id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20830 ChimeraX bug report submission chimerax-bug-report@… "{{{ The following bug report has been submitted: Platform: macOS-26.5.1-arm64-arm-64bit ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC) Description Last time you used ChimeraX it crashed. 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""e8717755549d2b003f7e9553f50423b49e76b713"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""642da32dea3b2418c750f848"", ""factorPackIds"" : [ ""66d8b2f77cd4b62688efd2cf"" ], ""deploymentId"" : 240000011 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000012 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.12 (2026-06-12) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs"" format > session > view name session-start opened ChimeraX session > hide #1 models > show #1 models > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > open > /Users/hwu/Downloads/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb > format pdb No such file/path: /Users/hwu/Downloads/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb > open ""/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs"" format > session > view name session-start opened ChimeraX session > open > /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_scores_rank_001_alphafold2_ptm_model_2_seed_000.json Opening an AlphaFold PAE file requires first opening the predicted atomic model. Did not find an open atomic model from the same directory. If the atomic model is already open choose it using menu Tools / Structure Prediction / AlphaFold Error Plot or use the open command structure option, for example open /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_scores_rank_001_alphafold2_ptm_model_2_seed_000.json structure #1 If you are trying to open a JSON file that is not AlphaFold PAE data then you need to specify the specific JSON format such as open mole_channels.json format mole > open > /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb Chain information for test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3 --- Chain | Description A | No description available Computing secondary structure > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3gjf, chain M (#2) with test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3), sequence alignment score = 622.8 RMSD between 102 pruned atom pairs is 0.290 angstroms; (across all 218 pairs: 25.827) > hide #1 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #!2 models > show #!2 models > hide #3 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #3 models > select #2/D:245 5 atoms, 4 bonds, 1 residue, 1 model selected > open /Users/hwu/Downloads/linker.fasta Failed opening file /Users/hwu/Downloads/linker.fasta: Sequence 'DP03824' differs in length from preceding sequences, and it is therefore impossible to open these sequences as an alignment. If you want to open the sequences individually, specify 'false' as the value of the 'alignment' keyword in the 'open' command. > open /Users/hwu/Downloads/linker.fasta Failed opening file /Users/hwu/Downloads/linker.fasta: Sequence 'DP03824' differs in length from preceding sequences, and it is therefore impossible to open these sequences as an alignment. If you want to open the sequences individually, specify 'false' as the value of the 'alignment' keyword in the 'open' command. > close session > open 1yjd Summary of feedback from opening 1yjd fetched from pdb --- note | Fetching compressed mmCIF 1yjd from http://files.rcsb.org/download/1yjd.cif 1yjd title: Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1) [more info...] Chain information for 1yjd #1 --- Chain | Description | UniProt C | T-cell-specific surface glycoprotein CD28 | CD28_HUMAN -1-134 H | Fab fragment of 5.11A1 antibody heavy chain | L | Fab fragment of 5.11A1 antibody light chain | Non-standard residues in 1yjd #1 --- 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) 1yjd mmCIF Assemblies --- 1| author_defined_assembly > select /C 1029 atoms, 1017 bonds, 159 residues, 1 model selected > select clear > select /C:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:118 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /C:14 12 atoms, 12 bonds, 1 residue, 1 model selected > select /C:14 12 atoms, 12 bonds, 1 residue, 1 model selected > color bfactor sel 12 atoms, 1 residues, atom bfactor range 48.7 to 64.7 > select clear > color bfactor 4493 atoms, 753 residues, atom bfactor range 25.8 to 100 > delete #1/A,B > delete #1/A > delete /A > select /L:110 8 atoms, 7 bonds, 1 residue, 1 model selected > delete #1/H > delete #1/L > sequence chain #1/C Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C > sequence chain #1/C Destroying pre-existing alignment with identifier 1/C Alignment identifier is 1/C > setattr /C uniprot Missing or invalid ""attrName"" argument: Expected a text string > setattr /C Missing or invalid ""target"" argument: Expected a text string > setattr #1/C uniprot Missing or invalid ""attrName"" argument: Expected a text string > setattr uniprot Missing or invalid ""attrName"" argument: Expected a text string > resnumbering Unknown command: resnumbering > setattr 1/C resnumbeirng Missing or invalid ""attrValue"" argument: Expected a text string > setattr 1/C resnumbering Missing or invalid ""attrValue"" argument: Expected a text string > setattr 1/C resnumbering=uniprot Missing or invalid ""attrValue"" argument: Expected a text string > open P10747 fromDatabase uniprot Summary of feedback from opening P10747 fetched from uniprot --- notes | Fetching compressed P10747 UniProt info from https://www.uniprot.org/uniprot/P10747.xml Alignment identifier is P10747 Associated 1yjd chain C to P10747 with 4 mismatches Opened UniProt P10747 > select /C:22,48,68,94 24 atoms, 22 bonds, 4 residues, 1 model selected > select /C:1-118 949 atoms, 972 bonds, 118 residues, 1 model selected > select /C:22,48,68,94 24 atoms, 22 bonds, 4 residues, 1 model selected > select /C:86-88 24 atoms, 23 bonds, 3 residues, 1 model selected > ~select Nothing selected > select /C:19,53,74,87,111 40 atoms, 35 bonds, 5 residues, 1 model selected > select /C:22,48,68,94 24 atoms, 22 bonds, 4 residues, 1 model selected > select /C:106 8 atoms, 7 bonds, 1 residue, 1 model selected > select /C:106-112 52 atoms, 51 bonds, 7 residues, 1 model selected > select clear > select /C:102 7 atoms, 7 bonds, 1 residue, 1 model selected > select /C:102-118 135 atoms, 138 bonds, 17 residues, 1 model selected > close session > open ""/Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs"" format > session No such file/path: /Users/hwu/Desktop/HeightDB/result-0nvi6/3GJF and 0nvi6.cxs > open > /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb > format pdb No such file/path: /Users/hwu/Desktop/HeightDB/test_77ace/test_77ace_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb > open ""/Users/hwu/Desktop/Structure prediction for > HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs"" > view name session-start opened ChimeraX session > hide #!2 models > show #!2 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > show #1 models > hide #1 models > open ""/Users/hwu/Desktop/Structure prediction for > HeightDB/AF2/test_d6f2a/test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"" Chain information for test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3 --- Chain | Description A | No description available Computing secondary structure > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3gjf, chain M (#2) with test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3), sequence alignment score = 631.1 RMSD between 101 pruned atom pairs is 0.315 angstroms; (across all 218 pairs: 26.487) > hide #3 models > show #3 models > hide #3 models > hide #!2 models > show #3 models > show #!2 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > hide #!2 models > show #!2 models > hide #!2 models > show #3 models > color bfactor #3 4550 atoms, 307 residues, atom bfactor range 30.4 to 98.6 > select #3/A:251 22 atoms, 21 bonds, 1 residue, 1 model selected > sequence chain #3/A Alignment identifier is 3/A > select #3/A:58 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:58-59 18 atoms, 17 bonds, 2 residues, 1 model selected > select > #3/A:5-9,12-14,20-27,35-41,47-53,60-62,70-75,80-85,94-101,115-119,147-150,156-161,173-178,185-188,202-207,210-215,224-232,235-238,242-246,268-270,288-290 1790 atoms, 1791 bonds, 114 residues, 1 model selected > select clear > select #3/A:251 22 atoms, 21 bonds, 1 residue, 1 model selected > info residues sel attribute bfactor > info residues sel attribute bfactor > ui tool show ""Render/Select by Attribute"" > select #3/A:199 14 atoms, 14 bonds, 1 residue, 1 model selected Populating font family aliases took 175 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > select clear > select #3/A:248 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #3/A:233 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:269 19 atoms, 18 bonds, 1 residue, 1 model selected > select #3/A:270 15 atoms, 14 bonds, 1 residue, 1 model selected > select clear > select #3/A:248 7 atoms, 6 bonds, 1 residue, 1 model selected > close session > open ""/Users/hwu/Desktop/Structure prediction for > HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs"" format session No such file/path: /Users/hwu/Desktop/Structure prediction for HeightDB/Boltz2/result-0nvi6/3GJF and 0nvi6.cxs > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF and 0nvi6.cxs"" > view name session-start opened ChimeraX session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/AF2/test_d6f2a/test_d6f2a_pae.png"" Image mode RGBA is not supported (L, P, I;16, I;16B, I;16L, I;16S, F, F;32BF, I, RGB) > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/AF2/test_d6f2a/test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"" Chain information for test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3 --- Chain | Description A | No description available Computing secondary structure > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 3gjf, chain M (#2) with test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb, chain A (#3), sequence alignment score = 631.1 RMSD between 101 pruned atom pairs is 0.315 angstroms; (across all 218 pairs: 26.487) > hide #1 models > hide #3 models > show #3 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"" > hide #!2 models > color bfactor #3 4550 atoms, 307 residues, atom bfactor range 30.4 to 98.6 > ui tool show Distances Exactly two atoms must be selected! > select #3/A:181 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:263 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #3/A:180 26 atoms, 25 bonds, 2 residues, 1 model selected > select add #3/A:181 33 atoms, 31 bonds, 3 residues, 1 model selected > select subtract #3/A:180 19 atoms, 17 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! > select clear > select #3/A:181 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #3/A:181 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:181 @Ca 1 atom, 1 residue, 1 model selected > select add #3/A:262 13 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > select #3/A:181 @Ca #3/A:262 @Ca 2 atoms, 2 residues, 1 model selected > distance #3/A:181@CA #3/A:262@CA Distance between test_d6f2a_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #3/A GLY 181 CA and ASP 262 CA: 31.177Å > ~distance #3/A:181@CA #3/A:262@CA > sequence chain #3/A Alignment identifier is 3/A > show #!2 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #3 models > show #3 models > copy #2 Unknown command: copy #2 > combine #2 > hide #!2 models > hide #3 models > select #4/M:48 7 atoms, 6 bonds, 1 residue, 1 model selected > delete #4/M > select #4/K:107 7 atoms, 6 bonds, 1 residue, 1 model selected > delete #4/K > show #3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > show #!4 models > hide #!4 models > hide #3 models > hide #!2 models > show #!4 models > show #!2 models > hide #!2 models > show #3 models > combine #23 No structures specified > combine #3 > combine #4 #5 > hide #5 models > hide #!4 models > hide #3 models > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"" > show #1 models > show #!2 models > hide #!2 models > hide #1 models > show #1 models > show #!2 models > show #3 models > hide #3 models > hide #!6 models > hide #!2 models > hide #1 models > select add #1 5078 atoms, 5211 bonds, 640 residues, 1 model selected > select add #2 12262 atoms, 11770 bonds, 2257 residues, 2 models selected > select add #3 16812 atoms, 16378 bonds, 2564 residues, 3 models selected > select add #4 20378 atoms, 19635 bonds, 3351 residues, 4 models selected > select add #5 24928 atoms, 24243 bonds, 3658 residues, 5 models selected > select subtract #5 20378 atoms, 19635 bonds, 3351 residues, 4 models selected > select add #5 24928 atoms, 24243 bonds, 3658 residues, 5 models selected > close #5 > close #1 > close #2 > close #3 > close #4 > show #!6 models > select add #6 8116 atoms, 7865 bonds, 1094 residues, 1 model selected > select clear > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/Sequences/rcsb_pdb_3GJF.fasta"" Failed opening file /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for HeightDB/Sequences/rcsb_pdb_3GJF.fasta: Sequence '3GJF_4|Chains G[auth K], H[auth L]|Antibody light chain|Homo sapiens (9606)' differs in length from preceding sequences, and it is therefore impossible to open these sequences as an alignment. If you want to open the sequences individually, specify 'false' as the value of the 'alignment' keyword in the 'open' command. > sequence chain #6/D Alignment identifier is 6/D > sequence chain #6/E Alignment identifier is 6/E > sequence chain #6/F Alignment identifier is 6/F > sequence chain #6/A Alignment identifier is 6/A > select /A:248 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:248-307 919 atoms, 935 bonds, 60 residues, 1 model selected > delete #6/A:248-307 > sequence chain #6/D Alignment identifier is 6/D > sequence chain #6/E Alignment identifier is 6/E > sequence chain #6/F Alignment identifier is 6/F > sequence chain #6/A Destroying pre-existing alignment with identifier 6/A Alignment identifier is 6/A > select /D:251 6 atoms, 5 bonds, 1 residue, 1 model selected > select /D:251-276 217 atoms, 224 bonds, 26 residues, 1 model selected > select /D:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /D:1-60 495 atoms, 512 bonds, 60 residues, 1 model selected > select clear > color bfactor 7197 atoms, 1034 residues, atom bfactor range 14.8 to 98.6 > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF d6f2a.cxs"" > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF d6f2a.cif"" relModel #6 Not saving entity_poly_seq for non-authoritative sequences > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"" > open 3GJF_d6f2a.cif Failed opening file /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc: No such file/path: 3GJF_d6f2a.cif > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"" > open 3GJF_d6f2a.cif No such file/path: 3GJF_d6f2a.cif > open /Users/hwu/Desktop/measure_ecd.py Traceback (most recent call last): File ""/Users/hwu/Desktop/measure_ecd.py"", line 26, in from Bio.PDB import PDBParser, MMCIFParser ModuleNotFoundError: No module named 'Bio' Failed opening file /Users/hwu/Desktop/measure_ecd.py: Error opening python file /Users/hwu/Desktop/measure_ecd.py > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"" > open 3GJF_d6f2a.cif Summary of feedback from opening 3GJF_d6f2a.cif --- warnings | Unknown polymer entity '4' on line 4488 Missing or incorrect sequence information. Inferred polymer connectivity. Atom H is not in the residue template for MET /A:1 Chain information for 3GJF_d6f2a.cif #1 --- Chain | Description A | No description available D | HLA class I histocompatibility antigen, A-2 alpha chain E | Beta-2-microglobulin F | NYESO-1 peptide > color #1 bychain > color ~#1:0-276 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint > -52.11,43.45,48.41 color yellow > shape sphere radius 2.5 center 38.94,2.55,29.79 color red > shape sphere radius 2.5 center -52.11,43.45,48.41 color red > 2dlabels text ""3GJF_d6f2a: 10.15 nm"" xpos 0.05 ypos 0.9 color black size 24 > view executed 3GJF_d6f2a_measure.cxc > ui tool show Distances > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF d6f2a.cif"" format mmcif No such file/path: /Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for Young-wook/Harry Wu/Collaborations/Structure prediction for HeightDB/ChimeraX/3GJF d6f2a.cif > open 3gjf 3gjf title: Rational development of high-affinity T-cell receptor-like antibodies [more info...] Chain information for 3gjf #1 --- Chain | Description | UniProt A D | HLA class I histocompatibility antigen, A-2 alpha chain | 1A02_HUMAN 1-276 B E | Beta-2-microglobulin | B2MG_HUMAN 1-99 C F | NYESO-1 peptide | H M | Antibody heavy chain | K L | Antibody light chain | 3gjf mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > hide surfaces > select ::name=""HOH"" 1603 atoms, 1603 residues, 1 model selected > select /D:1380@O 1 atom, 1 residue, 1 model selected > select ::name=""HOH"" 1603 atoms, 1603 residues, 1 model selected > hide sel > hide sel atoms > select clear > hide cartoons > show cartoons > hide surfaces > hide atoms > select clear > select /H:164 5 atoms, 4 bonds, 1 residue, 1 model selected > delete #1/H > select /L:73 5 atoms, 4 bonds, 1 residue, 1 model selected > delete #1/L > select /A:116 12 atoms, 12 bonds, 1 residue, 1 model selected > delete #1/A > select clear > select /C:3 8 atoms, 7 bonds, 1 residue, 1 model selected > delete #1/C > select /B:55 6 atoms, 5 bonds, 1 residue, 1 model selected > delete #1/B > select /M:48 7 atoms, 6 bonds, 1 residue, 1 model selected > delete #1/M > select /K:76 7 atoms, 6 bonds, 1 residue, 1 model selected > delete #1/K > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_HLA A*2:01_only.cif"" relModel #1 > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_HLA_A*201_only_measure.cxc"" > open 3GJF_HLA_A*201_only.cif Chain information for 3GJF_HLA_A*201_only.cif #1 --- Chain | Description D | HLA class I histocompatibility antigen, A-2 alpha chain E | Beta-2-microglobulin F | NYESO-1 peptide 3GJF_HLA_A*201_only.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > color #1 bychain > color ~#1:0-276 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 39.24,8.14,34.22 toPoint > -26.71,25.38,37.76 color yellow > shape sphere radius 2.5 center 39.24,8.14,34.22 color red > shape sphere radius 2.5 center -26.71,25.38,37.76 color red > 2dlabels text ""3GJF_HLA_A*201_only: 6.83 nm"" xpos 0.05 ypos 0.9 color black > size 24 > view executed 3GJF_HLA_A*201_only_measure.cxc > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge_measure.cxc"" > open CD2CD58merge.cif Summary of feedback from opening CD2CD58merge.cif --- warnings | Unknown polymer entity '1' on line 112 Unknown polymer entity '2' on line 1374 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for CD2CD58merge.cif #6 --- Chain | Description A | HUMAN CD2 PROTEIN B | HUMAN CD58 PROTEIN > color #1 bychain > color ~#1:1-215 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint > 68.86,44.41,-34.22 color yellow > shape sphere radius 2.5 center 6.92,-7.59,89.20 color red > shape sphere radius 2.5 center 68.86,44.41,-34.22 color red > 2dlabels text ""CD2CD58merge: 14.76 nm"" xpos 0.05 ypos 0.9 color black size > 24 > view executed CD2CD58merge_measure.cxc > select add #1 3566 atoms, 3257 bonds, 787 residues, 1 model selected > select add #2 3566 atoms, 3257 bonds, 787 residues, 2 models selected > select add #3 3566 atoms, 3257 bonds, 787 residues, 3 models selected > select add #4 3566 atoms, 3257 bonds, 787 residues, 4 models selected > select add #5 3566 atoms, 3257 bonds, 787 residues, 7 models selected > select clear > hide #1 models > hide #2 models > hide #4 models > hide #3 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > close session > open /Users/hwu/Desktop/HeightDB/CD2CD58merge_measure.cxc format cmd No such file/path: /Users/hwu/Desktop/HeightDB/CD2CD58merge_measure.cxc > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge_measure.cxc"" > open CD2CD58merge.cif Summary of feedback from opening CD2CD58merge.cif --- warnings | Unknown polymer entity '1' on line 112 Unknown polymer entity '2' on line 1374 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for CD2CD58merge.cif #1 --- Chain | Description A | HUMAN CD2 PROTEIN B | HUMAN CD58 PROTEIN > color #1 bychain > color ~#1:1-215 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint > 68.86,44.41,-34.22 color yellow > shape sphere radius 2.5 center 6.92,-7.59,89.20 color red > shape sphere radius 2.5 center 68.86,44.41,-34.22 color red > 2dlabels text ""CD2CD58merge: 14.76 nm"" xpos 0.05 ypos 0.9 color black size > 24 > view executed CD2CD58merge_measure.cxc > close session > alphafold fetch AF-Q9Y287-F1 Unrecognized format for AlphaFold id ""AF-Q9Y287-F1"". Example AlphaFold ids P29474, Q8N9C0-2, IGS22_HUMAN, AF-Q8N9C0-F1-v6, AF-Q8N9C0-2-F1-v6. > alphafold fetch AF-Q9Y287-F1-v6 Fetching compressed AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database6.json Fetching compressed AlphaFold Q9Y287 from https://alphafold.ebi.ac.uk/files/AF-Q9Y287-F1-model_v6.cif Chain information for AlphaFold Q9Y287 #1 --- Chain | Description | UniProt A | Integral membrane protein 2B | ITM2B_HUMAN 1-266 Color AlphaFold Q9Y287 by residue attribute pLDDT_score > ui tool show Distances > select clear > select /A:80 5 atoms, 4 bonds, 1 residue, 1 model selected > show sel atoms > select /A:200 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select /A:200 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:200 @Ca 1 atom, 1 residue, 1 model selected > select #1/A:80 @Ca 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select clear > select #1/A:200 @Ca 1 atom, 1 residue, 1 model selected > select #1/A:80 @Ca 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select #1/A:80@Ca 1 atom, 1 residue, 1 model selected > select #1/A:80@Ca #1/A:200 @Ca 2 atoms, 2 residues, 1 model selected > distance /A:80@CA /A:200@CA Distance between /A ALA 80 CA and HIS 200 CA: 40.325Å > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge_measure.cxc"" format cmd > open CD2CD58merge.cif Summary of feedback from opening CD2CD58merge.cif --- warnings | Unknown polymer entity '1' on line 112 Unknown polymer entity '2' on line 1374 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for CD2CD58merge.cif #1 --- Chain | Description A | HUMAN CD2 PROTEIN B | HUMAN CD58 PROTEIN > color #1 bychain > color ~#1:1-215 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint > 68.86,44.41,-34.22 color yellow > shape sphere radius 2.5 center 6.92,-7.59,89.20 color red > shape sphere radius 2.5 center 68.86,44.41,-34.22 color red > 2dlabels text ""CD2CD58merge: 14.76 nm"" xpos 0.05 ypos 0.9 color black size > 24 > view executed CD2CD58merge_measure.cxc > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_HLA A*2:01_only.cif"" format mmcif No such database '/users/hwu/library/cloudstorage/box-box/jun lab group folder/data for young-wook/harry wu/collaborations/structure prediction for heightdb/chimerax/3gjf_hla a*2' > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_HLA_A*201_only_measure.cxc"" format cmd > open 3GJF_HLA_A*201_only.cif Chain information for 3GJF_HLA_A*201_only.cif #1 --- Chain | Description D | HLA class I histocompatibility antigen, A-2 alpha chain E | Beta-2-microglobulin F | NYESO-1 peptide 3GJF_HLA_A*201_only.cif mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > color #1 bychain > color ~#1:0-276 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 39.24,8.14,34.22 toPoint > -26.71,25.38,37.76 color yellow > shape sphere radius 2.5 center 39.24,8.14,34.22 color red > shape sphere radius 2.5 center -26.71,25.38,37.76 color red > 2dlabels text ""3GJF_HLA_A*201_only: 6.83 nm"" xpos 0.05 ypos 0.9 color black > size 24 > view executed 3GJF_HLA_A*201_only_measure.cxc > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"" format cmd > open 3GJF_d6f2a.cif Summary of feedback from opening 3GJF_d6f2a.cif --- warnings | Unknown polymer entity '4' on line 4488 Missing or incorrect sequence information. Inferred polymer connectivity. Atom H is not in the residue template for MET /A:1 Chain information for 3GJF_d6f2a.cif #1 --- Chain | Description A | No description available D | HLA class I histocompatibility antigen, A-2 alpha chain E | Beta-2-microglobulin F | NYESO-1 peptide > color #1 bychain > color ~#1:0-276 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint > -52.11,43.45,48.41 color yellow > shape sphere radius 2.5 center 38.94,2.55,29.79 color red > shape sphere radius 2.5 center -52.11,43.45,48.41 color red > 2dlabels text ""3GJF_d6f2a: 10.15 nm"" xpos 0.05 ypos 0.9 color black size 24 > view executed 3GJF_d6f2a_measure.cxc > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF 0nvi6 d6f2a.cxs"" format session > view name session-start opened ChimeraX session > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/3GJF_d6f2a_measure.cxc"" format cmd > open 3GJF_d6f2a.cif Summary of feedback from opening 3GJF_d6f2a.cif --- warnings | Unknown polymer entity '4' on line 4488 Missing or incorrect sequence information. Inferred polymer connectivity. Atom H is not in the residue template for MET /A:1 Chain information for 3GJF_d6f2a.cif #1 --- Chain | Description A | No description available D | HLA class I histocompatibility antigen, A-2 alpha chain E | Beta-2-microglobulin F | NYESO-1 peptide > color #1 bychain > color ~#1:0-276 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 38.94,2.55,29.79 toPoint > -52.11,43.45,48.41 color yellow > shape sphere radius 2.5 center 38.94,2.55,29.79 color red > shape sphere radius 2.5 center -52.11,43.45,48.41 color red > 2dlabels text ""3GJF_d6f2a: 10.15 nm"" xpos 0.05 ypos 0.9 color black size 24 > view executed 3GJF_d6f2a_measure.cxc > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge_measure.cxc"" format cmd > open CD2CD58merge.cif Summary of feedback from opening CD2CD58merge.cif --- warnings | Unknown polymer entity '1' on line 112 Unknown polymer entity '2' on line 1374 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for CD2CD58merge.cif #1 --- Chain | Description A | HUMAN CD2 PROTEIN B | HUMAN CD58 PROTEIN > color #1 bychain > color ~#1:1-215 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 6.92,-7.59,89.20 toPoint > 68.86,44.41,-34.22 color yellow > shape sphere radius 2.5 center 6.92,-7.59,89.20 color red > shape sphere radius 2.5 center 68.86,44.41,-34.22 color red > 2dlabels text ""CD2CD58merge: 14.76 nm"" xpos 0.05 ypos 0.9 color black size > 24 > view executed CD2CD58merge_measure.cxc > select /B:186 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:182 10 atoms, 9 bonds, 1 residue, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select /B:172 6 atoms, 5 bonds, 1 residue, 1 model selected > close session > open /Users/hwu/Desktop/HeightDB/CD2CD58merge.cif format mmcif No such file/path: /Users/hwu/Desktop/HeightDB/CD2CD58merge.cif > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge.cxs"" > view name session-start opened ChimeraX session > select /B:209 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:209-215 58 atoms, 59 bonds, 7 residues, 1 model selected > select clear > select /B:209 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:209-215 58 atoms, 59 bonds, 7 residues, 1 model selected > delete sel > select clear > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge.cif"" relModel #5 Not saving entity_poly_seq for non-authoritative sequences > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/CD2CD58merge_measure.cxc"" > open CD2CD58merge.cif Summary of feedback from opening CD2CD58merge.cif --- warnings | Unknown polymer entity '1' on line 112 Unknown polymer entity '2' on line 1374 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for CD2CD58merge.cif #1 --- Chain | Description A | HUMAN CD2 PROTEIN B | HUMAN CD58 PROTEIN > color #1 bychain > color ~#1:1-208 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 6.45,-6.16,90.14 toPoint > 62.15,36.49,-20.74 color yellow > shape sphere radius 2.5 center 6.45,-6.16,90.14 color red > shape sphere radius 2.5 center 62.15,36.49,-20.74 color red > 2dlabels text ""CD2CD58merge: 13.12 nm"" xpos 0.05 ypos 0.9 color black size > 24 > view executed CD2CD58merge_measure.cxc > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/AF2/test_0d0a1/test_0d0a1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb"" Chain information for test_0d0a1_relaxed_rank_001_alphafold2_ptm_model_2_seed_000.pdb #1 --- Chain | Description A | No description available Computing secondary structure > color bfactor 4547 atoms, 311 residues, atom bfactor range 33.2 to 98.7 > close session > open /Users/hwu/Downloads/ChimeraX/AlphaFold/AF-Q9Y287-F1-model_v6.cif > format mmcif Chain information for AF-Q9Y287-F1-model_v6.cif #1 --- Chain | Description | UniProt A | Integral membrane protein 2B | ITM2B_HUMAN 1-266 Color AF-Q9Y287-F1-model_v6.cif by residue attribute pLDDT_score > color bfactor 2134 atoms, 266 residues, atom bfactor range 24.6 to 98 > close session > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/AF2/test_14818 (IgG1 CAR > ECD)/test_14818_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb"" Chain information for test_14818_relaxed_rank_001_alphafold2_ptm_model_4_seed_000.pdb #1 --- Chain | Description A | No description available Computing secondary structure > color bfactor 5811 atoms, 394 residues, atom bfactor range 24.4 to 98.4 > sequence chain #1/A Alignment identifier is 1/A > select /A:1 19 atoms, 18 bonds, 1 residue, 1 model selected > select /A:1-101 1478 atoms, 1491 bonds, 101 residues, 1 model selected > select clear > select /A:120-121 22 atoms, 21 bonds, 2 residues, 1 model selected > select /A:118-120 41 atoms, 40 bonds, 3 residues, 1 model selected > select /A:120-146 416 atoms, 418 bonds, 27 residues, 1 model selected > select /A:301 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:301-388 1322 atoms, 1337 bonds, 88 residues, 1 model selected > select clear > select /A:248 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:248-249 24 atoms, 23 bonds, 2 residues, 1 model selected > select /A:248-291 632 atoms, 644 bonds, 44 residues, 1 model selected > select /A:248 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:248-285 541 atoms, 551 bonds, 38 residues, 1 model selected > select /A:287 14 atoms, 14 bonds, 1 residue, 1 model selected > select /A:286 17 atoms, 16 bonds, 1 residue, 1 model selected > select /A:248-286 558 atoms, 568 bonds, 39 residues, 1 model selected > select clear > select /A:286 17 atoms, 16 bonds, 1 residue, 1 model selected > delete #1A:1-286 Missing or invalid ""atoms"" argument: invalid atoms specifier > delete #1/A:1-286 > select /A:394 23 atoms, 22 bonds, 1 residue, 1 model selected > select /A:387-394 122 atoms, 122 bonds, 8 residues, 1 model selected > select /A:385-394 146 atoms, 147 bonds, 10 residues, 1 model selected > select /A:394 23 atoms, 22 bonds, 1 residue, 1 model selected > select /A:388-394 108 atoms, 108 bonds, 7 residues, 1 model selected > delete sel > select clear > save ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/14818_IgG1_only.cif"" relModel #1 Not saving entity_poly_seq for non-authoritative sequences > open ""/Users/hwu/Library/CloudStorage/Box-Box/Jun Lab Group Folder/Data for > Young-wook/Harry Wu/Collaborations/Structure prediction for > HeightDB/ChimeraX/14818_IgG1_only_measure.cxc"" > open 14818_IgG1_only.cif Summary of feedback from opening 14818_IgG1_only.cif --- warnings | Unknown polymer entity '1' on line 106 Missing or incorrect sequence information. Inferred polymer connectivity. Chain information for 14818_IgG1_only.cif #2 --- Chain | Description A | No description available > color #1 bychain > color ~#1:287-387 #808080 transparency 70 target ac > shape cylinder radius 1.0 fromPoint 7.35,10.76,17.68 toPoint > -30.85,-9.09,17.28 color yellow > shape sphere radius 2.5 center 7.35,10.76,17.68 color red > shape sphere radius 2.5 center -30.85,-9.09,17.28 color red > 2dlabels text ""14818_IgG1_only: 4.31 nm"" xpos 0.05 ypos 0.9 color black size > 24 > view executed 14818_IgG1_only_measure.cxc ===== Log before crash end ===== Log: You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.12 (2026-06-12) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYD82LL/A Chip: Apple M1 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 8 GB System Firmware Version: 18000.120.36 OS Loader Version: 18000.120.36 Software: System Software Overview: System Version: macOS 26.5.1 (25F80) Kernel Version: Darwin 25.5.0 Time since boot: 54 days, 3 hours, 56 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.2 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.4.3 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12 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: 1.2.2 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.2 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.9 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.8 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.4.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.21 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.18 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.22.1 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.10.0 plotly: 6.8.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.18.0 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.32 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 2026.5.1 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.8.4 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.4 stack-data: 0.6.3 starlette: 1.3.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.7 tqdm: 4.68.2 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.49.0 wcwidth: 0.8.1 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.24.2 }}} " defect new normal Unassigned