > ui tool show Matchmaker > matchmaker #12 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1) with 8sax, chain C (#12), sequence alignment score = 647.8 RMSD between 126 pruned atom pairs is 0.769 angstroms; (across all 127 pairs: 0.792) > select add #12 23194 atoms, 23760 bonds, 2991 residues, 2 models selected > select #12/G:23@CE 1 atom, 1 residue, 1 model selected > select #12/G:23@CE 1 atom, 1 residue, 1 model selected > select add #12 19860 atoms, 20349 bonds, 2547 residues, 1 model selected > hide sel atoms > show sel cartoons > select clear > hide #!1 models > ui mousemode right select Drag select of 29 residues > select up 508 atoms, 510 bonds, 67 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8 > intraMol false intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.8 angstroms and 20 degrees Models used: 12 8sax 6 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 8sax #12/A LYS 327 NZ 8sax #12/C TYR 33 OH no hydrogen 3.095 N/A 8sax #12/A THR 415 OG1 8sax #12/N NAG 1 O5 no hydrogen 3.662 N/A 8sax #12/A THR 415 OG1 8sax #12/N NAG 1 O6 no hydrogen 3.431 N/A 8sax #12/C TYR 33 OH 8sax #12/A ASP 325 OD2 no hydrogen 2.827 N/A 8sax #12/N NAG 1 N2 8sax #12/A HIS 330 NE2 no hydrogen 3.281 N/A 8sax #12/N NAG 1 O6 8sax #12/A THR 415 OG1 no hydrogen 3.431 N/A 6 hydrogen bonds found > select up 60 atoms, 57 bonds, 6 residues, 1 model selected > style sel stick Changed 60 atom styles > color sel byhetero > select clear > select #12/A:414 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 73 atoms, 72 bonds, 9 residues, 1 model selected > select up 3582 atoms, 3664 bonds, 462 residues, 1 model selected > select down 73 atoms, 72 bonds, 9 residues, 1 model selected > select clear Drag select of 9 atoms, 43 residues, 7 bonds > select up 636 atoms, 638 bonds, 84 residues, 1 model selected > contacts sel restrict cross interModel false intraMol false > ignoreHiddenModels true select true color #ff2600 reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 31 contacts atom1 atom2 overlap distance 8sax #12/A ASN 332 ND2 8sax #12/N NAG 1 C1 1.117 2.403 8sax #12/A ASN 332 CG 8sax #12/N NAG 1 C1 0.545 2.945 8sax #12/A ASN 332 OD1 8sax #12/N NAG 1 C1 0.528 2.772 8sax #12/A ASN 332 ND2 8sax #12/N NAG 1 C2 0.307 3.213 8sax #12/A HIS 330 NE2 8sax #12/N NAG 1 C8 0.296 3.224 8sax #12/A HIS 330 CE1 8sax #12/C TYR 105 O 0.162 3.018 8sax #12/A THR 415 CG2 8sax #12/C TYR 105 CE1 0.118 3.522 8sax #12/A ASN 332 ND2 8sax #12/N NAG 1 C7 0.059 3.191 8sax #12/A HIS 330 CB 8sax #12/C TYR 105 CD1 0.051 3.589 8sax #12/A HIS 330 NE2 8sax #12/N NAG 1 N2 -0.001 3.281 8sax #12/A PRO 299 CG 8sax #12/C TYR 105 O -0.063 3.363 8sax #12/A HIS 330 ND1 8sax #12/C TYR 105 CD1 -0.063 3.463 8sax #12/A HIS 330 CE1 8sax #12/C TYR 105 CB -0.079 3.719 8sax #12/A ASN 332 ND2 8sax #12/N NAG 1 N2 -0.087 3.367 8sax #12/A THR 138 O 8sax #12/C GLY 57 CA -0.102 3.402 8sax #12/A ILE 323c CG2 8sax #12/D SER 96 CB -0.107 3.867 8sax #12/A ASN 332 ND2 8sax #12/N NAG 1 O7 -0.136 2.796 8sax #12/A HIS 330 CG 8sax #12/C TYR 105 CD1 -0.144 3.514 8sax #12/A THR 138 CG2 8sax #12/C ASN 59 ND2 -0.165 3.685 8sax #12/A HIS 330 CB 8sax #12/C TYR 105 CE1 -0.182 3.822 8sax #12/A HIS 330 ND1 8sax #12/C TYR 105 CB -0.258 3.778 8sax #12/A THR 297 CG2 8sax #12/N NAG 1 C8 -0.283 4.043 8sax #12/A LYS 327 CD 8sax #12/C LEU 104 CA -0.296 4.056 8sax #12/A THR 413 CG2 8sax #12/N NAG 1 O5 -0.304 3.644 8sax #12/A LYS 327 CE 8sax #12/C TYR 33 OH -0.323 3.663 8sax #12/A ASP 325 OD2 8sax #12/C TYR 33 OH -0.347 2.827 8sax #12/A HIS 330 CE1 8sax #12/C TYR 105 C -0.350 3.720 8sax #12/A THR 415 CG2 8sax #12/C TYR 105 CZ -0.354 3.844 8sax #12/A HIS 330 CE1 8sax #12/C TYR 105 CA -0.358 3.998 8sax #12/A ILE 323c CG2 8sax #12/D SER 96 CA -0.368 4.128 8sax #12/A LYS 327 NZ 8sax #12/C TYR 33 OH -0.395 3.095 31 contacts > select add #12 19860 atoms, 20349 bonds, 37 pseudobonds, 2547 residues, 3 models selected > style sel stick Changed 19860 atom styles > select clear > show #!1 models > hide #!1 models > select add #12 19860 atoms, 20349 bonds, 37 pseudobonds, 2547 residues, 3 models selected > color sel byhetero > select subtract #12 Nothing selected > hide #12.2 models > show #!1 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #12.2 models > hide #!12 models > show #1.3 models > hide #1.2 models > show #!12 models > hide #!1 models > show #!1 models > hide #!1 models > open pdb:9aug Summary of feedback from opening 9aug fetched from pdb --- note | Fetching compressed mmCIF 9aug from http://files.rcsb.org/download/9aug.cif 9aug title: Cryo-EM structure of CH848.d949.10.17.GS-DH270.UCA3.G57R [more info...] Chain information for 9aug #13 --- Chain | Description | UniProt A B C | HIV-1 BG505 DS-SOSIP glycoprotein gp120 | Q2N0S6_9HIV1 31-498 D E F | HIV-1 BG505 DS-SOSIP glycoprotein gp41 | Q2N0S6_9HIV1 512-664 G H I | UCA3.G57R heavy chain | J K L | UCA3.G57R light chain | Non-standard residues in 9aug #13 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > matchmaker #!13 to #1 & sel No 'to' model specified > show #!1 models > select #1/H:112D 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 181 atoms, 190 bonds, 22 residues, 1 model selected > select up 1725 atoms, 1772 bonds, 228 residues, 1 model selected > select up 4647 atoms, 4757 bonds, 608 residues, 1 model selected > select down 1725 atoms, 1772 bonds, 228 residues, 1 model selected > select subtract #1/H:74 1721 atoms, 1767 bonds, 227 residues, 1 model selected > select up 1725 atoms, 1772 bonds, 228 residues, 1 model selected > select add #1/L:56 1734 atoms, 1780 bonds, 229 residues, 1 model selected > select up 1828 atoms, 1876 bonds, 241 residues, 1 model selected > select up 3334 atoms, 3411 bonds, 444 residues, 1 model selected > select up 4647 atoms, 4757 bonds, 608 residues, 1 model selected > select down 3334 atoms, 3411 bonds, 444 residues, 1 model selected > matchmaker #!13 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 231023_poly310-DH270UCA3_refine_001.pdb, chain H (#1) with 9aug, chain G (#13), sequence alignment score = 999.8 RMSD between 125 pruned atom pairs is 0.728 angstroms; (across all 126 pairs: 0.755) > hide #!1 models > select add #1 4647 atoms, 4757 bonds, 71 pseudobonds, 608 residues, 4 models selected > select subtract #1 Nothing selected > select add #13 20211 atoms, 20745 bonds, 3 pseudobonds, 2544 residues, 2 models selected > show sel cartoons > style sel stick Changed 20211 atom styles > hide sel atoms > select clear > hide #!12 models Drag select of 32 residues > select up 392 atoms, 391 bonds, 53 residues, 1 model selected > hbonds sel color #ffd479 restrict cross interModel false distSlop 0.8 > intraMol false intraRes false select true reveal true log true Finding intramodel H-bonds Constraints relaxed by 0.8 angstroms and 20 degrees Models used: 13 9aug 12 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): 9aug #13/A SER 136 OG 9aug #13/G THR 58 O no hydrogen 3.683 N/A 9aug #13/A SER 136 OG 9aug #13/G THR 58 OG1 no hydrogen 3.145 N/A 9aug #13/A GLY 138 N 9aug #13/G SER 55 OG no hydrogen 3.662 N/A 9aug #13/A ASP 325 N 9aug #13/G ASP 107 OD2 no hydrogen 3.149 N/A 9aug #13/A LYS 327 NZ 9aug #13/G TYR 33 OH no hydrogen 3.222 N/A 9aug #13/A THR 415 OG1 9aug #13/G TYR 105 OH no hydrogen 3.764 N/A 9aug #13/G TYR 33 OH 9aug #13/A ASP 325 OD2 no hydrogen 2.362 N/A 9aug #13/G ASN 52 ND2 9aug #13/A ASP 325 OD1 no hydrogen 3.191 N/A 9aug #13/G SER 55 OG 9aug #13/A GLY 138 O no hydrogen 3.500 N/A 9aug #13/G ARG 57 NH2 9aug #13/A ILE 322 O no hydrogen 3.168 N/A 9aug #13/G THR 58 OG1 9aug #13/A SER 136 OG no hydrogen 3.145 N/A 9aug #13/G TYR 105 OH 9aug #13/A GLN 417 OE1 no hydrogen 3.170 N/A 12 hydrogen bonds found > select add #13 20211 atoms, 20745 bonds, 15 pseudobonds, 2544 residues, 3 models selected > color sel byhetero > select clear Drag select of 5 atoms, 15 residues, 3 bonds > select up 113 atoms, 105 bonds, 17 residues, 1 model selected > select up 128 atoms, 121 bonds, 17 residues, 1 model selected > select down 113 atoms, 105 bonds, 17 residues, 1 model selected > select #13/G:57 11 atoms, 10 bonds, 1 residue, 1 model selected > select #13/G:57 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear Drag select of 8 atoms, 33 residues, 7 bonds, 2 pseudobonds > select subtract #13/G:57 240 atoms, 5 bonds, 1 pseudobond, 33 residues, 2 models selected > select up 530 atoms, 533 bonds, 1 pseudobond, 72 residues, 2 models selected > contacts sel restrict cross interModel false intraMol false > ignoreHiddenModels true select true color #ff2600 reveal true log true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: False 25 contacts atom1 atom2 overlap distance 9aug #13/A ASP 325 CG 9aug #13/G ASN 52 ND2 0.265 3.255 9aug #13/A ASP 325 CG 9aug #13/G TYR 33 OH 0.200 3.140 9aug #13/A HIS 330 ND1 9aug #13/G TYR 105 CD1 0.133 3.267 9aug #13/A ILE 326 CG1 9aug #13/G ARG 57 NH1 0.123 3.397 9aug #13/A ASP 325 OD2 9aug #13/G TYR 33 OH 0.118 2.362 9aug #13/A ASP 325 OD2 9aug #13/G ASN 52 ND2 0.066 2.594 9aug #13/A HIS 330 CE1 9aug #13/G TYR 105 CB 0.064 3.576 9aug #13/A GLN 417 OE1 9aug #13/G TYR 105 CE1 0.062 3.118 9aug #13/A GLY 324 CA 9aug #13/J SER 97 OG 0.047 3.293 9aug #13/A ILE 323 CG2 9aug #13/J SER 96 CA 0.041 3.719 9aug #13/A GLY 137 CA 9aug #13/G ARG 57 CD 0.022 3.738 9aug #13/A LYS 327 CD 9aug #13/G LEU 104 CA 0.006 3.754 9aug #13/A HIS 330 CE1 9aug #13/G TYR 105 O -0.009 3.189 9aug #13/A ILE 323 CG2 9aug #13/J SER 96 CB -0.042 3.802 9aug #13/A HIS 330 CE1 9aug #13/G TYR 105 CD1 -0.045 3.565 9aug #13/A LYS 327 CE 9aug #13/G TYR 106 O -0.048 3.348 9aug #13/A ASP 325 CB 9aug #13/G TYR 33 OH -0.116 3.456 9aug #13/A SER 136 CB 9aug #13/G THR 58 OG1 -0.136 3.476 9aug #13/A ILE 326 CD1 9aug #13/G ARG 57 NH1 -0.178 3.698 9aug #13/A ILE 323 CG2 9aug #13/J SER 96 O -0.194 3.494 9aug #13/A HIS 330 CE1 9aug #13/G TYR 105 CA -0.208 3.848 9aug #13/A ILE 323 CG2 9aug #13/J SER 96 C -0.226 3.716 9aug #13/A HIS 330 CG 9aug #13/G TYR 105 CD1 -0.287 3.657 9aug #13/A LYS 327 CE 9aug #13/G LEU 104 CA -0.364 4.124 9aug #13/A GLY 324 C 9aug #13/G TRP 50 CH2 -0.385 3.755 25 contacts > select clear > hide #13.3 models > hide #13.2 models > show #13.3 models > show #13.2 models > hide #13.3 models Desktop color scheme is dark Desktop color scheme is light > open pdb:6QWL 6qwl title: Influenza B virus (B/Panama/45) polymerase Hetermotrimer in complex with 3'5' cRNA promoter [more info...] Chain information for 6qwl #14 --- Chain | Description | UniProt E | Polymerase acidic protein | PA_INBP9 1-726 K | RNA-directed RNA polymerase catalytic subunit | RDRP_INBP9 1-752 Q | Polymerase basic protein 2 | PB2_INBP9 1-770 T | 3' cRNA | W | 5' cRNA | > hide #!13 models > select add #14 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected > view orient > select clear > select #14/E:549@NH1 1 atom, 1 residue, 1 model selected > select add #14/K:331@CD1 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #14/E:549@NH1 #14/K:331@CD1 Distance between 6qwl #14/E ARG 549 NH1 and /K ILE 331 CD1: 104.224Å > open > /Users/oswanson/Downloads/fold_lee_rdrp_trimer_dimer/fold_lee_rdrp_trimer_dimer_model_0.cif Chain information for fold_lee_rdrp_trimer_dimer_model_0.cif #16 --- Chain | Description A B | . C D | . E F | . > select clear > select add #16 35830 atoms, 36512 bonds, 4496 residues, 1 model selected > select subtract #16 Nothing selected > select add #16 35830 atoms, 36512 bonds, 4496 residues, 1 model selected > view orient > hide #!14 models > view orient > select clear > select #16/D:196@NH1 1 atom, 1 residue, 1 model selected > select add #16/C:196@NH2 2 atoms, 2 residues, 1 model selected > distance #16/D:196@NH1 #16/C:196@NH2 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/D ARG 196 NH1 and /C ARG 196 NH2: 197.716Å > select #16/A:621@OE1 1 atom, 1 residue, 1 model selected > select add #16/E:631@ND2 2 atoms, 2 residues, 1 model selected > distance #16/A:621@OE1 #16/E:631@ND2 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/A GLU 621 OE1 and /E ASN 631 ND2: 126.822Å > select clear > select #16/A:621@OE1 1 atom, 1 residue, 1 model selected > select add #16/E:631@CB 2 atoms, 2 residues, 1 model selected > distance #16/A:621@OE1 #16/E:631@CB Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/A GLU 621 OE1 and /E ASN 631 CB: 128.258Å > select #16/B:321@CG 1 atom, 1 residue, 1 model selected > select add #16/B:100@O 2 atoms, 2 residues, 1 model selected > distance #16/B:321@CG #16/B:100@O Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/B ASP 321 CG and GLY 100 O: 131.686Å > select #16/D:194@CE 1 atom, 1 residue, 1 model selected > select add #16/B:206@OE1 2 atoms, 2 residues, 1 model selected > distance #16/D:194@CE #16/B:206@OE1 Distance between fold_lee_rdrp_trimer_dimer_model_0.cif #16/D LYS 194 CE and /B GLN 206 OE1: 62.308Å > select add #16 35830 atoms, 36512 bonds, 5 pseudobonds, 4496 residues, 2 models selected > hide sel atoms > show sel cartoons Computing secondary structure > select clear Desktop color scheme is dark > molmap #16 4 Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 4 as #17, grid size 142,148,110, pixel 1.33, shown at level 0.102, step 1, values float32 > hide #!17 models > select add #16 35830 atoms, 36512 bonds, 5 pseudobonds, 4496 residues, 2 models selected > color sel bychain > select clear Desktop color scheme is light > show #!17 models > molmap #16 8 Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size 80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32 > save > /Users/oswanson/Desktop/Primocalins/Structures/initial_models_plusRdRp.cxs Cell requested for row 0 is out of bounds for table with 28 rows! Resizing table model. > show #!14 models > hide #!15 models > show #!13 models > hide #!14 models > hide #16 models > hide #!17 models > close #1-2,4-5,8,10,16#3,6-7,9,11-15,17 > open > /Users/oswanson/Desktop/Primocalins/Structures/initial_models_plusRdRp.cxs > format session Opened fold_lee_rdrp_trimer_dimer_model_0.cif map 8 as #17, grid size 80,83,64, pixel 2.67, shown at level 0.0919, step 1, values float32 > view name session-start opened ChimeraX session > close #1 > close #2,4-5,8#3,6-7,9-12 > show #!13 models > close #13 > show #!14 models > ui tool show Matchmaker > matchmaker #!14 to #16 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 fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#16) with 6qwl, chain K (#14), sequence alignment score = 3220.4 RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs: 3.053) > hide #!17 models > select add #14 10408 atoms, 10668 bonds, 25 pseudobonds, 1270 residues, 4 models selected > show sel cartoons > hide sel atoms > hide #!14 models > hide #!15 models > close #15 > select subtract #14 Nothing selected > show #!17 models > hide #!17 models > open /Users/oswanson/Downloads/cryosparc_P605_J23_class_00_final_volume.mrc Opened cryosparc_P605_J23_class_00_final_volume.mrc as #1, grid size 128,128,128, pixel 2.9, shown at level 0.115, step 1, values float32 > select add #14 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected > select add #16 46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 4 models selected > select add #17 46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 6 models selected > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.28748,0.86499,0.41127,16.771,0.95617,0.23429,0.17561,44.158,0.055546,0.44373,-0.89444,263.76,#16,1,0,0,135.5,0,1,0,277.63,0,0,1,187.37,#17,1,0,0,135.5,0,1,0,277.63,0,0,1,187.37 > ui mousemode right ""rotate selected models"" > view matrix models > #14,0.18687,0.24553,0.95121,-76.618,0.83833,0.46491,-0.2847,108.53,-0.51213,0.85063,-0.11895,196.06,#16,0.54986,0.40325,-0.73147,138.69,0.044048,0.86052,0.50751,275.9,0.8341,-0.31128,0.4554,187.63,#17,0.54986,0.40325,-0.73147,138.69,0.044048,0.86052,0.50751,275.9,0.8341,-0.31128,0.4554,187.63 > volume #1 level 0.2269 > volume #1 level 0.1301 > ui mousemode right ""translate selected models"" > view matrix models > #14,0.18687,0.24553,0.95121,-30.788,0.83833,0.46491,-0.2847,26.758,-0.51213,0.85063,-0.11895,210.32,#16,0.54986,0.40325,-0.73147,184.52,0.044048,0.86052,0.50751,194.12,0.8341,-0.31128,0.4554,201.88,#17,0.54986,0.40325,-0.73147,184.52,0.044048,0.86052,0.50751,194.12,0.8341,-0.31128,0.4554,201.88 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.12079,0.25201,0.96015,23.371,0.64731,0.75331,-0.11629,-0.5835,-0.7526,0.60747,-0.25413,305.87,#16,0.6476,0.11216,-0.75368,184.02,0.41769,0.77501,0.47423,193.72,0.6373,-0.62192,0.45505,201.57,#17,0.6476,0.11216,-0.75368,184.02,0.41769,0.77501,0.47423,193.72,0.6373,-0.62192,0.45505,201.57 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.12079,0.25201,0.96015,17.372,0.64731,0.75331,-0.11629,-0.15817,-0.7526,0.60747,-0.25413,290.4,#16,0.6476,0.11216,-0.75368,178.02,0.41769,0.77501,0.47423,194.15,0.6373,-0.62192,0.45505,186.1,#17,0.6476,0.11216,-0.75368,178.02,0.41769,0.77501,0.47423,194.15,0.6373,-0.62192,0.45505,186.1 > transparency #1.1 50 > ui tool show ""Fit in Map"" > fitmap #14 inMap #17 Fit molecule 6qwl (#14) to map fold_lee_rdrp_trimer_dimer_model_0.cif map 8 (#17) using 10408 atoms average map value = 0.2949, steps = 52 shifted from previous position = 2.8 rotated from previous position = 3.66 degrees atoms outside contour = 973, contour level = 0.091911 Position of 6qwl (#14) relative to fold_lee_rdrp_trimer_dimer_model_0.cif map 8 (#17) coordinates: Matrix rotation and translation -0.26601820 0.86761118 0.42010137 -122.48682198 0.96396267 0.24087630 0.11293618 -224.65998238 -0.00320777 0.43500512 -0.90042227 84.96204885 Axis 0.59580861 0.78309703 0.17824460 Axis point 35.35475112 0.00000000 66.57258889 Rotation angle (degrees) 164.31913872 Shift along axis -233.76524286 > fitmap #14 inMap #1 Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 10408 atoms average map value = 0.1799, steps = 200 shifted from previous position = 21.9 rotated from previous position = 74.3 degrees atoms outside contour = 3991, contour level = 0.1301 Position of 6qwl (#14) relative to cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.60115416 -0.46274634 0.65152091 74.63506249 0.78882591 0.21309401 -0.57649340 125.49176200 0.12793501 0.86049798 0.49312866 20.61803554 Axis 0.72713451 0.26494062 0.63331026 Axis point 0.00000000 83.73335535 57.16462029 Rotation angle (degrees) 81.15926345 Shift along axis 100.57520736 > fitmap #16 inMap #1 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 35830 atoms average map value = 0.1462, steps = 80 shifted from previous position = 14.2 rotated from previous position = 7.6 degrees atoms outside contour = 19724, contour level = 0.1301 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation 0.64553227 0.15603228 -0.74762425 188.80351799 0.47289373 0.68702028 0.55170161 187.23326867 0.59971628 -0.70968801 0.36970707 192.28999636 Axis -0.67358407 -0.71948199 0.16920452 Axis point -224.98972481 0.00000000 152.57508207 Rotation angle (degrees) 69.44356542 Shift along axis -229.34967086 > volume #1 level 0.1887 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.65777,0.35349,-0.66512,321.14,-0.567,0.34891,0.74617,136.4,0.49583,0.86793,-0.029068,32.827,#16,-0.73375,-0.11951,0.66882,185.61,-0.032984,-0.97698,-0.21076,187.23,0.67862,-0.17671,0.71292,192.09,#17,-0.73654,-0.090736,0.67028,196.56,0.033703,-0.99465,-0.097612,178.17,0.67555,-0.049305,0.73566,192.58 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.65777,0.35349,-0.66512,319.91,-0.567,0.34891,0.74617,141.42,0.49583,0.86793,-0.029068,31.088,#16,-0.73375,-0.11951,0.66882,184.37,-0.032984,-0.97698,-0.21076,192.24,0.67862,-0.17671,0.71292,190.35,#17,-0.73654,-0.090736,0.67028,195.33,0.033703,-0.99465,-0.097612,183.18,0.67555,-0.049305,0.73566,190.84 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.74976,0.28884,-0.59534,331.34,-0.64787,-0.13743,0.74925,206.52,0.1346,0.94746,0.29017,33.245,#16,-0.80043,-0.17992,0.57178,184.62,-0.25408,-0.76212,-0.5955,193.91,0.54291,-0.62193,0.56431,190.19,#17,-0.79743,-0.16606,0.58011,194.68,-0.19374,-0.84002,-0.50679,184.4,0.57146,-0.51652,0.63768,186.94 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.74976,0.28884,-0.59534,331.45,-0.64787,-0.13743,0.74925,197.96,0.1346,0.94746,0.29017,40.397,#16,-0.80043,-0.17992,0.57178,184.73,-0.25408,-0.76212,-0.5955,185.35,0.54291,-0.62193,0.56431,197.34,#17,-0.79743,-0.16606,0.58011,194.79,-0.19374,-0.84002,-0.50679,175.84,0.57146,-0.51652,0.63768,194.09 > fitmap #16 inMap #1 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 35830 atoms average map value = 0.15, steps = 292 shifted from previous position = 5.36 rotated from previous position = 54.4 degrees atoms outside contour = 24089, contour level = 0.18871 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation -0.74059655 -0.66117825 -0.11983354 184.20616119 0.24333744 -0.09766510 -0.96501213 188.58923260 0.62634147 -0.74384464 0.23321986 194.00978837 Axis 0.18534914 -0.62533104 0.75802823 Axis point 18.57115180 211.97461864 0.00000000 Rotation angle (degrees) 143.37150914 Shift along axis 63.27664874 > vop flip #1 Opened cryosparc_P605_J23_class_00_final_volume.mrc z flip as #2, grid size 128,128,128, pixel 2.9, shown at step 1, values float32 > fitmap #16 inMap #2 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 35830 atoms average map value = 0.1442, steps = 120 shifted from previous position = 22.3 rotated from previous position = 13.4 degrees atoms outside contour = 24593, contour level = 0.18871 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates: Matrix rotation and translation -0.76940695 -0.57566756 -0.27680282 185.63600251 0.42188903 -0.13261273 -0.89689660 187.73379770 0.47960670 -0.80685855 0.34490098 171.96023011 Axis 0.07173535 -0.60264858 0.79477590 Axis point 38.45425971 199.68363632 0.00000000 Rotation angle (degrees) 141.12885946 Shift along axis 36.84900469 > ui mousemode right ""rotate selected models"" > view matrix models > #14,0.20753,0.35524,-0.91145,232.73,-0.91446,-0.26044,-0.30972,368.73,-0.3474,0.89776,0.2708,112.41,#16,-0.69418,-0.24771,0.67584,183.35,-0.66486,-0.13916,-0.7339,188.3,0.27584,-0.95879,-0.06809,173.1,#17,-0.16546,0.59462,0.78679,200.35,-0.97326,-0.22734,-0.032866,180.69,0.15933,-0.77119,0.61634,192.29 > view matrix models > #14,0.87363,0.2703,0.40461,-4.3424,0.4065,0.05162,-0.91219,232.85,-0.26745,0.96139,-0.064779,135.31,#16,0.7382,0.11433,0.66482,182.59,-0.67451,0.11071,0.72992,184.5,0.0098543,-0.98725,0.15884,172.66,#17,0.99092,0.13415,-0.0092278,189.53,-0.10914,0.84245,0.5276,194.59,0.078551,-0.5218,0.84944,196.43 > view matrix models > #14,0.86818,-0.2967,0.39778,46.324,0.47562,0.2688,-0.83757,195.92,0.14158,0.91636,0.37449,32.278,#16,0.6312,0.62944,0.45321,184.13,-0.54308,-0.058522,0.83764,183.79,0.55376,-0.77484,0.3049,172.06,#17,0.79169,0.37475,-0.48249,176.8,0.056498,0.74147,0.6686,199.04,0.60831,-0.55658,0.56584,192.76 > volume #2 level 0.08303 > view matrix models > #14,0.88761,-0.18414,0.42218,31.08,0.45951,0.41684,-0.78428,179.04,-0.031558,0.89013,0.45461,48.68,#16,0.68024,0.5349,0.50116,183.79,-0.47455,-0.1997,0.85727,183.44,0.55864,-0.82097,0.11799,172.51,#17,0.85733,0.32231,-0.40137,179.18,0.12,0.6331,0.76471,201.94,0.50058,-0.70378,0.5041,191.26 > ui mousemode right ""translate selected models"" > view matrix models > #14,0.88761,-0.18414,0.42218,32.772,0.45951,0.41684,-0.78428,182.06,-0.031558,0.89013,0.45461,51.466,#16,0.68024,0.5349,0.50116,185.49,-0.47455,-0.1997,0.85727,186.45,0.55864,-0.82097,0.11799,175.3,#17,0.85733,0.32231,-0.40137,180.87,0.12,0.6331,0.76471,204.95,0.50058,-0.70378,0.5041,194.05 > view matrix models > #14,0.88761,-0.18414,0.42218,23.115,0.45951,0.41684,-0.78428,185.33,-0.031558,0.89013,0.45461,47.88,#16,0.68024,0.5349,0.50116,175.83,-0.47455,-0.1997,0.85727,189.72,0.55864,-0.82097,0.11799,171.71,#17,0.85733,0.32231,-0.40137,171.21,0.12,0.6331,0.76471,208.23,0.50058,-0.70378,0.5041,190.46 > ui mousemode right ""rotate selected models"" > view matrix models > #14,0.86299,-0.34605,0.3681,46.814,0.49877,0.46748,-0.72986,169.24,0.080484,0.81346,0.57603,25.104,#16,0.59358,0.67207,0.44269,176.3,-0.40157,-0.22936,0.88664,189.52,0.69743,-0.70407,0.13374,171.72,#17,0.75616,0.41265,-0.50788,167.94,0.19549,0.59823,0.77712,209.02,0.62451,-0.68691,0.37168,188 > view matrix models > #14,0.86747,-0.34312,0.36023,46.873,0.49054,0.46937,-0.7342,170.7,0.082836,0.81361,0.57548,24.836,#16,0.58855,0.67116,0.45072,176.28,-0.40824,-0.23449,0.88225,189.53,0.69782,-0.70325,0.13598,171.72,#17,0.75683,0.41946,-0.50125,168.07,0.18739,0.59546,0.78123,209.08,0.62617,-0.68519,0.37206,188.01 > ui mousemode right ""translate selected models"" > view matrix models > #14,0.86747,-0.34312,0.36023,51.075,0.49054,0.46937,-0.7342,166.39,0.082836,0.81361,0.57548,26.91,#16,0.58855,0.67116,0.45072,180.49,-0.40824,-0.23449,0.88225,185.21,0.69782,-0.70325,0.13598,173.79,#17,0.75683,0.41946,-0.50125,172.27,0.18739,0.59546,0.78123,204.77,0.62617,-0.68519,0.37206,190.08 > fitmap #16 inMap #2 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 35830 atoms average map value = 0.1527, steps = 196 shifted from previous position = 10.3 rotated from previous position = 52.9 degrees atoms outside contour = 14387, contour level = 0.083025 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates: Matrix rotation and translation 0.79116208 0.47083690 -0.39035262 189.77020175 0.21834466 0.37874623 0.89937584 187.56612037 0.57130392 -0.79678347 0.19684494 171.28797258 Axis -0.86270884 -0.48912245 -0.12842384 Axis point 0.00000000 134.63132621 35.34050310 Rotation angle (degrees) 79.43349915 Shift along axis -277.45669015 > volume #2 level 0.1415 > select subtract #16 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 5 models selected > select add #16 46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 6 models selected > select subtract #17 46238 atoms, 47180 bonds, 24 pseudobonds, 5766 residues, 4 models selected > select subtract #14 35830 atoms, 36512 bonds, 4496 residues, 1 model selected > color bfactor sel 35830 atoms, 4496 residues, atom bfactor range 19 to 94.1 > hide #16 models > show #!14 models > fitmap #14 inMap #2 Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 10408 atoms average map value = 0.2296, steps = 172 shifted from previous position = 24.9 rotated from previous position = 29.8 degrees atoms outside contour = 3623, contour level = 0.14146 Position of 6qwl (#14) relative to cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates: Matrix rotation and translation 0.84866127 0.13336671 0.51184702 -23.71765426 0.43643228 0.37015506 -0.82006835 194.27778117 -0.29883258 0.91934680 0.25593073 86.01589402 Axis 0.89529654 0.41726591 0.15599126 Axis point 0.00000000 49.60474067 161.53558806 Rotation angle (degrees) 76.26842446 Shift along axis 73.24888814 > select subtract #16 Nothing selected > select add #14 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected > show #16 models > hide #16 models > ui mousemode right ""rotate selected models"" > view matrix models > #14,0.87735,0.17176,0.44806,-23.989,0.34241,0.43009,-0.83533,201.02,-0.33618,0.8863,0.31853,86.902 > volume #2 level 0.1999 > view matrix models > #14,-0.97442,-0.15226,0.16529,311.43,-0.082037,-0.44376,-0.89238,385.87,0.20922,-0.88312,0.41992,239.92 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.97442,-0.15226,0.16529,227.79,-0.082037,-0.44376,-0.89238,431.33,0.20922,-0.88312,0.41992,236.53 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.12974,-0.15321,-0.97964,272.18,0.89189,0.41365,-0.18281,83.262,0.43323,-0.89745,0.082977,254.85 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.12974,-0.15321,-0.97964,351.43,0.89189,0.41365,-0.18281,35.006,0.43323,-0.89745,0.082977,278.16 > view matrix models > #14,-0.12974,-0.15321,-0.97964,358.16,0.89189,0.41365,-0.18281,31.031,0.43323,-0.89745,0.082977,268.4 > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.003597,-0.27496,-0.96145,355.08,0.85574,0.49662,-0.14523,19.411,0.5174,-0.82327,0.23351,225.91 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.003597,-0.27496,-0.96145,354.62,0.85574,0.49662,-0.14523,17.032,0.5174,-0.82327,0.23351,217.48 > fitmap #14 inMap #2 Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 10408 atoms average map value = 0.2172, steps = 100 shifted from previous position = 8.52 rotated from previous position = 14.8 degrees atoms outside contour = 5286, contour level = 0.1999 Position of 6qwl (#14) relative to cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates: Matrix rotation and translation 0.13567298 -0.47227038 -0.87094978 355.00638729 0.86038618 0.49204153 -0.13278088 19.43382005 0.49125194 -0.73133837 0.47309165 171.17570398 Axis -0.29965963 -0.68196767 0.66717629 Axis point 38.44526890 0.00000000 367.58717042 Rotation angle (degrees) 87.11089207 Shift along axis -5.42994726 > fitmap #14 inMap #2 Fit molecule 6qwl (#14) to map cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) using 10408 atoms average map value = 0.2172, steps = 44 shifted from previous position = 0.0432 rotated from previous position = 0.058 degrees atoms outside contour = 5294, contour level = 0.1999 Position of 6qwl (#14) relative to cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates: Matrix rotation and translation 0.13636012 -0.47157692 -0.87121818 354.83006149 0.86025263 0.49250116 -0.13193943 19.24156614 0.49129556 -0.73147646 0.47283281 171.21387534 Axis -0.30015678 -0.68213925 0.66677729 Axis point 38.31968328 0.00000000 367.40995255 Rotation angle (degrees) 87.08542200 Shift along axis -5.46855382 > hide #!2 models > show #16 models > matchmaker #16 to #14 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 6qwl, chain K (#14) with fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#16), sequence alignment score = 3220.4 RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs: 3.053) > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > volume #2 level 0.3317 > hide #!14 models > show #!14 models > hide #16 models > volume #2 level 0.1962 > show #!17 models > molmap #14 8 Opened 6qwl map 8 as #3, grid size 51,53,56, pixel 2.67, shown at level 0.0839, step 1, values float32 > hide #!17 models > hide #!14 models > show #!14 models > select subtract #14 Nothing selected > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.12389,-0.51731,-0.84678,359.36,0.92551,0.36802,-0.089421,21.402,0.35789,-0.77263,0.52437,187.81 > fitmap #3 inMap #2 Fit map 6qwl map 8 in map cryosparc_P605_J23_class_00_final_volume.mrc z flip using 12587 points correlation = 0.7629, correlation about mean = 0.09084, overlap = 759.9 steps = 84, shift = 1.08, angle = 9.77 degrees Position of 6qwl map 8 (#3) relative to cryosparc_P605_J23_class_00_final_volume.mrc z flip (#2) coordinates: Matrix rotation and translation 0.15606119 -0.44984957 -0.87936356 349.86982704 0.85254165 0.51093661 -0.11007501 14.36108019 0.49881623 -0.73251562 0.46325287 171.75362759 Axis -0.31188241 -0.69055588 0.65258098 Axis point 35.44588963 0.00000000 361.38339726 Rotation angle (degrees) 86.26595020 Shift along axis -6.95222053 > hide #!14 models > hide #!3 models > show #16 models > show #!14 models > hide #!14 models > show #!1 models > hide #!2 models > combine #14 > select subtract #3 Nothing selected > hide #16 models > select add #4 10408 atoms, 10668 bonds, 24 pseudobonds, 1270 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #4,0.13636,-0.47158,-0.87122,406.48,0.86025,0.4925,-0.13194,-67.544,0.4913,-0.73148,0.47283,172.74 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.7157,-0.37195,-0.59113,469.87,0.59514,0.11815,-0.79489,111.74,0.3655,-0.9207,0.1368,262.37 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.7157,-0.37195,-0.59113,454.84,0.59514,0.11815,-0.79489,208.5,0.3655,-0.9207,0.1368,283.3 > view matrix models > #4,-0.7157,-0.37195,-0.59113,419.53,0.59514,0.11815,-0.79489,213.45,0.3655,-0.9207,0.1368,289.75 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.69442,-0.3599,-0.6231,419.44,0.58127,0.22986,-0.78057,198.11,0.42415,-0.90423,0.04958,291.65 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.69442,-0.3599,-0.6231,418.63,0.58127,0.22986,-0.78057,183.26,0.42415,-0.90423,0.04958,291.57 > fitmap #4 inMap #1 Fit molecule copy of 6qwl (#4) to map cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 10408 atoms average map value = 0.2096, steps = 144 shifted from previous position = 6.47 rotated from previous position = 64.2 degrees atoms outside contour = 4629, contour level = 0.18871 Position of copy of 6qwl (#4) relative to cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation -0.14347824 -0.98911909 0.03251793 336.65894023 0.42613730 -0.09140306 -0.90002915 264.97601036 0.89320826 -0.11527749 0.43461489 61.69787383 Axis 0.42814429 -0.46957486 0.77213465 Axis point 25.50671173 281.72175705 0.00000000 Rotation angle (degrees) 113.58650590 Shift along axis 67.35159673 > volume #1 level 0.3031 > volume #1 color #76765d80 > volume #1 color #807f6480 > volume #1 color #807f645d > volume #1 color #d6d6d6 > volume #1 color silver > volume #1 color #c0c0c08c > volume #1 color #76d6ff > volume #1 color #76d6ff43 > volume #1 color darkgrey > volume #1 color #a9a9a987 > volume #1 color #a9a9a98f > lighting soft > lighting simple > volume #1 level 0.2683 > fitmap #4 inMap #1 Fit molecule copy of 6qwl (#4) to map cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 10408 atoms average map value = 0.2096, steps = 44 shifted from previous position = 0.0604 rotated from previous position = 0.0648 degrees atoms outside contour = 7386, contour level = 0.26829 Position of copy of 6qwl (#4) relative to cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation -0.14358010 -0.98907322 0.03345021 336.54517646 0.42657360 -0.09235260 -0.89972549 264.94152825 0.89298360 -0.11491370 0.43517252 61.59581517 Axis 0.42822749 -0.46899885 0.77243854 Axis point 25.58148056 281.48695698 0.00000000 Rotation angle (degrees) 113.60194188 Shift along axis 67.43960578 > combine #16 > matchmaker #5 to #4 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 copy of 6qwl, chain K (#4) with copy of fold_lee_rdrp_trimer_dimer_model_0.cif, chain C (#5), sequence alignment score = 3220.4 RMSD between 301 pruned atom pairs is 1.204 angstroms; (across all 539 pairs: 3.053) > fitmap #5 inMap #1 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) to map cryosparc_P605_J23_class_00_final_volume.mrc (#1) using 35830 atoms average map value = 0.08176, steps = 132 shifted from previous position = 7.76 rotated from previous position = 5.08 degrees atoms outside contour = 32465, contour level = 0.26829 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) relative to cryosparc_P605_J23_class_00_final_volume.mrc (#1) coordinates: Matrix rotation and translation -0.80899717 -0.29911248 -0.50601906 198.65812349 -0.58098274 0.27603427 0.76567887 194.08321522 -0.08934550 0.91342039 -0.39709013 277.46996867 Axis 0.28178569 -0.79471666 -0.53760789 Axis point 121.61319452 0.00000000 95.61507287 Rotation angle (degrees) 164.80219121 Shift along axis -247.43219487 > hide #!4 models > volume #1 level 0.1367 > open pdb:3J9B Summary of feedback from opening 3J9B fetched from pdb --- note | Fetching compressed mmCIF 3j9b from http://files.rcsb.org/download/3j9b.cif 3j9b title: Electron cryo-microscopy of an RNA polymerase [more info...] Chain information for 3j9b #6 --- Chain | Description | UniProt A H | Polymerase | Q91R78_9INFA 259-716 B I | RNA-directed RNA polymerase catalytic subunit | RDRP_I96A0 1-24 C J | Polymerase basic protein 2 | D K | RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') | E | RNA (5'-R(*UP*UP*UP*UP*UP*A)-3') | L | RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3') | > matchmaker #!6 to #5 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 copy of fold_lee_rdrp_trimer_dimer_model_0.cif, chain A (#5) with 3j9b, chain A (#6), sequence alignment score = 1181.1 RMSD between 246 pruned atom pairs is 1.151 angstroms; (across all 454 pairs: 4.689) > hide #!6 models > show #!6 models > select add #6 23262 atoms, 23718 bonds, 31 pseudobonds, 3244 residues, 5 models selected > select clear > select add #6 12854 atoms, 13050 bonds, 7 pseudobonds, 1974 residues, 2 models selected > show sel cartoons > hide sel atoms > hide #!1 models > show #!1 models > hide #!6 models > show #!6 models > hide #!6 models > open /Users/oswanson/Downloads/cryosparc_P605_J45_class_00_final_volume.mrc Opened cryosparc_P605_J45_class_00_final_volume.mrc as #7, grid size 256,256,256, pixel 1.45, shown at level 0.0414, step 1, values float32 > transparency #7.1 50 > volume #7 level 0.1009 > volume #7 level 0.1726 > hide #5 models > volume #7 level 0.1498 > show #5 models > fitmap #5 inMap #7 Fit molecule copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) to map cryosparc_P605_J45_class_00_final_volume.mrc (#7) using 35830 atoms average map value = 0.05264, steps = 764 shifted from previous position = 14 rotated from previous position = 10.2 degrees atoms outside contour = 30732, contour level = 0.14976 Position of copy of fold_lee_rdrp_trimer_dimer_model_0.cif (#5) relative to cryosparc_P605_J45_class_00_final_volume.mrc (#7) coordinates: Matrix rotation and translation -0.72693585 -0.40409826 -0.55521965 189.47473641 -0.68191939 0.32950002 0.65300511 201.23646391 -0.08093334 0.85330788 -0.51508782 269.53556139 Axis 0.34238374 -0.81071233 -0.47488830 Axis point 122.28388606 0.00000000 100.44646883 Rotation angle (degrees) 162.99158906 Shift along axis -226.27109781 > show #16 models > select clear > select add #16 35830 atoms, 36512 bonds, 4496 residues, 1 model selected > view matrix models > #16,-0.80542,-0.1331,0.57757,92.095,0.12444,0.91477,0.38433,139.56,-0.5795,0.38142,-0.72021,113.29 > view matrix models > #16,-0.80542,-0.1331,0.57757,165.41,0.12444,0.91477,0.38433,167.11,-0.5795,0.38142,-0.72021,104.45 > fitmap #16 inMap #7 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map cryosparc_P605_J45_class_00_final_volume.mrc (#7) using 35830 atoms average map value = 0.05062, steps = 2000 shifted from previous position = 25.2 rotated from previous position = 30.1 degrees atoms outside contour = 31031, contour level = 0.14976 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to cryosparc_P605_J45_class_00_final_volume.mrc (#7) coordinates: Matrix rotation and translation -0.45526558 -0.47379441 0.75382498 189.36681218 0.00872221 0.84424206 0.53589109 169.24944743 -0.89031296 0.25054779 -0.38022182 98.42982751 Axis -0.16426646 0.94649747 0.27777521 Axis point 126.23588556 0.00000000 -41.59599197 Rotation angle (degrees) 119.71081820 Shift along axis 156.42892503 > fitmap #16 inMap #7 Fit molecule fold_lee_rdrp_trimer_dimer_model_0.cif (#16) to map cryosparc_P605_J45_class_00_final_volume.mrc (#7) using 35830 atoms average map value = 0.05056, steps = 2000 shifted from previous position = 0.55 rotated from previous position = 0.731 degrees atoms outside contour = 31068, contour level = 0.14976 Position of fold_lee_rdrp_trimer_dimer_model_0.cif (#16) relative to cryosparc_P605_J45_class_00_final_volume.mrc (#7) coordinates: Matrix rotation and translation -0.45390691 -0.47418558 0.75439814 189.45692177 0.02001012 0.84100233 0.54066133 169.71982871 -0.89082440 0.26050551 -0.37224826 98.18257195 Axis -0.16095929 0.94523772 0.28393266 Axis point 125.64106046 0.00000000 -42.66603170 Rotation angle (degrees) 119.51006315 Shift along axis 157.80797159 > select clear > ui mousemode right select Drag select of 2294 residues, 7 cryosparc_P605_J45_class_00_final_volume.mrc > select up 21255 atoms, 21646 bonds, 2671 residues, 4 models selected > select up 35830 atoms, 36512 bonds, 4496 residues, 4 models selected > select up 71660 atoms, 73024 bonds, 8992 residues, 4 models selected > select down 35830 atoms, 36512 bonds, 4496 residues, 4 models selected > combine selection Expected a keyword > combine sel name Lee_init Remapping chain ID 'A' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'G' Remapping chain ID 'B' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'H' Remapping chain ID 'C' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'I' Remapping chain ID 'D' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'J' Remapping chain ID 'E' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'K' Remapping chain ID 'F' in fold_lee_rdrp_trimer_dimer_model_0.cif #16 to 'L' > hide #5 models > hide #16 models > select clear > select #8/I:535 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 899 residues > select up 8410 atoms, 8550 bonds, 1056 residues, 1 model selected > select up 17915 atoms, 18256 bonds, 2248 residues, 1 model selected > delete atoms sel > delete bonds sel Drag select of 1990 residues > select up 16641 atoms, 16952 bonds, 2086 residues, 1 model selected > select up 17915 atoms, 18256 bonds, 2248 residues, 1 model selected > select up 53745 atoms, 54768 bonds, 6744 residues, 1 model selected > select down 17915 atoms, 18256 bonds, 2248 residues, 1 model selected > delete atoms sel > delete bonds sel > color #8 bychain > hide #!7 models > show #!7 models > select #8/L:270 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 130 atoms, 129 bonds, 16 residues, 1 model selected > select up 6170 atoms, 6275 bonds, 770 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > show #!4 models > hide #!4 models > show #!6 models > hide #!6 models > sequence chain #16/E #16/F #5/E #5/F #8/E #8/L Alignment identifier is 1 > select #16/E-F:770 #5/E-F:770 #8/E,L:770 42 atoms, 36 bonds, 6 residues, 3 models selected > select #16/E-F #5/E-F #8/E,L 37020 atoms, 37650 bonds, 4620 residues, 3 models selected . [ID: 1] region 6 chains [1-770] RMSD: 123.980 > select clear > hide #8 models > show #8 models Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) Window position QRect(2319,365 600x300) outside any known screen, using primary screen OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 98, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/ui/statusbar.py"", line 164, in status r.draw_background() File ""/Applications/ChimeraX-1.10.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 59, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10 (2025-06-26) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,13 Model Number: Z1BP0006TLL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 24 GB System Firmware Version: 13822.1.2 OS Loader Version: 13822.1.2 Software: System Software Overview: System Version: macOS 26.0.1 (25A362) Kernel Version: Darwin 25.0.0 Time since boot: 26 days, 9 hours, 8 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 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: 2880 x 1864 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.4.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.5.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.18 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10 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: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-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: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 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: 1.45.2 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.9.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.4 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.0 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX