id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16805 Selection intersection problem isaphan@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.7.3-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description The intersect selection does not seem to be working. For example, I want to colour the sidechains of residues in one chain that contact another chain: 1. select (replace) contacts between 2 chains : selects several residues in both chains. OK 2. select (substract) 1 chain : only contact residues in 1 chain are shown, including sidechains. OK 3. select (intersect) sidechain only: removes all selection! ctrl-Z does not restore selection :( There are workaround, but still it would be really helpful to have the intersect selection work. Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open > /Users/iphan/Documents/ssgcid/OQ8b_HIP_42_neuraminidase/documents/neuraminidase_svtd.cxs Log from Wed May 1 10:43:48 2024UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/neuraminidase.cxs"" format session Log from Wed Dec 13 18:08:18 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/neuraminidase.cxs"" Log from Fri Dec 1 10:04:32 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/neuraminidase.cxs"" format session Log from Wed Nov 29 16:58:50 2023UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/iphan/Documents/BaseJ/PAF1C/sequences/LEO1_PAF1_colabfold_batch/LEO1_Q8IJJ3_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb Chain information for LEO1_Q8IJJ3_unrelaxed_alphafold2_multimer_v3_model_1_seed_000.pdb #1 --- Chain | Description A | No description available B | No description available > select add #1 6436 atoms, 6566 bonds, 760 residues, 1 model selected > color sel bychain > select clear [Repeated 1 time(s)] > select add #1 6436 atoms, 6566 bonds, 760 residues, 1 model selected > color bfactor sel 6436 atoms, 760 residues, atom bfactor range 14.5 to 95.4 > select clear > color bychain > close > open 6hg0 Summary of feedback from opening 6hg0 fetched from pdb --- warnings | Unable to fetch template for 'BMA': might have incorrect bonds Unable to fetch template for 'MAN': might have incorrect bonds Unable to fetch template for 'PO4': might have incorrect bonds Unable to fetch template for 'SIA': might have incorrect bonds Unable to fetch template for 'K': might have incorrect bonds note | Fetching compressed mmCIF 6hg0 from http://files.rcsb.org/download/6hg0.cif 6hg0 title: Influenza A Virus N9 Neuraminidase complex with NANA (Tern/Australia). [more info...] Chain information for 6hg0 #1 --- Chain | Description | UniProt A | Neuraminidase | NRAM_I75A5 83-470 Non-standard residues in 6hg0 #1 --- BMA — beta-D-mannopyranose CA — calcium ion GOL — glycerol (glycerin; propane-1,2,3-triol) K — potassium ion MAN — alpha-D-mannopyranose NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose PO4 — phosphate ion SIA — N-acetyl-alpha-neuraminic acid 6hg0 mmCIF Assemblies --- 1| author_and_software_defined_assembly > select #1:119,120,135,152,153,181,227,228,229,279,294,351,372,406 130 atoms, 121 bonds, 14 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select add #1 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 2 models selected > mlp sel Map values for surface ""6hg0_A SES surface"": minimum -29.21, mean -5.382, maximum 24.5 To also show corresponding color key, enter the above mlp command and add key true > select #1:119,120,135,152,153,181,227,228,229,279,294,351,372,406 130 atoms, 121 bonds, 14 residues, 1 model selected > color (#!1 & sel) red > undo > select intersect sideonly 61 bonds, 1 model selected > hide #1.2 models > color sel red > undo > select #1:119,120,135,152,153,181,227,228,229,279,294,351,372,406 130 atoms, 121 bonds, 14 residues, 1 model selected > select intersect sideonly 61 bonds, 1 model selected > color sel red [Repeated 1 time(s)] > select up 74 atoms, 61 bonds, 14 residues, 1 model selected > select down 61 bonds, 2 models selected > select up 74 atoms, 61 bonds, 14 residues, 1 model selected > color (#!1 & sel) red > show #1.2 models > select /A:467@OE2 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 58 atoms, 59 bonds, 6 residues, 2 models selected > select up 3067 atoms, 3159 bonds, 388 residues, 2 models selected > select up 3868 atoms, 3225 bonds, 1125 residues, 2 models selected > select up 4040 atoms, 3411 bonds, 1139 residues, 2 models selected > select up 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 3 models selected > select up 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 3 models selected > select up 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 3 models selected > select up 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 3 models selected > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > select /A:224@CD1 1 atom, 1 residue, 1 model selected > select add /A:151@CE1 2 atoms, 2 residues, 2 models selected > select up 18 atoms, 17 bonds, 2 residues, 2 models selected > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select add /A:153@NH1 19 atoms, 17 bonds, 3 residues, 2 models selected > select up 29 atoms, 27 bonds, 3 residues, 2 models selected > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > undo [Repeated 8 time(s)] > redo > undo > redo [Repeated 7 time(s)] > ~label (#!1 & sel) residues > select /A:348@ND2 1 atom, 1 residue, 1 model selected > select add /A:372@CD 2 atoms, 2 residues, 2 models selected > select add /A:434@NZ 3 atoms, 3 residues, 2 models selected > select up 28 atoms, 25 bonds, 3 residues, 2 models selected > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > ui mousemode right ""move label"" > select /A:328@CD 1 atom, 1 residue, 1 model selected > select /A:328@CG 1 atom, 1 residue, 1 model selected > lighting full > select /A:328@CB 1 atom, 1 residue, 1 model selected > select /A:328@O 1 atom, 1 residue, 1 model selected > select /A:328@CD 1 atom, 1 residue, 1 model selected > select clear > save ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/neuraminidase.cxs"" ——— End of log from Wed Nov 29 16:58:50 2023 ——— opened ChimeraX session > hide #1.2 models > show #1.2 models > select /A:372@NE 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > select add /A:294@NH1 12 atoms, 10 bonds, 2 residues, 2 models selected > select up 22 atoms, 20 bonds, 2 residues, 2 models selected > select add /A:119@NH2 23 atoms, 20 bonds, 3 residues, 2 models selected > select up 33 atoms, 30 bonds, 3 residues, 2 models selected > select add /A:152@OD2 34 atoms, 30 bonds, 4 residues, 2 models selected > select up 41 atoms, 37 bonds, 4 residues, 2 models selected > select add /A:153@NH1 42 atoms, 37 bonds, 5 residues, 2 models selected > select up 52 atoms, 48 bonds, 5 residues, 2 models selected > hide #1.2 models Drag select of 2 residues > undo > select up 54 atoms, 49 bonds, 6 residues, 2 models selected > select up 64 atoms, 60 bonds, 6 residues, 2 models selected > select add /A:279@CD 65 atoms, 60 bonds, 7 residues, 2 models selected > select up 73 atoms, 68 bonds, 7 residues, 2 models selected > show #1.2 models > select add /A:229@CD 74 atoms, 68 bonds, 8 residues, 2 models selected > select up 82 atoms, 76 bonds, 8 residues, 2 models selected > select up 522 atoms, 526 bonds, 66 residues, 2 models selected > select down 82 atoms, 76 bonds, 8 residues, 2 models selected > select add /A:120@CG 83 atoms, 76 bonds, 9 residues, 2 models selected > select up 91 atoms, 85 bonds, 9 residues, 2 models selected > select up 522 atoms, 526 bonds, 66 residues, 2 models selected > select down 91 atoms, 85 bonds, 9 residues, 2 models selected > hide #1.2 models > show sel atoms > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > show #1.2 models > select #1:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > select clear > select #1:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/flu_neuraminidase_100_hotspots_all_rfd.result/flu_neuraminidase_100_hotspots_all_rfd/best.pdb"" Chain information for best.pdb #2 --- Chain | Description A | No description available B | No description available > hide #1.3 models > hide #!1 models > select add #2 4014 atoms, 4097 bonds, 497 residues, 3 models selected > select subtract #1.2 3923 atoms, 4012 bonds, 488 residues, 2 models selected > view sel > cofr sel > hide #2 models > select subtract #2 Nothing selected > show #!1 models > hide #!1 models > show #!1 models > show #1.3 models > select add #1 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 3 models selected > view sel > cofr sel > select #2/A 3066 atoms, 3149 bonds, 388 residues, 1 model selected > hide #1.2 models > select #1/A 3868 atoms, 3225 bonds, 9 pseudobonds, 1125 residues, 2 models selected > select intersect > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 3159 bonds, 1 model selected > select ~sel 7963 atoms, 7423 bonds, 14 pseudobonds, 1627 residues, 4 models selected > select clear > select intersect #1/A Nothing selected > select #1/A 3868 atoms, 3225 bonds, 9 pseudobonds, 1125 residues, 2 models selected > select intersect main 3159 bonds, 1 model selected > select up 3067 atoms, 3159 bonds, 388 residues, 1 model selected > select up 3868 atoms, 3225 bonds, 1125 residues, 2 models selected > select down 3067 atoms, 3159 bonds, 388 residues, 2 models selected > save ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/6hg0_protein_monomer.pdb"" models #1 selectedOnly true > relModel #1 > hide #!1 models > hide #1.1 models > hide #1.3 models > select add #1 4040 atoms, 3411 bonds, 14 pseudobonds, 1139 residues, 4 models selected > select subtract #1 1 model selected > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/6hg0_protein_monomer.pdb"" Summary of feedback from opening /Users/iphan/Documents/ssgcid/Flu project/neuraminidase/6hg0_protein_monomer.pdb --- warnings | Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (2 ) 23 messages similar to the above omitted Chain information for 6hg0_protein_monomer.pdb #3 --- Chain | Description A | No description available > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > select #1:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > select #2:119,120,152,153,229,279,294,372,406 64 atoms, 60 bonds, 8 residues, 1 model selected > select #3:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > show sel atoms > color sel red > select add #3 3067 atoms, 3157 bonds, 2 pseudobonds, 388 residues, 2 models selected > mlp sel Map values for surface ""6hg0_protein_monomer.pdb_A SES surface"": minimum -29.21, mean -5.382, maximum 24.5 To also show corresponding color key, enter the above mlp command and add key true > select #3:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > color (#!3 & sel) red > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > show #!1 models > show #1.2 models > show #!3 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.1 models > hide #1.1 models > hide #!3 models > select add #3.1 91 atoms, 85 bonds, 2 pseudobonds, 9 residues, 3 models selected > select subtract #3.1 91 atoms, 85 bonds, 9 residues, 2 models selected > hide #3.1 models > show #!3 models > hide #3.2 models > show #1.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > select #1/A:181@CB 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 2 models selected > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > hide #!3 models > select #1/A:153@N 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > select up 86 atoms, 87 bonds, 10 residues, 2 models selected > select down 11 atoms, 10 bonds, 1 residue, 2 models selected > hide #1.2 models > show #1.2 models > show #3.1 models > hide #3.1 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > hide #!3 models > select up 86 atoms, 87 bonds, 10 residues, 2 models selected > select down 11 atoms, 10 bonds, 1 residue, 2 models selected > select up 86 atoms, 87 bonds, 10 residues, 2 models selected > select up 3067 atoms, 3159 bonds, 388 residues, 2 models selected > select down 86 atoms, 87 bonds, 10 residues, 2 models selected > select down 11 atoms, 10 bonds, 1 residue, 2 models selected > color (#!1 & sel) red > show #1.3 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #3.2 models > show #3.2 models > hide #1.2 models > hide #!1 models > select #3:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > hide #3.2 models > hide #!3 models > show #1.2 models > hide #!1 models > show #!1 models > hide #1.2 models > hide #1.3 models > hide #!1 models > open > /Users/iphan/Documents/BaseJ/PAF1C/sequences/LEO1_PAF1_colabfold_batch/LEO1_Q8I3K1_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb > /Users/iphan/Documents/BaseJ/PAF1C/sequences/LEO1_PAF1_colabfold_batch/LEO1_Q8I3K1_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb > /Users/iphan/Documents/BaseJ/PAF1C/sequences/LEO1_PAF1_colabfold_batch/LEO1_Q8I3K1_unrelaxed_rank_003_alphafold2_multimer_v3_model_1_seed_000.pdb > /Users/iphan/Documents/BaseJ/PAF1C/sequences/LEO1_PAF1_colabfold_batch/LEO1_Q8I3K1_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb > /Users/iphan/Documents/BaseJ/PAF1C/sequences/LEO1_PAF1_colabfold_batch/LEO1_Q8I3K1_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb Chain information for LEO1_Q8I3K1_unrelaxed_rank_001_alphafold2_multimer_v3_model_3_seed_000.pdb #4 --- Chain | Description A | No description available B | No description available Chain information for LEO1_Q8I3K1_unrelaxed_rank_002_alphafold2_multimer_v3_model_4_seed_000.pdb #5 --- Chain | Description A | No description available B | No description available Chain information for LEO1_Q8I3K1_unrelaxed_rank_003_alphafold2_multimer_v3_model_1_seed_000.pdb #6 --- Chain | Description A | No description available B | No description available Chain information for LEO1_Q8I3K1_unrelaxed_rank_004_alphafold2_multimer_v3_model_5_seed_000.pdb #7 --- Chain | Description A | No description available B | No description available Chain information for LEO1_Q8I3K1_unrelaxed_rank_005_alphafold2_multimer_v3_model_2_seed_000.pdb #8 --- Chain | Description A | No description available B | No description available > hide #5 models > hide #6 models > hide #7 models > hide #8 models > show #5 models > show #6 models > show #7 models > show #8 models > select add #4 6503 atoms, 6614 bonds, 777 residues, 3 models selected > select add #5 12915 atoms, 13143 bonds, 1545 residues, 4 models selected > select subtract #3.2 12824 atoms, 13058 bonds, 1536 residues, 3 models selected > select add #6 19236 atoms, 19587 bonds, 2304 residues, 3 models selected > select add #7 25648 atoms, 26116 bonds, 3072 residues, 4 models selected > select add #8 32060 atoms, 32645 bonds, 3840 residues, 5 models selected > color sel bychain > hide #8 models > hide #7 models > hide #6 models > hide #5 models > show #5 models > hide #4 models > show #6 models > hide #5 models > show #7 models > hide #6 models > lighting simple > show #8 models > hide #7 models > close #4-8 > show #!3 models > show #3.1 models > show #3.2 models > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/flu_neuraminidase_10_hotspots_9_rfd_beta.result/flu_neuraminidase_10_hotspots_9_rfd_beta/best.pdb"" Chain information for best.pdb #4 --- Chain | Description A | No description available B | No description available > hide #!3 models > hide #3.1 models > hide #3.2 models > select add #4 3136 atoms, 3219 bonds, 398 residues, 1 model selected > cofr sel > view sel > color sel bychain > select #4:119,120,152,153,229,279,294,372,406 64 atoms, 60 bonds, 8 residues, 1 model selected > select #4:119,120,152,153,229,279,294,372,406 64 atoms, 60 bonds, 8 residues, 1 model selected > select #4:119,120,152,153,229,279,294,372,406 64 atoms, 60 bonds, 8 residues, 1 model selected > select #4:119,120,152,153,229,279,294,372,406 64 atoms, 60 bonds, 8 residues, 1 model selected > show #!1 models > select #1:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > select #4:119,120,152,153,229,279,294,372,406 64 atoms, 60 bonds, 8 residues, 1 model selected > open ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/6hg0_protein_monomer.pdb"" Summary of feedback from opening /Users/iphan/Documents/ssgcid/Flu project/neuraminidase/6hg0_protein_monomer.pdb --- warnings | Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (1 ) Cannot find LINK/SSBOND residue NAG (2 ) 23 messages similar to the above omitted Chain information for 6hg0_protein_monomer.pdb #5 --- Chain | Description A | No description available > ui tool show ""Show Sequence Viewer"" > sequence chain #5/A Alignment identifier is 5/A > ui tool show ""Renumber Residues"" > renumber #4/A seqStart 83 388 residues renumbered > select #4:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > show sel atoms > select #4/B:10 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 70 atoms, 70 bonds, 10 residues, 1 model selected > show sel atoms > color sel byhetero > select #4:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > color sel byhetero > select clear > select #4/B:5 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 70 atoms, 70 bonds, 10 residues, 1 model selected > select up 3136 atoms, 3219 bonds, 398 residues, 1 model selected > select down 70 atoms, 70 bonds, 10 residues, 1 model selected > hide sel cartoons > select #4:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > select clear > select #4/A:346 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 293 atoms, 301 bonds, 39 residues, 1 model selected > select up 3066 atoms, 3149 bonds, 388 residues, 1 model selected > mlp sel Map values for surface ""best.pdb_A SES surface"": minimum -27.51, mean -5.14, maximum 24.64 To also show corresponding color key, enter the above mlp command and add key true > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 70 atoms, 70 bonds, 10 residues, 1 model selected > surface sel > transparency (#!4 & sel) 40 > select #4/A:348@ND2 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > select up 293 atoms, 301 bonds, 39 residues, 2 models selected > select up 3066 atoms, 3149 bonds, 388 residues, 2 models selected > select down 293 atoms, 301 bonds, 39 residues, 2 models selected > select #4/A:346@O 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 2 models selected > select up 293 atoms, 301 bonds, 39 residues, 2 models selected > select up 3066 atoms, 3149 bonds, 388 residues, 2 models selected > select down 293 atoms, 301 bonds, 39 residues, 2 models selected > hide #!5 models > select add #4 3136 atoms, 3219 bonds, 398 residues, 2 models selected > hide #4.1 models > show #4.1 models > surface style #4 mesh > undo > redo > surface style #4 solid > select subtract #4.1 70 atoms, 70 bonds, 10 residues, 3 models selected > select add #4.1 3136 atoms, 70 bonds, 398 residues, 2 models selected > select subtract #4.2 3066 atoms, 388 residues, 3 models selected > select add #4 3136 atoms, 3219 bonds, 398 residues, 2 models selected > select subtract #4 2 models selected > select add #4.1 3066 atoms, 388 residues, 1 model selected > select subtract #4.1 1 model selected > select add #4.2 70 atoms, 10 residues, 1 model selected > select subtract #4.2 1 model selected > select add #4.1 3066 atoms, 388 residues, 1 model selected > select subtract #4.1 1 model selected > hide #4.1 models > select #4/A:405 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 67 atoms, 69 bonds, 8 residues, 2 models selected > select up 3066 atoms, 3149 bonds, 388 residues, 2 models selected > select up 3136 atoms, 3219 bonds, 398 residues, 2 models selected > select down 3066 atoms, 3149 bonds, 388 residues, 3 models selected > hide #4.2 models > show #4.2 models > show #4.1 models > transparency (#!4 & sel) 40 > hide #!1 models > select #4/A:328@CB 1 atom, 1 residue, 1 model selected > ui tool show ""Side View"" > select #4:119,120,152,153,229,279,294,372,406 91 atoms, 85 bonds, 9 residues, 1 model selected > hide #!4.1 models > select #4:153,406 23 atoms, 22 bonds, 2 residues, 1 model selected > select #4:153,372,406 34 atoms, 32 bonds, 3 residues, 1 model selected > save ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/neuraminidase.cxs"" ——— End of log from Fri Dec 1 10:04:32 2023 ——— opened ChimeraX session > lighting full > select clear > select #4/A:279@CD 1 atom, 1 residue, 1 model selected > select add #4/A:229@CD 2 atoms, 2 residues, 2 models selected > select add #4/A:406@OH 3 atoms, 1 bond, 3 residues, 2 models selected > select add #4/A:372@CZ 4 atoms, 1 bond, 4 residues, 2 models selected > select up 6 atoms, 1 bond, 5 residues, 2 models selected > select up 8 atoms, 2 bonds, 6 residues, 2 models selected > select up 63 atoms, 58 bonds, 6 residues, 2 models selected > select up 65 atoms, 59 bonds, 7 residues, 2 models selected > select up 72 atoms, 67 bonds, 7 residues, 2 models selected > select up 74 atoms, 68 bonds, 8 residues, 2 models selected > select up 83 atoms, 77 bonds, 8 residues, 2 models selected > ui tool show ""Side View"" > set bgColor white > set bgColor black > set bgColor white > save /Users/iphan/Desktop/image1.png supersample 3 > show #2 models > hide #!4 models > select add #4 3136 atoms, 3219 bonds, 398 residues, 2 models selected > show #!4 models > ui tool show Matchmaker > matchmaker #2 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 best.pdb, chain A (#4) with best.pdb, chain A (#2), sequence alignment score = 2075.4 RMSD between 388 pruned atom pairs is 0.092 angstroms; (across all 388 pairs: 0.092) > hide #!4 models > select #2/A:263 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 293 atoms, 301 bonds, 39 residues, 1 model selected > select up 3066 atoms, 3149 bonds, 388 residues, 1 model selected > select up 3923 atoms, 4012 bonds, 488 residues, 1 model selected > select down 3066 atoms, 3149 bonds, 388 residues, 1 model selected > color sel bychain > select clear > show #!4 models > select add #4/A:229@CG 1 atom, 1 residue, 1 model selected > select add #4/A:279@CG 2 atoms, 2 residues, 2 models selected > select add #4/A:153@CZ 3 atoms, 3 residues, 2 models selected > hide #!4 models > select add #2/B:61 12 atoms, 10 bonds, 4 residues, 3 models selected > select up 16 atoms, 10 bonds, 6 residues, 3 models selected > select up 59 atoms, 54 bonds, 6 residues, 3 models selected > select up 852 atoms, 860 bonds, 101 residues, 3 models selected > select up 3923 atoms, 4012 bonds, 488 residues, 3 models selected > surface (#2 & sel) > transparency (#!2 & sel) 30 > select clear > select #2/B:59@OE1 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 2 models selected > select up 380 atoms, 383 bonds, 42 residues, 2 models selected > select up 857 atoms, 863 bonds, 100 residues, 2 models selected > transparency (#!2 & sel) 50 > select clear > show #!4 models > select add #4/A:135 8 atoms, 9 bonds, 1 residue, 1 model selected > undo > select add #4/A:120@CG 1 atom, 2 bonds, 1 residue, 1 model selected > select add #4/A:294@CZ 2 atoms, 2 bonds, 2 residues, 2 models selected > select up 10 atoms, 4 bonds, 6 residues, 2 models selected > select up 63 atoms, 58 bonds, 6 residues, 2 models selected > list selected Unknown command: list selected > list res selected Unknown command: list res selected > list Unknown command: list > info selection atom id #4/A:120@N idatm_type Npl atom id #4/A:120@CA idatm_type C3 atom id #4/A:120@C idatm_type C2 atom id #4/A:120@CB idatm_type C3 atom id #4/A:120@O idatm_type O2 atom id #4/A:120@CG idatm_type C3 atom id #4/A:120@CD idatm_type Cac atom id #4/A:120@OE1 idatm_type O2- atom id #4/A:120@OE2 idatm_type O2- atom id #4/A:153@N idatm_type Npl atom id #4/A:153@CA idatm_type C3 atom id #4/A:153@C idatm_type C2 atom id #4/A:153@CB idatm_type C3 atom id #4/A:153@O idatm_type O2 atom id #4/A:153@CG idatm_type C3 atom id #4/A:153@CD idatm_type C3 atom id #4/A:153@NE idatm_type Ng+ atom id #4/A:153@NH1 idatm_type Ng+ atom id #4/A:153@NH2 idatm_type Ng+ atom id #4/A:153@CZ idatm_type C2 atom id #4/A:229@N idatm_type Npl atom id #4/A:229@CA idatm_type C3 atom id #4/A:229@C idatm_type C2 atom id #4/A:229@CB idatm_type C3 atom id #4/A:229@O idatm_type O2 atom id #4/A:229@CG idatm_type C3 atom id #4/A:229@CD idatm_type Cac atom id #4/A:229@OE1 idatm_type O2- atom id #4/A:229@OE2 idatm_type O2- atom id #4/A:294@N idatm_type Npl atom id #4/A:294@CA idatm_type C3 atom id #4/A:294@C idatm_type C2 atom id #4/A:294@CB idatm_type C3 atom id #4/A:294@O idatm_type O2 atom id #4/A:294@CG idatm_type C3 atom id #4/A:294@CD idatm_type C3 atom id #4/A:294@NE idatm_type Ng+ atom id #4/A:294@NH1 idatm_type Ng+ atom id #4/A:294@NH2 idatm_type Ng+ atom id #4/A:294@CZ idatm_type C2 atom id #4/A:372@N idatm_type Npl atom id #4/A:372@CA idatm_type C3 atom id #4/A:372@C idatm_type C2 atom id #4/A:372@CB idatm_type C3 atom id #4/A:372@O idatm_type O2 atom id #4/A:372@CG idatm_type C3 atom id #4/A:372@CD idatm_type C3 atom id #4/A:372@NE idatm_type Ng+ atom id #4/A:372@NH1 idatm_type Ng+ atom id #4/A:372@NH2 idatm_type Ng+ atom id #4/A:372@CZ idatm_type C2 atom id #4/A:406@N idatm_type Npl atom id #4/A:406@CA idatm_type C3 atom id #4/A:406@C idatm_type C2 atom id #4/A:406@CB idatm_type C3 atom id #4/A:406@O idatm_type O2 atom id #4/A:406@CG idatm_type Car atom id #4/A:406@CD1 idatm_type Car atom id #4/A:406@CD2 idatm_type Car atom id #4/A:406@CE1 idatm_type Car atom id #4/A:406@CE2 idatm_type Car atom id #4/A:406@OH idatm_type O3 atom id #4/A:406@CZ idatm_type Car > hide #!4 models > select #2/A:120,153,229,294,372,406, Expected an objects specifier or a keyword > select #2/A:120,153,229,294,372,406 43 atoms, 40 bonds, 5 residues, 1 model selected > show #!4 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/A Alignment identifier is 4/A > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > ui tool show ""Renumber Residues"" > renumber #2/A seqStart 83 388 residues renumbered > select #2/A:120,153,229,294,372,406 63 atoms, 58 bonds, 6 residues, 1 model selected > hide #!4 models > show sel atoms > color sel byhetero > lighting full > lighting simple > lighting full > save ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/test_rfdesign_protein100.png"" width 831 height 739 > supersample 3 > save ""/Users/iphan/Documents/ssgcid/Flu > project/neuraminidase/neuraminidase.cxs"" ——— End of log from Wed Dec 13 18:08:18 2023 ——— opened ChimeraX session > hide #!2 models > select add #2 3923 atoms, 4012 bonds, 488 residues, 1 model selected > show #!1 models > select subtract #2 1 model selected > close #1-5 > open 6LXI format mmcif fromDatabase pdb 6lxi title: Crystal structure of Z2B3 Fab in complex with influenza virus neuraminidase from A/Brevig Mission/1/1918 (H1N1) [more info...] Chain information for 6lxi #1 --- Chain | Description | UniProt A B | Neuraminidase | NRAM_I18A0 1-469 C H | Heavy chain of Z2B3 Fab | D L | Light chain of Z2B3 Fab | Non-standard residues in 6lxi #1 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CA — calcium ion FUC — alpha-L-fucopyranose (alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose) 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) 6lxi mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > select /C:69@CG2 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 42 atoms, 41 bonds, 6 residues, 1 model selected > select up 1095 atoms, 1123 bonds, 145 residues, 1 model selected > select up 1101 atoms, 1128 bonds, 146 residues, 1 model selected > select up 1611 atoms, 1652 bonds, 214 residues, 1 model selected > hide sel atoms > show sel cartoons > select /D:2@N 1 atom, 1 residue, 1 model selected > select up 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 49 atoms, 49 bonds, 7 residues, 1 model selected > select up 1108 atoms, 1135 bonds, 151 residues, 1 model selected > select up 1112 atoms, 1138 bonds, 152 residues, 1 model selected > select up 1325 atoms, 1357 bonds, 179 residues, 1 model selected > hide sel atoms > select /H:204@CG 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 73 atoms, 74 bonds, 10 residues, 1 model selected > select up 1727 atoms, 1771 bonds, 232 residues, 1 model selected > select up 1796 atoms, 1771 bonds, 301 residues, 1 model selected > select up 12997 atoms, 12773 bonds, 2206 residues, 1 model selected > select down 1796 atoms, 1771 bonds, 301 residues, 1 model selected > hide sel atoms > select /L:208@CE 1 atom, 1 residue, 1 model selected > select up 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 52 atoms, 51 bonds, 7 residues, 1 model selected > select up 1563 atoms, 1602 bonds, 211 residues, 1 model selected > select up 1609 atoms, 1602 bonds, 257 residues, 1 model selected > select up 12997 atoms, 12773 bonds, 2206 residues, 1 model selected > select down 1609 atoms, 1602 bonds, 257 residues, 1 model selected > hide sel atoms > select /D:203@CA 1 atom, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 43 atoms, 43 bonds, 6 residues, 1 model selected > select up 122 atoms, 123 bonds, 17 residues, 1 model selected > hide sel atoms > select /A:389@CG2 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 92 atoms, 93 bonds, 11 residues, 1 model selected > select up 2980 atoms, 3069 bonds, 387 residues, 1 model selected > hide sel atoms > select solvent 565 atoms, 565 residues, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 60 atoms, 64 bonds, 5 residues, 1 model selected > hide sel atoms > select /A:501@CA 1 atom, 1 residue, 1 model selected > select add /A:502@CA 2 atoms, 2 residues, 1 model selected > hide sel atoms > select /C:112 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /C:111 10 atoms, 8 bonds, 2 residues, 1 model selected > select add /C:110 18 atoms, 15 bonds, 3 residues, 1 model selected > select add /C:109 26 atoms, 22 bonds, 4 residues, 1 model selected > select add /C:108 37 atoms, 32 bonds, 5 residues, 1 model selected > select add /B:368@NH1 38 atoms, 32 bonds, 6 residues, 1 model selected > select subtract /B:368@NH1 37 atoms, 32 bonds, 5 residues, 1 model selected > select add /C:107 45 atoms, 39 bonds, 6 residues, 1 model selected > select add /C:106 52 atoms, 45 bonds, 7 residues, 1 model selected > select add /C:105 60 atoms, 52 bonds, 8 residues, 1 model selected > select add /C:104 67 atoms, 59 bonds, 9 residues, 1 model selected > select add /C:103 74 atoms, 65 bonds, 10 residues, 1 model selected > select add /C:113 86 atoms, 77 bonds, 11 residues, 1 model selected > select add /C:114 98 atoms, 89 bonds, 12 residues, 1 model selected > color sel lime > select /B:200@ND2 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 36 atoms, 36 bonds, 6 residues, 1 model selected > select up 2980 atoms, 3069 bonds, 387 residues, 1 model selected > select down 36 atoms, 36 bonds, 6 residues, 1 model selected > select add /B:217@CD 37 atoms, 36 bonds, 7 residues, 1 model selected > select up 45 atoms, 44 bonds, 7 residues, 1 model selected > select up 91 atoms, 90 bonds, 13 residues, 1 model selected > select up 2980 atoms, 3069 bonds, 387 residues, 1 model selected > mlp sel Map values for surface ""6lxi_B SES surface"": minimum -30.24, mean -5.764, maximum 24.54 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!1 & sel) 40 > hide #1.2 models > hide #1.1 models > hide sel atoms > select /C:106 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /C:107 15 atoms, 13 bonds, 2 residues, 1 model selected > select add /C:109 23 atoms, 20 bonds, 3 residues, 1 model selected > select add /C:111 27 atoms, 23 bonds, 4 residues, 1 model selected > select add /C:110 35 atoms, 30 bonds, 5 residues, 1 model selected > select subtract /C:111 31 atoms, 27 bonds, 4 residues, 1 model selected > select add /C:111 35 atoms, 30 bonds, 5 residues, 1 model selected > select add /C:112 41 atoms, 35 bonds, 6 residues, 1 model selected > select add /C:113 53 atoms, 47 bonds, 7 residues, 1 model selected > select add /C:114 65 atoms, 59 bonds, 8 residues, 1 model selected > select add /C:103 72 atoms, 65 bonds, 9 residues, 1 model selected > select add /C:104 79 atoms, 72 bonds, 10 residues, 1 model selected > select add /C:105 87 atoms, 79 bonds, 11 residues, 1 model selected > select add /C:108 98 atoms, 89 bonds, 12 residues, 1 model selected > color sel red > select clear > lighting full > ui tool show ""Side View"" > hide #!1 models > show #!1 models > select add #1.3 2980 atoms, 387 residues, 2 models selected > coulombic sel The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics: /B LYS 469 OXT Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 6lxi_B SES surface #1.3: minimum, -16.06, mean -2.44, maximum 9.17 To also show corresponding color key, enter the above coulombic command and add key true > select clear > select add /C:114 12 atoms, 12 bonds, 1 residue, 1 model selected > select add /C:113 24 atoms, 24 bonds, 2 residues, 1 model selected > select add /B:399@CE3 25 atoms, 24 bonds, 3 residues, 1 model selected > select subtract /B:399@CE3 24 atoms, 24 bonds, 2 residues, 2 models selected > select add /C:112 30 atoms, 29 bonds, 3 residues, 1 model selected > select add /C:111 34 atoms, 32 bonds, 4 residues, 1 model selected > select add /C:110 42 atoms, 39 bonds, 5 residues, 1 model selected > select add /C:109 50 atoms, 46 bonds, 6 residues, 1 model selected > select add /C:108 61 atoms, 56 bonds, 7 residues, 1 model selected > select add /C:107 69 atoms, 63 bonds, 8 residues, 1 model selected > select add /C:106 76 atoms, 69 bonds, 9 residues, 1 model selected > select add /C:105 84 atoms, 76 bonds, 10 residues, 1 model selected > select add /C:104 91 atoms, 83 bonds, 11 residues, 1 model selected > select add /C:103 98 atoms, 89 bonds, 12 residues, 1 model selected > color sel lime > select /B:467@O 1 atom, 1 residue, 1 model selected > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 11 bonds, 1 residue, 1 model selected > select up 60 atoms, 64 bonds, 5 residues, 1 model selected > hide sel atoms > select /C:114 12 atoms, 12 bonds, 1 residue, 1 model selected > select add /C:113 24 atoms, 24 bonds, 2 residues, 1 model selected > select add /C:112 30 atoms, 29 bonds, 3 residues, 1 model selected > select add /C:111 34 atoms, 32 bonds, 4 residues, 1 model selected > select add /C:110 42 atoms, 39 bonds, 5 residues, 1 model selected > select add /B:118@NH1 43 atoms, 39 bonds, 6 residues, 1 model selected > select subtract /B:118@NH1 42 atoms, 39 bonds, 5 residues, 2 models selected > select add /C:108 53 atoms, 49 bonds, 6 residues, 1 model selected > select add /C:109 61 atoms, 56 bonds, 7 residues, 1 model selected > select add /C:107 69 atoms, 63 bonds, 8 residues, 1 model selected > select add /C:106 76 atoms, 69 bonds, 9 residues, 1 model selected > select add /B:399@CZ3 77 atoms, 69 bonds, 10 residues, 1 model selected > select subtract /B:399@CZ3 76 atoms, 69 bonds, 9 residues, 2 models selected > select add /C:105 84 atoms, 76 bonds, 10 residues, 1 model selected > select add /C:104 91 atoms, 83 bonds, 11 residues, 1 model selected > select add /C:103 98 atoms, 89 bonds, 12 residues, 1 model selected > show sel atoms > style sel ball Changed 98 atom styles > color sel byhetero > select clear > select /C:114@CA 1 atom, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > hide sel atoms > ui tool show ""Color Actions"" [Repeated 1 time(s)] > color sel plum > select clear > save ""/Users/iphan/Documents/ssgcid/Flu > project/documents/neuraminidase_svtd.cxs"" ——— End of log from Wed May 1 10:43:48 2024 ——— opened ChimeraX session > select /C:58 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 34 atoms, 34 bonds, 4 residues, 1 model selected > select up 1095 atoms, 1123 bonds, 145 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B Alignment identifier is 1 > sequence chain /H /C Alignment identifier is 2 > interfaces select /C & ::polymer_type>0 contacting /B & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > hide #1.3.1 models > hide #!1.3 models > show #1.3 models > select add #1.3 3099 atoms, 402 residues, 3 models selected > select subtract #1.3 119 atoms, 15 residues, 2 models selected > undo [Repeated 1 time(s)] > toolshed show > ui tool show Log > select up 944 atoms, 960 bonds, 124 residues, 2 models selected > select down 250 atoms, 30 residues, 2 models selected > select intersect sideonly 59 atoms, 15 residues, 1 model selected > hide #!1.3 models > show #1.2 models > hide #1.2 models > show #1.3 models > hide #1.3.1 models > hide #!1.3 models > hide #!1 models > show #!1 models > show #1.3 models > select intersect /C 59 atoms, 15 residues, 1 model selected > show sel cartoons > hide #!1.3 models > show #1.3 models > hide #!1.3 models > select /C 1657 atoms, 1652 bonds, 2 pseudobonds, 260 residues, 2 models selected > show #1.3 models > select /B 3147 atoms, 3069 bonds, 13 pseudobonds, 554 residues, 2 models selected > show sel cartoons > hide #!1.3 models > select subtract #1.3 167 atoms, 3 pseudobonds, 167 residues, 3 models selected > select add #1.1 167 atoms, 25 pseudobonds, 167 residues, 2 models selected > select add #1 12997 atoms, 12773 bonds, 29 pseudobonds, 2206 residues, 3 models selected > select subtract #1 1 model selected > interfaces select /C & ::polymer_type>0 contacting /B & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > select intersect sideonly 59 atoms, 15 residues, 1 model selected > undo [Repeated 1 time(s)] > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > select intersect sideonly 59 atoms, 15 residues, 1 model selected > undo > select clear > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > show sel atoms > select up 944 atoms, 960 bonds, 124 residues, 2 models selected > select down 250 atoms, 30 residues, 2 models selected > style sel stick Changed 250 atom styles > select up 944 atoms, 960 bonds, 124 residues, 2 models selected > select down 250 atoms, 30 residues, 2 models selected > color (#!1 & sel) red > undo > select intersect /B Nothing selected > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > select subtract /C/H 131 atoms, 15 residues, 2 models selected > select up 673 atoms, 683 bonds, 89 residues, 2 models selected > select down 131 atoms, 15 residues, 2 models selected > color (#!1 & sel) red > color (#!1 & sel) yellow > set bgColor black > select intersect sidechain Nothing selected > undo > select clear > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > select subtract backbone 130 atoms, 30 residues, 2 models selected > undo [Repeated 5 time(s)] > select clear > interfaces select /B & ::polymer_type>0 contacting /C & ::polymer_type>0 > areaCutoff 0 bothSides true 30 contacting residues > select subtract /C 131 atoms, 15 residues, 2 models selected > select subtract backbone 71 atoms, 15 residues, 2 models selected > color (#!1 & sel) byhetero > color (#!1 & sel) light gray > undo > select subtract backbone 71 atoms, 15 residues, 2 models selected > select subtract backbone 71 atoms, 15 residues, 2 models selected > color (#!1 & sel) light gray > color (#!1 & sel) byhetero > style sel sphere Changed 71 atom styles > style sel sphere Changed 71 atom styles > style sel sphere Changed 71 atom styles > style sel ball Changed 71 atom styles > style sel stick Changed 71 atom styles > label (#!1 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select clear > undo > list residues sel Unknown command: list residues sel > list residues Unknown command: list residues > list re Unknown command: list re > list res Unknown command: list res > info residues sel residue id /B:118 name ARG index 117 residue id /B:149 name VAL index 148 residue id /B:150 name LYS index 149 residue id /B:151 name ASP index 150 residue id /B:152 name ARG index 151 residue id /B:223 name ILE index 222 residue id /B:225 name ARG index 224 residue id /B:247 name SER index 246 residue id /B:344 name ASN index 343 residue id /B:368 name ARG index 367 residue id /B:430 name GLN index 429 residue id /B:431 name PRO index 430 residue id /B:432 name LYS index 431 residue id /B:434 name ASN index 433 residue id /B:436 name ILE index 435 > select /C 1657 atoms, 1652 bonds, 2 pseudobonds, 260 residues, 2 models selected > select /B 3147 atoms, 3069 bonds, 13 pseudobonds, 554 residues, 2 models selected > select intersect backbone 1547 bonds, 1 model selected > ui tool show ""Color Actions"" > select clear > select /B 3147 atoms, 3069 bonds, 13 pseudobonds, 554 residues, 2 models selected > select subtract sideonly 1715 atoms, 1547 bonds, 8 pseudobonds, 554 residues, 3 models selected > color (#!1 & sel) cornflower blue > ui tool show ""Color Actions"" > color sel sky blue > select clear OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15G001WALL/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 11881.81.2 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.3 (23H417) Kernel Version: Darwin 23.6.0 Time since boot: 2 days, 8 hours Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Structure Analysis can't reproduce Eric Pettersen all ChimeraX