id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8813 Crash using color chooser chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_MspA.pdb"" AF_MspA.pdb title: Alphafold monomer V2.0 prediction for porin MSPA (A0QR29) [more info...] Chain information for AF_MspA.pdb #1 --- Chain | Description | UniProt A | porin MSPA | MSPA_MYCS2 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:65 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:65-79 126 atoms, 130 bonds, 15 residues, 1 model selected > select /A:138-139 11 atoms, 11 bonds, 2 residues, 1 model selected > select /A:138-148 71 atoms, 71 bonds, 11 residues, 1 model selected > select /A:138-139 11 atoms, 11 bonds, 2 residues, 1 model selected > select /A:138-147 63 atoms, 63 bonds, 10 residues, 1 model selected > select /A:140 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:140-149 64 atoms, 63 bonds, 10 residues, 1 model selected > select /A:148 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:140-148 60 atoms, 59 bonds, 9 residues, 1 model selected > select > /A:29-36,42-48,51-55,65-78,86-96,99-108,139-148,152-163,166-171,174-178,186-195,200-204 785 atoms, 790 bonds, 103 residues, 1 model selected > select /A:148 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:139-148 64 atoms, 63 bonds, 10 residues, 1 model selected > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_MdtP.pdb"" AF_MdtP.pdb title: Alphafold monomer V2.0 prediction for multidrug resistance outer membrane protein MDTP (P32714) [more info...] Chain information for AF_MdtP.pdb #2 --- Chain | Description | UniProt A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI > select #1/A:78 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:65-78 122 atoms, 126 bonds, 14 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:328-329 17 atoms, 17 bonds, 2 residues, 1 model selected > select #2/A:328-339 95 atoms, 97 bonds, 12 residues, 1 model selected > log metadata #1 Metadata for AF_MspA.pdb #1 --- Title | Alphafold monomer V2.0 prediction for porin MSPA (A0QR29) Source (natural) | Mycolicibacterium smegmatis (strain ATCC 700084 / MC(2)155) > log chains #1 Chain information for AF_MspA.pdb #1 --- Chain | Description | UniProt A | porin MSPA | MSPA_MYCS2 > select #1/A:86-87 13 atoms, 12 bonds, 2 residues, 1 model selected > select #1/A:86-96 82 atoms, 82 bonds, 11 residues, 1 model selected > close > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_TolC.pdb"" AF_TolC.pdb title: Alphafold monomer V2.0 prediction for outer membrane protein tolc (P02930) [more info...] Chain information for AF_TolC.pdb #1 --- Chain | Description | UniProt A | outer membrane protein tolc | TOLC_ECOLI > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_HofQ.pdb"" AF_HofQ.pdb title: Alphafold monomer V2.0 prediction for DNA utilization protein hofq (P34749) [more info...] Chain information for AF_HofQ.pdb #2 --- Chain | Description | UniProt A | DNA utilization protein hofq | HOFQ_ECOLI Drag select of 18 residues > select clear > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A:269 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:269-284 113 atoms, 113 bonds, 16 residues, 1 model selected > select #1/A:289 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:288-289 18 atoms, 17 bonds, 2 residues, 1 model selected > select #1/A:284 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:269-284 113 atoms, 113 bonds, 16 residues, 1 model selected > select #1/A:299 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:299-311 94 atoms, 94 bonds, 13 residues, 1 model selected > select #1/A:270 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:270-285 110 atoms, 110 bonds, 16 residues, 1 model selected > select #1/A:83 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:83-98 117 atoms, 117 bonds, 16 residues, 1 model selected > select #1/A:74 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:63-74 91 atoms, 92 bonds, 12 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select #2/A:315 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:315-327 110 atoms, 111 bonds, 13 residues, 1 model selected > select #2/A:180 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:180-183 33 atoms, 32 bonds, 4 residues, 1 model selected > select #2/A:261 5 atoms, 4 bonds, 1 residue, 1 model selected > select #2/A:254-261 64 atoms, 63 bonds, 8 residues, 1 model selected > select #2/A:262 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:262-263 13 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:242 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:242-250 71 atoms, 70 bonds, 9 residues, 1 model selected > select #2/A:239 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:230-239 78 atoms, 79 bonds, 10 residues, 1 model selected > close #1 > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_MdtP.pdb"" AF_MdtP.pdb title: Alphafold monomer V2.0 prediction for multidrug resistance outer membrane protein MDTP (P32714) [more info...] Chain information for AF_MdtP.pdb #1 --- Chain | Description | UniProt A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > select #1/A:107 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:107-119 100 atoms, 99 bonds, 13 residues, 1 model selected > select #1/A:141 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:141-155 115 atoms, 117 bonds, 15 residues, 1 model selected > select #1/A:328 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:328-339 95 atoms, 97 bonds, 12 residues, 1 model selected > select #1/A:359 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:351-359 77 atoms, 79 bonds, 9 residues, 1 model selected > close #2 > close > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_MspA.pdb"" AF_MspA.pdb title: Alphafold monomer V2.0 prediction for porin MSPA (A0QR29) [more info...] Chain information for AF_MspA.pdb #1 --- Chain | Description | UniProt A | porin MSPA | MSPA_MYCS2 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:65-66 20 atoms, 19 bonds, 2 residues, 1 model selected > select /A:65-78 122 atoms, 126 bonds, 14 residues, 1 model selected > select /A:42 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:42-46 38 atoms, 37 bonds, 5 residues, 1 model selected > select /A:86-87 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:86-96 82 atoms, 82 bonds, 11 residues, 1 model selected > select /A:99 14 atoms, 15 bonds, 1 residue, 1 model selected > select /A:99-108 76 atoms, 78 bonds, 10 residues, 1 model selected > select /A:139-140 11 atoms, 10 bonds, 2 residues, 1 model selected > select /A:139-148 64 atoms, 63 bonds, 10 residues, 1 model selected > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_GspD.pdb"" AF_GspD.pdb title: Alphafold monomer V2.0 prediction for curli production assembly/transport component CSGG (P0AEA2) [more info...] Chain information for AF_GspD.pdb #2 --- Chain | Description | UniProt A | curli production assembly/transport component CSGG | CSGG_ECOLI > close #1 > open /Users/benjin/Downloads/pdb3m2l.ent pdb3m2l.ent title: Crystal structure of the M113F mutant of α-hemolysin [more info...] Chain information for pdb3m2l.ent #1 --- Chain | Description | UniProt A B C D E F G | α-hemolysin | HLA_STAAU > show cartoons > hide cartoons > hide atoms > show cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #1/D #1/E #1/F #1/G Alignment identifier is 1 > select #1/A-G:132-133 84 atoms, 77 bonds, 14 residues, 1 model selected > select #1/A-G:132-152 1057 atoms, 1071 bonds, 147 residues, 1 model selected > select #1/A-G:109 49 atoms, 42 bonds, 7 residues, 1 model selected > select #1/A-G:109-127 1038 atoms, 1059 bonds, 133 residues, 1 model selected > close #1 > mlp Map values for surface ""AF_GspD.pdb_A SES surface"": minimum -25.74, mean -4.26, maximum 23.78 To also show corresponding color key, enter the above mlp command and add key true > transparency 80 > transparency 50 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 2/A > select /A:161-162 12 atoms, 11 bonds, 2 residues, 1 model selected > select /A:161-180 156 atoms, 156 bonds, 20 residues, 1 model selected > select /A:180 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:169-180 94 atoms, 93 bonds, 12 residues, 1 model selected > select /A:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:161-169 70 atoms, 70 bonds, 9 residues, 1 model selected > select /A:136 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:136-146 83 atoms, 83 bonds, 11 residues, 1 model selected > select /A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:161 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:161-169 70 atoms, 70 bonds, 9 residues, 1 model selected > select /A:136 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:136-146 83 atoms, 83 bonds, 11 residues, 1 model selected > select /A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:186-191 43 atoms, 42 bonds, 6 residues, 1 model selected > select /A:192-193 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:192-199 63 atoms, 63 bonds, 8 residues, 1 model selected > select /A:201 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:201-210 81 atoms, 82 bonds, 10 residues, 1 model selected > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_CusC.pdb"" AF_CusC.pdb title: Alphafold monomer V2.0 prediction for cation efflux system protein cusc (P77211) [more info...] Chain information for AF_CusC.pdb #1 --- Chain | Description | UniProt A | cation efflux system protein cusc | CUSC_ECOLI > close #2 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:101 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:101-111 78 atoms, 79 bonds, 11 residues, 1 model selected > select /A:121 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:121-134 109 atoms, 110 bonds, 14 residues, 1 model selected > select /A:318 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:307-318 77 atoms, 76 bonds, 12 residues, 1 model selected > select /A:330-331 12 atoms, 11 bonds, 2 residues, 1 model selected > select /A:330-340 94 atoms, 97 bonds, 11 residues, 1 model selected > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Multimeric/AF_MdtP.pdb"" AF_MdtP.pdb title: Alphafold monomer V2.0 prediction for multidrug resistance outer membrane protein MDTP (P32714) [more info...] Chain information for AF_MdtP.pdb #2 --- Chain | Description | UniProt A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI > log metadata #2 Metadata for AF_MdtP.pdb #2 --- Title | Alphafold monomer V2.0 prediction for multidrug resistance outer membrane protein MDTP (P32714) Source (natural) | Escherichia coli (strain K12) > log chains #2 Chain information for AF_MdtP.pdb #2 --- Chain | Description | UniProt A | multidrug resistance outer membrane protein MDTP | MDTP_ECOLI > open /Users/benjin/Downloads/AF-Q51487-F1-model_v4.pdb AF-Q51487-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for outer membrane protein OPRM (Q51487) [more info...] Chain information for AF-Q51487-F1-model_v4.pdb #3 --- Chain | Description | UniProt A | outer membrane protein OPRM | OPRM_PSEAE > open /Users/benjin/Downloads/AF-Q51487-F1-model_v4.pdb AF-Q51487-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for outer membrane protein OPRM (Q51487) [more info...] Chain information for AF-Q51487-F1-model_v4.pdb #4 --- Chain | Description | UniProt A | outer membrane protein OPRM | OPRM_PSEAE > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A #4/A Alignment identifier is 1 > select #3/A:105-106 #4/A:105-106 24 atoms, 22 bonds, 4 residues, 2 models selected > select #3/A:105-116 #4/A:105-116 174 atoms, 172 bonds, 24 residues, 2 models selected Outer Membrane Protein OPRM [ID: 1] region 2 chains [105-116] RMSD: 0.000 > close #1 > close #2 > close #4 > select /A:327 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:316-327 78 atoms, 77 bonds, 12 residues, 1 model selected > select /A:348 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:339-348 81 atoms, 84 bonds, 10 residues, 1 model selected > select /A:127 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:127-143 126 atoms, 128 bonds, 17 residues, 1 model selected > select /A:116 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:105-116 87 atoms, 86 bonds, 12 residues, 1 model selected > open /Users/benjin/Downloads/pdb3d5k.ent pdb3d5k.ent title: Crystal structure of the OPRM channel In A non-symmetrical space group [more info...] Chain information for pdb3d5k.ent #1 --- Chain | Description | UniProt A B C | OPRM | OPRM_PSEAE Non-standard residues in pdb3d5k.ent #1 --- CL — chloride ion NA — sodium ion > close #3 > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B /C Alignment identifier is 1 > select /A-C:110-111 39 atoms, 36 bonds, 6 residues, 1 model selected > select /A-C:110-126 378 atoms, 384 bonds, 51 residues, 1 model selected > select /A-C:88 24 atoms, 21 bonds, 3 residues, 1 model selected > select /A-C:88-99 261 atoms, 258 bonds, 36 residues, 1 model selected > select /A-C:299 18 atoms, 15 bonds, 3 residues, 1 model selected > select /A-C:299-310 234 atoms, 231 bonds, 36 residues, 1 model selected > select /A-C:336 21 atoms, 18 bonds, 3 residues, 1 model selected > select /A-C:322-336 366 atoms, 381 bonds, 45 residues, 1 model selected > open /Users/benjin/Downloads/AF-I6X9D2-F1-model_v4.pdb AF-I6X9D2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for mce-family related protein (I6X9D2) [more info...] Chain information for AF-I6X9D2-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | mce-family related protein | I6X9D2_MYCTU > close #1 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 2/A > select /A:59 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:54-59 46 atoms, 45 bonds, 6 residues, 1 model selected > open /Users/benjin/Downloads/AF-Q6MX49-F1-model_v4.pdb AF-Q6MX49-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more info...] Chain information for AF-Q6MX49-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE5 | Q6MX49_MYCTU > select add #2 649 atoms, 665 bonds, 84 residues, 1 model selected > select add #1 15905 atoms, 16224 bonds, 2288 residues, 2 models selected > mlp sel Map values for surface ""AF-Q6MX49-F1-model_v4.pdb_A SES surface"": minimum -28.28, mean -2.941, maximum 25.4 Map values for surface ""AF-I6X9D2-F1-model_v4.pdb_A SES surface"": minimum -24.87, mean -2.315, maximum 22.55 To also show corresponding color key, enter the above mlp command and add key true > undo > redo > undo > close #2 > open ""/Users/benjin/Desktop/Multimeric candiates/AF-I6X8E6-F1-model_v4 > (1).pdb"" AF-I6X8E6-F1-model_v4 (1).pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6X8E6) [more info...] Chain information for AF-I6X8E6-F1-model_v4 (1).pdb #2 --- Chain | Description | UniProt A | uncharacterized protein | I6X8E6_MYCTU > close #1 > select clear > mlp Map values for surface ""AF-I6X8E6-F1-model_v4 (1).pdb_A SES surface"": minimum -23.36, mean -2.949, maximum 23.22 To also show corresponding color key, enter the above mlp command and add key true > mlp Map values for surface ""AF-I6X8E6-F1-model_v4 (1).pdb_A SES surface"": minimum -23.36, mean -2.949, maximum 23.22 To also show corresponding color key, enter the above mlp command and add key true > undo > redo > hide surfaces Drag select of 14 residues > select clear > select add #2 832 atoms, 868 bonds, 112 residues, 1 model selected > color byattribute pLddt No known/registered numeric attribute pLddt > close #2 > ui tool show AlphaFold Fetching I6X8E6 UniProt info from https://www.uniprot.org/uniprot/I6X8E6.xml > alphafold match I6X8E6 Fetching AlphaFold database settings from https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json Fetching compressed AlphaFold I6X8E6 from https://alphafold.ebi.ac.uk/files/AF-I6X8E6-F1-model_v2.cif 1 AlphaFold model found using UniProt identifier: I6X8E6 (UniProt I6X8E6) Opened 1 AlphaFold model > alphafold pae #1 uniprotId I6X8E6 Fetching compressed AlphaFold PAE I6X8E6 from https://alphafold.ebi.ac.uk/files/AF-I6X8E6-F1-predicted_aligned_error_v2.json > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:86 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:64-86 205 atoms, 217 bonds, 23 residues, 1 model selected > select /A:64-86 205 atoms, 217 bonds, 23 residues, 1 model selected > select /A:46 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:46-86 344 atoms, 361 bonds, 41 residues, 1 model selected > select /A:112 8 atoms, 8 bonds, 1 residue, 1 model selected > select /A:1-112 832 atoms, 868 bonds, 112 residues, 1 model selected > select /A:112 8 atoms, 8 bonds, 1 residue, 1 model selected > select /A:1-112 832 atoms, 868 bonds, 112 residues, 1 model selected > mlp sel Map values for surface ""AlphaFold I6X8E6_A SES surface"": minimum -23.36, mean -2.949, maximum 23.22 To also show corresponding color key, enter the above mlp command and add key true > transparency (#!1 & sel) 50 > undo > redo > undo > redo > hide sel surfaces > select /A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:1-112 832 atoms, 868 bonds, 112 residues, 1 model selected > hide sel surfaces > select subtract #1 1 model selected > alphafold pae #1 uniprotId I6X8E6 > open ""/Users/benjin/Desktop/Monomeric candidates/AF-I6X7P2-F1-model_v4.pdb"" AF-I6X7P2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6X7P2) [more info...] Chain information for AF-I6X7P2-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | uncharacterized protein | I6X7P2_MYCTU > close #1 > mlp Map values for surface ""AF-I6X7P2-F1-model_v4.pdb_A SES surface"": minimum -27.75, mean -4.872, maximum 22.4 To also show corresponding color key, enter the above mlp command and add key true > open /Users/benjin/Downloads/AF-I6XHD1-F1-model_v4.pdb AF-I6XHD1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6XHD1) [more info...] Chain information for AF-I6XHD1-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | I6XHD1_MYCTU > close #1 > close #2 > open /Users/benjin/Downloads/AF-I6XHD1-F1-model_v4.pdb AF-I6XHD1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6XHD1) [more info...] Chain information for AF-I6XHD1-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | I6XHD1_MYCTU > mlp Map values for surface ""AF-I6XHD1-F1-model_v4.pdb_A SES surface"": minimum -26.88, mean -5.195, maximum 21.67 To also show corresponding color key, enter the above mlp command and add key true > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for AF-I6XHD1-F1-model_v4.pdb_A SES surface #1.1: minimum, -14.29, mean -1.41, maximum 9.56 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""AF-I6XHD1-F1-model_v4.pdb_A SES surface"": minimum -26.88, mean -5.195, maximum 21.67 To also show corresponding color key, enter the above mlp command and add key true > close #1 > open /Users/benjin/Desktop/Structure/PDB/pdb1uun.ent format pdb No such file/path: /Users/benjin/Desktop/Structure/PDB/pdb1uun.ent > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Monomeric /12_AF_Tsx.pdb"" 12_AF_Tsx.pdb title: Alphafold monomer V2.0 prediction for nucleoside-specific channel- forming protein TSX (P0A927) [more info...] Chain information for 12_AF_Tsx.pdb #1 --- Chain | Description | UniProt A | nucleoside-specific channel-forming protein TSX | TSX_ECOLI > mlp Map values for surface ""12_AF_Tsx.pdb_A SES surface"": minimum -29.57, mean -2.558, maximum 24.84 To also show corresponding color key, enter the above mlp command and add key true > open ""/Users/benjin/Desktop/1. Write up/0. Bioinformatics/0. Structure-based > homology search/Monomeric /8_AF_YfaZ.pdb"" 8_AF_YfaZ.pdb title: Alphafold monomer V2.0 prediction for outer membrane protein yfaz (P76471) [more info...] Chain information for 8_AF_YfaZ.pdb #2 --- Chain | Description | UniProt A | outer membrane protein yfaz | YFAZ_ECOLI > close #1 > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 8_AF_YfaZ.pdb_A SES surface #2.1: minimum, -20.75, mean -2.68, maximum 13.99 To also show corresponding color key, enter the above coulombic command and add key true > mlp Map values for surface ""8_AF_YfaZ.pdb_A SES surface"": minimum -27.7, mean -4.367, maximum 23.12 To also show corresponding color key, enter the above mlp command and add key true > close #2 > open /Users/benjin/Downloads/AF-I6XHD1-F1-model_v4.pdb AF-I6XHD1-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6XHD1) [more info...] Chain information for AF-I6XHD1-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | I6XHD1_MYCTU > mlp Map values for surface ""AF-I6XHD1-F1-model_v4.pdb_A SES surface"": minimum -26.88, mean -5.195, maximum 21.67 To also show corresponding color key, enter the above mlp command and add key true > open ""/Users/benjin/Desktop/Monomeric candidates/AF-I6X7P2-F1-model_v4.pdb"" AF-I6X7P2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6X7P2) [more info...] Chain information for AF-I6X7P2-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | uncharacterized protein | I6X7P2_MYCTU > close #1 > mlp Map values for surface ""AF-I6X7P2-F1-model_v4.pdb_A SES surface"": minimum -27.75, mean -4.872, maximum 22.4 To also show corresponding color key, enter the above mlp command and add key true > open ""/Users/benjin/Desktop/Monomeric candidates/AF-I6X7P2-F1-model_v4.pdb"" AF-I6X7P2-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (I6X7P2) [more info...] Chain information for AF-I6X7P2-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | I6X7P2_MYCTU > select add #2 1313 atoms, 1345 bonds, 176 residues, 1 model selected > close #2 > mlp Map values for surface ""AF-I6X7P2-F1-model_v4.pdb_A SES surface"": minimum -27.75, mean -4.872, maximum 22.4 To also show corresponding color key, enter the above mlp command and add key true > open /Users/benjin/Downloads/AF-O06555-F1-model_v4.pdb AF-O06555-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for conserved ala-, pro-rich protein (O06555) [more info...] Chain information for AF-O06555-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | conserved ala-, pro-rich protein | O06555_MYCTU > close #1 > mlp Map values for surface ""AF-O06555-F1-model_v4.pdb_A SES surface"": minimum -26.21, mean -4.743, maximum 24.43 To also show corresponding color key, enter the above mlp command and add key true > open /Users/benjin/Downloads/AF-O05592-F1-model_v4.pdb AF-O05592-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (O05592) [more info...] Chain information for AF-O05592-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | O05592_MYCTU > close #2 > mlp Map values for surface ""AF-O05592-F1-model_v4.pdb_A SES surface"": minimum -30.36, mean -6.171, maximum 24.45 To also show corresponding color key, enter the above mlp command and add key true > open /Users/benjin/Downloads/AF-O69715-F1-model_v4.pdb AF-O69715-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (O69715) [more info...] Chain information for AF-O69715-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | uncharacterized protein | O69715_MYCTU > close #2 > close #1 > open /Users/benjin/Downloads/AF-O69715-F1-model_v4.pdb AF-O69715-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (O69715) [more info...] Chain information for AF-O69715-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | O69715_MYCTU > mlp Map values for surface ""AF-O69715-F1-model_v4.pdb_A SES surface"": minimum -24.49, mean -5.122, maximum 21.92 To also show corresponding color key, enter the above mlp command and add key true > open /Users/benjin/Downloads/AF-O53527-F1-model_v4.pdb AF-O53527-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (O53527) [more info...] Chain information for AF-O53527-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | uncharacterized protein | O53527_MYCTU > select add #1 898 atoms, 917 bonds, 119 residues, 1 model selected > select subtract #1 1 model selected > hide #2 models > close #2 > undo > close #1 > open /Users/benjin/Downloads/AF-O53527-F1-model_v4.pdb AF-O53527-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for uncharacterized protein (O53527) [more info...] Chain information for AF-O53527-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | uncharacterized protein | O53527_MYCTU > mlp Map values for surface ""AF-O53527-F1-model_v4.pdb_A SES surface"": minimum -26.94, mean -4.219, maximum 23.46 To also show corresponding color key, enter the above mlp command and add key true > close #1 > open /Users/benjin/Downloads/AF-Q6MX48-F1-model_v4.pdb AF-Q6MX48-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more info...] Chain information for AF-Q6MX48-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE6 | Q6MX48_MYCTU > mlp Map values for surface ""AF-Q6MX48-F1-model_v4.pdb_A SES surface"": minimum -28.82, mean -3.232, maximum 23.35 To also show corresponding color key, enter the above mlp command and add key true > hide surfaces > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:503-504 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:503-510 61 atoms, 61 bonds, 8 residues, 1 model selected > select /A:565 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:565-566 9 atoms, 8 bonds, 2 residues, 1 model selected > select /A:701 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:701-702 15 atoms, 15 bonds, 2 residues, 1 model selected > select /A:416-417 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:416-510 696 atoms, 713 bonds, 95 residues, 1 model selected > select add #1 6993 atoms, 7158 bonds, 963 residues, 2 models selected > select subtract #1 1 model selected > save /Users/benjin/Desktop/image1.png supersample 3 > open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb AF-Q6MX49-PPE5.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more info...] Chain information for AF-Q6MX49-PPE5.pdb #2 --- Chain | Description | UniProt A | ppe family protein PPE5 | Q6MX49_MYCTU > close #2 > close #1 > open /Users/benjin/Downloads/AF-Q6MX48-F1-model_v4.pdb AF-Q6MX48-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more info...] Chain information for AF-Q6MX48-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE6 | Q6MX48_MYCTU > close > open /Users/benjin/Desktop/AF-Q6MX48-F1-model_v4.pdb AF-Q6MX48-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more info...] Chain information for AF-Q6MX48-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE6 | Q6MX48_MYCTU > close > open /Users/benjin/Desktop/AF-Q6MX48-PPE6.pdb AF-Q6MX48-PPE6.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more info...] Chain information for AF-Q6MX48-PPE6.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE6 | Q6MX48_MYCTU > close > open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb AF-Q6MX49-PPE5.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more info...] Chain information for AF-Q6MX49-PPE5.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE5 | Q6MX49_MYCTU > mlp Map values for surface ""AF-Q6MX49-PPE5.pdb_A SES surface"": minimum -28.28, mean -2.941, maximum 25.4 To also show corresponding color key, enter the above mlp command and add key true > undo Undo failed, probably because structures have been modified. > close #1 > open /Users/benjin/Desktop/AF-Q6MX48-PPE6.pdb AF-Q6MX48-PPE6.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more info...] Chain information for AF-Q6MX48-PPE6.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE6 | Q6MX48_MYCTU > open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb AF-Q6MX49-PPE5.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more info...] Chain information for AF-Q6MX49-PPE5.pdb #2 --- Chain | Description | UniProt A | ppe family protein PPE5 | Q6MX49_MYCTU > close #1 > open /Users/benjin/Desktop/AF-Q6MX49-PPE5.pdb AF-Q6MX49-PPE5.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE5 (Q6MX49) [more info...] Chain information for AF-Q6MX49-PPE5.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE5 | Q6MX49_MYCTU Fetching Q6MX49 UniProt info from https://www.uniprot.org/uniprot/Q6MX49.xml > alphafold match Q6MX49 Fetching compressed AlphaFold Q6MX49 from https://alphafold.ebi.ac.uk/files/AF-Q6MX49-F1-model_v2.cif 1 AlphaFold model found using UniProt identifier: Q6MX49 (UniProt Q6MX49) Opened 1 AlphaFold model > close #1 > hide #2 models > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f Must choose path to predicted aligned file File ""Q6MX49"" does not exist. > alphafold pae #3 uniprotId Q6MX49 Fetching compressed AlphaFold PAE Q6MX49 from https://alphafold.ebi.ac.uk/files/AF-Q6MX49-F1-predicted_aligned_error_v2.json > color bfactor #3 palette alphafold 15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5 > alphafold pae #3 colorDomains true > color bfactor #3 palette alphafold 15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5 > alphafold pae #3 uniprotId Q6MX49 > undo > alphafold pae #3 uniprotId Q6MX49 > alphafold pae #3 colorDomains true > color bfactor #3 palette alphafold 15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5 > alphafold pae #3 colorDomains true > color bfactor #3 palette alphafold 15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5 > alphafold pae #3 uniprotId Q6MX49 > color bfactor #3 palette alphafold 15256 atoms, 2204 residues, atom bfactor range 20.9 to 92.5 > save /Users/benjin/Desktop/image1.png supersample 3 > open /Users/benjin/Downloads/uniprot- > compressed_true_download_true_fields_accession_2Creviewed_2C-2023.04.10-09.06.15.31.xlsx/[Content_Types].xml Opened [Content_Types].xml > open /Users/benjin/Downloads/uniprot- > compressed_true_download_true_fields_accession_2Creviewed_2C-2023.04.10-09.06.15.31.xlsx/xl/worksheets/sheet1.xml Opened sheet1.xml > mlp #3 Map values for surface ""AlphaFold Q6MX49_A SES surface"": minimum -28.28, mean -2.941, maximum 25.4 To also show corresponding color key, enter the above mlp command and add key true > close #2 > close > open /Users/benjin/Desktop/AF-Q6MX48-PPE6.pdb AF-Q6MX48-PPE6.pdb title: Alphafold monomer V2.0 prediction for ppe family protein PPE6 (Q6MX48) [more info...] Chain information for AF-Q6MX48-PPE6.pdb #1 --- Chain | Description | UniProt A | ppe family protein PPE6 | Q6MX48_MYCTU > alphafold pae #1 uniprotId Q6MX48 Fetching compressed AlphaFold PAE Q6MX48 from https://alphafold.ebi.ac.uk/files/AF-Q6MX48-F1-predicted_aligned_error_v2.json > alphafold pae #1 colorDomains true > color bfactor #1 palette alphafold 6993 atoms, 963 residues, atom bfactor range 22.1 to 98.5 > save /Users/benjin/Desktop/image1.png supersample 3 > help help:user/tools/alphafold.html#pae > alphafold pae #1 uniprotId Q6MX48 > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:205 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:205-207 16 atoms, 15 bonds, 3 residues, 1 model selected > select /A:205 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:205-440 1673 atoms, 1709 bonds, 236 residues, 1 model selected > select /A:205 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:205-255 352 atoms, 357 bonds, 51 residues, 1 model selected > select /A:416 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:416-511 703 atoms, 721 bonds, 96 residues, 1 model selected > select /A:417-418 16 atoms, 15 bonds, 2 residues, 1 model selected > select /A:417-449 247 atoms, 252 bonds, 33 residues, 1 model selected > select /A:416 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:416-454 290 atoms, 296 bonds, 39 residues, 1 model selected > select /A:416 5 atoms, 4 bonds, 1 residue, 1 model selected > select /A:416-511 703 atoms, 721 bonds, 96 residues, 1 model selected > alphafold pae #1 uniprotId Q6MX48 > color bfactor #1 palette alphafold 6993 atoms, 963 residues, atom bfactor range 22.1 to 98.5 > help help:user/tools/alphafold.html#pae > Extended β-strands Unknown command: Extended β-strands > (416-511) Unknown command: (416-511) > color bfactor palette alphafold 6993 atoms, 963 residues, atom bfactor range 22.1 to 98.5 > key red:low orange: yellow: cornflowerblue: blue:high > select clear > open ""/Users/benjin/Desktop/Part III Project/Presentation/20230113 > Biochemistry Symposium/MmpL5_coiled conservation_AlphaFold.pdb"" MmpL5_coiled conservation_AlphaFold.pdb title: Alphafold monomer V2.0 prediction for siderophore exporter MMPL5 (P9WJV1) [more info...] Chain information for MmpL5_coiled conservation_AlphaFold.pdb #3 --- Chain | Description | UniProt A | siderophore exporter MMPL5 | MMPL5_MYCTU > close #1 > hide #3 models > close > open ""/Users/benjin/Desktop/Part III Project/0. Bioinformatics seq /MmpL Mtb > analysis_Adam/AF_MmpL5_conserved between paralogues.pdb"" AF_MmpL5_conserved between paralogues.pdb title: Alphafold monomer V2.0 prediction for siderophore exporter MMPL5 (P9WJV1) [more info...] Chain information for AF_MmpL5_conserved between paralogues.pdb #1 --- Chain | Description | UniProt A | siderophore exporter MMPL5 | MMPL5_MYCTU > open ""/Users/benjin/Desktop/Part III Project/0. Bioinformatics seq /MmpL Mtb > analysis_Adam/Mtb MmpL5 coiled coil aligned paralogue.cxs"" opened ChimeraX session > open ""/Users/benjin/Desktop/1. Write up/TrimericS5L5 2.pdb"" Summary of feedback from opening /Users/benjin/Desktop/1. Write up/TrimericS5L5 2.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ILE B 2 ARG B 7 1 6 Start residue of secondary structure not found: HELIX 2 2 TRP B 9 THR B 30 1 22 Start residue of secondary structure not found: HELIX 3 3 PHE C 23 THR C 30 1 8 Start residue of secondary structure not found: HELIX 4 4 ALA C 32 THR C 49 1 18 Start residue of secondary structure not found: HELIX 5 5 LEU C 53 ILE C 59 1 7 46 messages similar to the above omitted Chain information for TrimericS5L5 2.pdb --- Chain | Description 3.1/B 3.2/B 3.3/B | No description available 3.4/B 3.4/C 3.4/D | No description available 3.1/C 3.2/C 3.3/C | No description available 3.4/E 3.4/F 3.4/G | No description available Associated TrimericS5L5 2.pdb (3.1) chain C to MmpL5 with 0 mismatches Associated TrimericS5L5 2.pdb (3.2) chain C to MmpL5 with 0 mismatches Associated TrimericS5L5 2.pdb (3.3) chain C to MmpL5 with 0 mismatches Associated TrimericS5L5 2.pdb (3.4) chain B to MmpL5 with 0 mismatches Associated TrimericS5L5 2.pdb (3.4) chain C to MmpL5 with 0 mismatches Associated TrimericS5L5 2.pdb (3.4) chain D to MmpL5 with 0 mismatches > close #1-2 > ui tool show ""AlphaFold Error Plot"" > help help:user/tools/alphafold.html#pae > color bfactor palette alphafold 31974 atoms, 4170 residues, atom bfactor range 24.5 to 98.8 > hide surfaces > select add #3 31974 atoms, 32598 bonds, 4170 residues, 5 models selected > hide sel surfaces > show sel surfaces > hide sel surfaces > undo > hide #!3.1 models > show #!3.1 models > hide #!3.1 models > show #!3.1 models > hide #!3.3 models > show #!3.3 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > show #!3.4 models > hide #!3.4 models > color bfactor palette alphafold 31974 atoms, 4170 residues, 12 surfaces, atom bfactor range 24.5 to 98.8 > save /Users/benjin/Desktop/image1.png supersample 3 > save /Users/benjin/Desktop/image2.png supersample 3 > save /Users/benjin/Desktop/image3.png supersample 3 > hide #!3.1 models > show #!3.1 models > hide #!3.2 models > show #!3.2 models > hide #!3.2 models > show #!3.2 models > show #!3.4 models > hide #!3.4 models > hide #!3 models > show #!3 models > show #!3.4 models > hide #!3.4 models > ui tool show ""Color Actions"" > color bychain > undo > save /Users/benjin/Desktop/image1.png supersample 3 > ui tool show ""Color Actions"" > color bypolymer > color bychain > color bypolymer > color bychain > color #3.1 #ff40ff transparency 0 > color #3.1 #ff2600 transparency 0 > color #3.1 #fffb00 transparency 0 > color #3.1 #c13a5b transparency 0 > color #3.1 #4498d8 transparency 0 > color #3.2 #4498d8 transparency 0 > color #3.3 #4498d8 transparency 0 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 17 days 9:34 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Platform can't reproduce Tom Goddard all ChimeraX