id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7885 unwanted whole-chain selection klazowski@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.0-arm64-arm-64bit ChimeraX Version: 1.5rc202210241843 (2022-10-24 18:43:45 UTC) Description I selected a residue /H:167 in the structure PDB 7Z13 and then tried to select residues with Zone but it selects the whole chain. In the Zone window it says ""<5,000 angstroms"" which might mean it tries to select eveyrthing within 5 thousand A instead of 5. I cannot put a dot ""."" there, only comma "","". It might be related to the fact that in my language settings I use "","" as decimal separator and the program is confused about this. Log: UCSF ChimeraX version: 1.5rc202210241843 (2022-10-24) © 2016-2022 Regents of the University of California. All rights reserved. > open /Users/krystian/Desktop/PSF1_human_yeast.cxs Log from Tue Oct 25 15:49:36 2022 Startup Messages --- note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.5rc202210241843 (2022-10-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > 2E9X Unknown command: 2E9X > fetch 2E9X Unknown command: fetch 2E9X > close session > open 2E9X Summary of feedback from opening 2E9X fetched from pdb --- notes | Fetching compressed mmCIF 2e9x from http://files.rcsb.org/download/2e9x.cif Fetching CCD SO4 from http://ligand-expo.rcsb.org/reports/S/SO4/SO4.cif 2e9x title: The crystal structure of human GINS core complex [more info...] Chain information for 2e9x #1 --- Chain | Description | UniProt A E | DNA replication complex GINS protein PSF1 | PSF1_HUMAN B F | DNA replication complex GINS protein PSF2 | PSF2_HUMAN C G | GINS complex subunit 3 | Q9BRX5_HUMAN D H | GINS complex subunit 4 | Q9BRT9_HUMAN Non-standard residues in 2e9x #1 --- SO4 — sulfate ion 2e9x mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| software_defined_assembly 4| software_defined_assembly > hide atoms > show atoms > show cartoons > hide atoms > toolshed show > ui tool show AlphaFold > hbonds reveal true 2811 hydrogen bonds found > hbonds reveal true 2811 hydrogen bonds found > hbonds reveal false 2811 hydrogen bonds found > undo > redo > ~hbonds > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 2e9x_A SES surface #1.2: minimum, -13.71, mean 0.18, maximum 13.10 Coulombic values for 2e9x_B SES surface #1.3: minimum, -16.69, mean -1.17, maximum 13.91 Coulombic values for 2e9x_C SES surface #1.4: minimum, -17.68, mean -2.33, maximum 11.98 Coulombic values for 2e9x_D SES surface #1.5: minimum, -22.67, mean -3.72, maximum 16.46 Coulombic values for 2e9x_E SES surface #1.6: minimum, -15.33, mean -0.16, maximum 13.33 Coulombic values for 2e9x_F SES surface #1.7: minimum, -15.50, mean -1.43, maximum 10.33 Coulombic values for 2e9x_G SES surface #1.8: minimum, -20.48, mean -2.64, maximum 8.72 Coulombic values for 2e9x_H SES surface #1.9: minimum, -21.80, mean -3.38, maximum 11.77 To also show corresponding color key, enter the above coulombic command and add key true > undo > show cartoons > hide atoms > style stick Changed 11975 atom styles > hide surfaces > show surfaces > hide surfaces > show atoms > hide atoms > open 7QHS Summary of feedback from opening 7QHS fetched from pdb --- notes | Fetching compressed mmCIF 7qhs from http://files.rcsb.org/download/7qhs.cif Fetching CCD ATP from http://ligand-expo.rcsb.org/reports/A/ATP/ATP.cif Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif Fetching CCD ADP from http://ligand-expo.rcsb.org/reports/A/ADP/ADP.cif 7qhs title: S. cerevisiae CMGE nucleating origin DNA melting [more info...] Chain information for 7qhs #2 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 3 | DNA replication licensing factor MCM3 | MCM3_YEAST 4 | DNA replication licensing factor MCM4 | MCM4_YEAST 5 | DNA replication licensing factor MCM5 | A0A6A5PUY8_YEASX 6 | DNA replication licensing factor MCM6 | MCM6_YEAST 7 | DNA replication licensing factor MCM7 | MCM7_YEAST A | DNA (26-MER) | B | DNA (26-MER) | C | DNA replication complex GINS protein PSF3 | PSF3_YEAST D | DNA replication complex GINS protein SLD5 | SLD5_YEAST E | Cell division control protein 45 | CDC45_YEAST F | DNA polymerase epsilon subunit B | DPB2_YEAST G | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST H | DNA replication complex GINS protein PSF1 | A0A6A5Q203_YEASX I | DNA replication complex GINS protein PSF2 | A0A6A5PX40_YEASX Non-standard residues in 7qhs #2 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide surfaces > hide atoms > hide cartoons > show cartoons > select #2/2 5263 atoms, 5352 bonds, 5 pseudobonds, 662 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/A#2/B 1066 atoms, 1194 bonds, 33 pseudobonds, 52 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/E 4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/G 6115 atoms, 6250 bonds, 11 pseudobonds, 758 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/F 4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/3 4990 atoms, 5077 bonds, 6 pseudobonds, 635 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/4 4878 atoms, 4950 bonds, 7 pseudobonds, 611 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/5 5483 atoms, 5563 bonds, 11 pseudobonds, 693 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/6 5000 atoms, 5080 bonds, 8 pseudobonds, 631 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/7 5214 atoms, 5294 bonds, 9 pseudobonds, 661 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #1/A 1247 atoms, 1216 bonds, 198 residues, 1 model selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/B 1477 atoms, 1454 bonds, 228 residues, 1 model selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/C 1548 atoms, 1524 bonds, 1 pseudobond, 246 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/D 1713 atoms, 1655 bonds, 1 pseudobond, 286 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2e9x, chain F (#1) with 7qhs, chain I (#2), sequence alignment score = 337.6 RMSD between 127 pruned atom pairs is 1.255 angstroms; (across all 159 pairs: 2.471) > select #1/E 1240 atoms, 1208 bonds, 199 residues, 1 model selected > color (#!1 & sel) #9437ffff > color (#!1 & sel) #7a81ffff > color (#!1 & sel) #0096ffff > select #2/H 1697 atoms, 1719 bonds, 208 residues, 1 model selected > color sel #73fdffff > select #1/F 1503 atoms, 1458 bonds, 250 residues, 1 model selected > color (#!1 & sel) #ff9300ff > select #2/I 1581 atoms, 1613 bonds, 1 pseudobond, 189 residues, 2 models selected > color (#!2 & sel) #ffd479ff > select #2/C 1398 atoms, 1431 bonds, 2 pseudobonds, 173 residues, 2 models selected > color (#!2 & sel) #531b93ff > select #1/G 1534 atoms, 1501 bonds, 1 pseudobond, 250 residues, 2 models selected > color (#!1 & sel) #d783ffff > select #1/G 1534 atoms, 1501 bonds, 1 pseudobond, 250 residues, 2 models selected > select #2/D 1990 atoms, 2032 bonds, 242 residues, 1 model selected > color sel #008f00ff > color sel #4f8f00ff > select #1/H 1713 atoms, 1659 bonds, 1 pseudobond, 282 residues, 2 models selected > color (#!1 & sel) #d4fb79ff > select clear > background color white Unknown command: background color white > set background color white Expected a keyword > set bgColor white > lighting soft > lighting simple > lighting full > lighting flat > lighting full > lighting shadows false > lighting flat [Repeated 1 time(s)] > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting shadows true > graphics silhouettes false > lighting full > select #1/E#2/H 2937 atoms, 2927 bonds, 407 residues, 2 models selected > save /Users/krystian/Desktop/GINS_human_yeast.cxs > select #1/F#2/I 3084 atoms, 3071 bonds, 1 pseudobond, 439 residues, 3 models selected > delete atoms (#!1-2 & sel) > delete bonds (#!1-2 & sel) > select #2/C 1398 atoms, 1431 bonds, 2 pseudobonds, 173 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/D 1990 atoms, 2032 bonds, 242 residues, 1 model selected > delete atoms sel > delete bonds sel > select #1/G 1534 atoms, 1501 bonds, 1 pseudobond, 250 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/H 1713 atoms, 1659 bonds, 1 pseudobond, 282 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2e9x, chain E (#1) with 7qhs, chain H (#2), sequence alignment score = 245.9 RMSD between 109 pruned atom pairs is 1.065 angstroms; (across all 142 pairs: 2.411) > set bgColor gray > set bgColor white > set bgColor gray > volume style surface No volumes specified > show surfaces > hide surfaces Hide dust shortcut requires a displayed map surface > volume style mesh No volumes specified > volume style mesh No volumes specified Hide dust shortcut requires a displayed map surface > select 84.e Expected an objects specifier or a keyword > select :84.e Expected an objects specifier or a keyword > select :84/E 1251 atoms, 1218 bonds, 200 residues, 2 models selected > select :84.E Expected an objects specifier or a keyword > select :84#1 1251 atoms, 1218 bonds, 200 residues, 2 models selected > select :84 19 atoms, 17 bonds, 2 residues, 2 models selected > select #1/E 1240 atoms, 1208 bonds, 199 residues, 1 model selected > select clear > save /Users/krystian/Desktop/PSF1_human_yeast.cxs ——— End of log from Tue Oct 25 15:49:36 2022 ——— opened ChimeraX session > select :84 19 atoms, 17 bonds, 2 residues, 2 models selected > select :83 20 atoms, 18 bonds, 2 residues, 2 models selected > select :84 19 atoms, 17 bonds, 2 residues, 2 models selected > select clear > select :152 6 atoms, 5 bonds, 1 residue, 1 model selected > open 2q9q Summary of feedback from opening 2q9q fetched from pdb --- note | Fetching compressed mmCIF 2q9q from http://files.rcsb.org/download/2q9q.cif 2q9q title: The crystal structure of full length human GINS complex [more info...] Chain information for 2q9q #3 --- Chain | Description | UniProt A E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN B F | GINS complex subunit 4 | Q9BRT9_HUMAN C G | DNA replication complex GINS protein PSF1 | PSF1_HUMAN D H | GINS complex subunit 3 | Q9BRX5_HUMAN 2q9q mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > show sel cartoons > hide sel surfaces > hide sel atoms [Repeated 1 time(s)] > hide sel surfaces > hide sel cartoons > show sel cartoons > select 14820 atoms, 14593 bonds, 4 pseudobonds, 2264 residues, 4 models selected > hide sel atoms > show sel cartoons > hide sel surfaces > select #3/D#3/H 3072 atoms, 3046 bonds, 2 pseudobonds, 466 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #3/B#3/F 3374 atoms, 3290 bonds, 2 pseudobonds, 538 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #1/E 1240 atoms, 1208 bonds, 199 residues, 1 model selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #3/A#3/E 2969 atoms, 2908 bonds, 471 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/G 1233 atoms, 1211 bonds, 190 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/C 1235 atoms, 1211 bonds, 192 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #0096ffff > matchmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 2q9q, chain C (#3) with 7qhs, chain H (#2), sequence alignment score = 286.7 RMSD between 106 pruned atom pairs is 1.064 angstroms; (across all 142 pairs: 4.078) > select :152 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/C 1235 atoms, 1211 bonds, 192 residues, 1 model selected > delete atoms sel > delete bonds sel > open 7PFO Summary of feedback from opening 7PFO fetched from pdb --- notes | Fetching compressed mmCIF 7pfo from http://files.rcsb.org/download/7pfo.cif Fetching CCD ANP from http://ligand-expo.rcsb.org/reports/A/ANP/ANP.cif 7pfo title: Core human replisome [more info...] Chain information for 7pfo #1 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN C | Cell division control protein 45 homolog,Cell division control protein 45 homolog | CDC45_HUMAN D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN K | Protein timeless homolog | TIM_HUMAN L | TIMELESS-interacting protein | TIPIN_HUMAN M | Leading strand DNA | N | Lagging Strand DNA | Q | Claspin | CLSPN_HUMAN Non-standard residues in 7pfo #1 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion SO4 — sulfate ion ZN — zinc ion > select 69751 atoms, 71186 bonds, 120 pseudobonds, 8642 residues, 5 models selected > show sel surfaces > hide sel surfaces > hide sel atoms > show sel cartoons > select #1/C 4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/Q 683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/B 6062 atoms, 6180 bonds, 17 pseudobonds, 760 residues, 3 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/A 4204 atoms, 4314 bonds, 528 residues, 1 model selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > select ~sel 51152 atoms, 52203 bonds, 100 pseudobonds, 6338 residues, 4 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #2/H 1697 atoms, 1719 bonds, 208 residues, 1 model selected > color (#!2 & sel) #011993ff > color (#!2 & sel) #0096ffff > color (#!2 & sel) #73fdffff > select #1/D 1606 atoms, 1638 bonds, 195 residues, 1 model selected > color (#!1 & sel) #0096ffff > matchmaker #1 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7qhs, chain H (#2) with 7pfo, chain D (#1), sequence alignment score = 334.1 RMSD between 107 pruned atom pairs is 0.909 angstroms; (across all 190 pairs: 3.777) > select :152 12 atoms, 10 bonds, 2 residues, 2 models selected > select #2/H:166 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:168 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/D:153 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/D:151 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/H:166 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > label (#!1 & sel) attribute name > label (#!1 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > label (#!2 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > select clear > select #1/D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > color (#!1 & sel) forest green > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!2 & sel) lime > select clear > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color (#!2 & sel) #73fa79ff > select :83 20 atoms, 18 bonds, 2 residues, 2 models selected > select #1/D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #2/H:93 22 atoms, 20 bonds, 2 residues, 3 models selected > label (#!1-2 & sel) text ""{0.name} {0.number}{0.insertion_code}"" > select clear > select #1/D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) #9437ffff > select #2/H:93 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!2 & sel) #d783ffff > color (#!2 & sel) #ff8ad8ff > select clear > select #2/H:93 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!2 & sel) #d783ffff > color (#!2 & sel) #afafafff [Repeated 1 time(s)] > color (#!2 & sel) #b1b1b1ff > color (#!2 & sel) #b5b5b5ff > color (#!2 & sel) #bcbcbcff > color (#!2 & sel) #bfbfbfff > color (#!2 & sel) #c3c3c3ff > color (#!2 & sel) #c6c6c6ff > color (#!2 & sel) #c5c5c5ff [Repeated 1 time(s)] > color (#!2 & sel) #c4c4c4ff > color (#!2 & sel) #c3c3c3ff > color (#!2 & sel) #c2c2c2ff > color (#!2 & sel) #c0c0c0ff > color (#!2 & sel) #bfbfbfff > color (#!2 & sel) #bababaff > color (#!2 & sel) #b9b9b9ff > color (#!2 & sel) #b5b5b5ff > color (#!2 & sel) #b3b3b3ff [Repeated 1 time(s)] > color (#!2 & sel) #b2b2b2ff > color (#!2 & sel) #b0b0b0ff > color (#!2 & sel) #adadadff > color (#!2 & sel) #abababff > color (#!2 & sel) #aaaaaaff > color (#!2 & sel) #a7a7a7ff [Repeated 1 time(s)] > color (#!2 & sel) #d783ffff > color (#!2 & sel) #e2b5f8ff [Repeated 1 time(s)] > color (#!2 & sel) #e1b5f8ff [Repeated 1 time(s)] > color (#!2 & sel) #e0b5f8ff > select #1/D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!1 & sel) #dd91f8ff > color (#!1 & sel) #dc91f8ff > color (#!1 & sel) #db91f8ff > color (#!1 & sel) #d791f8ff > color (#!1 & sel) #d192f8ff > color (#!1 & sel) #d092f8ff > color (#!1 & sel) #cf92f8ff > color (#!1 & sel) #d093f8ff > color (#!1 & sel) #d195f8ff [Repeated 1 time(s)] > color (#!1 & sel) #d196f8ff > color (#!1 & sel) #d298f8ff > color (#!1 & sel) #d399f8ff > color (#!1 & sel) #d59df8ff > color (#!1 & sel) #d9a0f8ff > color (#!1 & sel) #dd9df8ff > color (#!1 & sel) #d88cf8ff > color (#!1 & sel) #d683f8ff > color (#!1 & sel) #d47ff8ff > color (#!1 & sel) #d27af8ff > color (#!1 & sel) #cf75f8ff > color (#!1 & sel) #ce6df8ff > color (#!1 & sel) #cc64f8ff > color (#!1 & sel) #cc5ff8ff > color (#!1 & sel) #cb5bf8ff > color (#!1 & sel) #cb57f8ff > color (#!1 & sel) #cb54f8ff > color (#!1 & sel) #ca4ff8ff > color (#!1 & sel) #c94af8ff > color (#!1 & sel) #c848f8ff > color (#!1 & sel) #c847f8ff > color (#!1 & sel) #c747f8ff [Repeated 1 time(s)] > color (#!1 & sel) #dd58f8ff > color (#!1 & sel) #dc59f8ff > color (#!1 & sel) #d95af8ff > color (#!1 & sel) #d35cf8ff > color (#!1 & sel) #d25cf8ff > color (#!1 & sel) #d15cf8ff > color (#!1 & sel) #ce5df8ff > color (#!1 & sel) #c55ef8ff > color (#!1 & sel) #ba5ff8ff > color (#!1 & sel) #b85ff8ff > color (#!1 & sel) #b55df8ff > color (#!1 & sel) #b35df8ff > color (#!1 & sel) #b05cf8ff > color (#!1 & sel) #ad5cf8ff > color (#!1 & sel) #ac5bf8ff > color (#!1 & sel) #a858f8ff > color (#!1 & sel) #a455f8ff > color (#!1 & sel) #a052f8ff > color (#!1 & sel) #9e50f8ff > color (#!1 & sel) #9d4ff8ff > color (#!1 & sel) #9d4ef8ff > color (#!1 & sel) #9c4df8ff > color (#!1 & sel) #9b4cf8ff > color (#!1 & sel) #9a4bf8ff [Repeated 1 time(s)] > color (#!1 & sel) #994af8ff > color (#!1 & sel) #9949f8ff > color (#!1 & sel) #994af8ff > color (#!1 & sel) #9a4bf8ff > color (#!1 & sel) #a551f8ff > color (#!1 & sel) #a953f8ff [Repeated 1 time(s)] > color (#!1 & sel) #aa53f8ff [Repeated 1 time(s)] > color (#!1 & sel) #aa54f8ff > color (#!1 & sel) #a954f8ff [Repeated 1 time(s)] > select clear > select :84 19 atoms, 17 bonds, 2 residues, 2 models selected > ui tool show ""Side View"" > set bgColor white > select clear Drag select of 5 residues > select clear > select #1/D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > ui mousemode right ""move planes"" [Repeated 1 time(s)] > ui tool show ""Blast Protein"" [Repeated 1 time(s)] > blastprotein #2/H database pdb cutoff 1e-3 matrix BLOSUM62 maxSeqs 100 name > bp1 Webservices job id: 9Z39200QRDDK53EE Alignment identifier is bp1 [1] Associated 7qhs chain H to #2/H with 0 mismatches Associated 7pfo chain D to 7PFO_D with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment bp1 [1] > set bgColor gray > set bgColor white > save /Users/krystian/Desktop/image1.png supersample 3 > save /Users/krystian/Desktop/image2.png supersample 3 > save /Users/krystian/Desktop/image3.png supersample 3 > save /Users/krystian/Desktop/image4.png supersample 3 > save /Users/krystian/Desktop/PSF1_human_yeast_2.cxs > close session > open 7PFO 7pfo title: Core human replisome [more info...] Chain information for 7pfo #1 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN C | Cell division control protein 45 homolog,Cell division control protein 45 homolog | CDC45_HUMAN D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN K | Protein timeless homolog | TIM_HUMAN L | TIMELESS-interacting protein | TIPIN_HUMAN M | Leading strand DNA | N | Lagging Strand DNA | Q | Claspin | CLSPN_HUMAN Non-standard residues in 7pfo #1 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion SO4 — sulfate ion ZN — zinc ion > hide surfaces > show cartoons > hide atoms > set bgColor white > select /Q 683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /N 438 atoms, 488 bonds, 22 residues, 1 model selected > delete atoms sel > delete bonds sel > select /M 662 atoms, 738 bonds, 1 pseudobond, 32 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /K 5215 atoms, 5317 bonds, 2 pseudobonds, 636 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > delete atoms > delete bonds > open 7PFO 7pfo title: Core human replisome [more info...] Chain information for 7pfo #1 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN C | Cell division control protein 45 homolog,Cell division control protein 45 homolog | CDC45_HUMAN D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN K | Protein timeless homolog | TIM_HUMAN L | TIMELESS-interacting protein | TIPIN_HUMAN M | Leading strand DNA | N | Lagging Strand DNA | Q | Claspin | CLSPN_HUMAN Non-standard residues in 7pfo #1 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion SO4 — sulfate ion ZN — zinc ion > open 7PFO 7pfo title: Core human replisome [more info...] Chain information for 7pfo #2 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN C | Cell division control protein 45 homolog,Cell division control protein 45 homolog | CDC45_HUMAN D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN K | Protein timeless homolog | TIM_HUMAN L | TIMELESS-interacting protein | TIPIN_HUMAN M | Leading strand DNA | N | Lagging Strand DNA | Q | Claspin | CLSPN_HUMAN Non-standard residues in 7pfo #2 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion SO4 — sulfate ion ZN — zinc ion > hide atoms > show cartoons > close session > open 7PFO 7pfo title: Core human replisome [more info...] Chain information for 7pfo #1 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_HUMAN 3 | DNA replication licensing factor MCM3 | MCM3_HUMAN 4 | DNA replication licensing factor MCM4 | MCM4_HUMAN 5 | DNA replication licensing factor MCM5 | MCM5_HUMAN 6 | DNA replication licensing factor MCM6 | MCM6_HUMAN 7 | DNA replication licensing factor MCM7 | MCM7_HUMAN A | DNA polymerase epsilon subunit 2 | DPOE2_HUMAN B | DNA polymerase epsilon catalytic subunit A | DPOE1_HUMAN C | Cell division control protein 45 homolog,Cell division control protein 45 homolog | CDC45_HUMAN D | DNA replication complex GINS protein PSF1 | PSF1_HUMAN E | DNA replication complex GINS protein PSF2 | PSF2_HUMAN F | DNA replication complex GINS protein PSF3 | PSF3_HUMAN G | DNA replication complex GINS protein SLD5 | SLD5_HUMAN H I J | WD repeat and HMG-box DNA-binding protein 1 | WDHD1_HUMAN K | Protein timeless homolog | TIM_HUMAN L | TIMELESS-interacting protein | TIPIN_HUMAN M | Leading strand DNA | N | Lagging Strand DNA | Q | Claspin | CLSPN_HUMAN Non-standard residues in 7pfo #1 --- ANP — phosphoaminophosphonic acid-adenylate ester MG — magnesium ion SO4 — sulfate ion ZN — zinc ion > select /N 438 atoms, 488 bonds, 22 residues, 1 model selected > delete atoms sel > delete bonds sel > hide atoms > show cartoons > set bgColor white > select /C 4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected > select /Q 683 atoms, 693 bonds, 2 pseudobonds, 79 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /M 662 atoms, 738 bonds, 1 pseudobond, 32 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /H/I/J 9507 atoms, 9732 bonds, 1203 residues, 1 model selected > delete atoms sel > delete bonds sel > select /K 5215 atoms, 5317 bonds, 2 pseudobonds, 636 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select /L 735 atoms, 750 bonds, 87 residues, 1 model selected > delete atoms sel > delete bonds sel > select /D 1606 atoms, 1638 bonds, 195 residues, 1 model selected > select :83.D Expected an objects specifier or a keyword > select :83/D 1686 atoms, 1711 bonds, 204 residues, 1 model selected > select clear > select :83/D 1686 atoms, 1711 bonds, 204 residues, 1 model selected > select :83 91 atoms, 83 bonds, 10 residues, 1 model selected > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 11 atom styles > select /D:22 7 atoms, 7 bonds, 1 residue, 1 model selected > select /D:23 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /D:22 12 atoms, 11 bonds, 2 residues, 1 model selected > select add /D:24 23 atoms, 22 bonds, 3 residues, 1 model selected > style sel stick Changed 23 atom styles > show sel atoms > select /D:107 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /D:106 13 atoms, 11 bonds, 2 residues, 1 model selected > show sel atoms > show sel cartoons > style sel stick Changed 13 atom styles > style sel ball Changed 13 atom styles > style sel stick Changed 13 atom styles > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel red > color sel orange > select clear > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > select add /D:106 8 atoms, 8 bonds, 1 residue, 1 model selected > select add /D:23 13 atoms, 12 bonds, 2 residues, 1 model selected > select add /D:24 24 atoms, 23 bonds, 3 residues, 1 model selected > select add /D:22 31 atoms, 30 bonds, 4 residues, 1 model selected > color sel byhetero > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > color sel byhetero > select /5:394 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show ""Change Chain IDs"" > ui tool show ""Build Structure"" > select /D:22 7 atoms, 7 bonds, 1 residue, 1 model selected > select add /D:24 18 atoms, 18 bonds, 2 residues, 1 model selected > select add /D:83 29 atoms, 28 bonds, 3 residues, 1 model selected > select add /D:107 34 atoms, 32 bonds, 4 residues, 1 model selected > select add /D:106 42 atoms, 39 bonds, 5 residues, 1 model selected > select ~sel 50772 atoms, 51701 bonds, 65 pseudobonds, 6370 residues, 3 models selected > show sel surfaces > hide sel surfaces > select clear > select /D:83 11 atoms, 10 bonds, 1 residue, 1 model selected > select /D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 6 atom styles > color (#!1 & sel) byhetero > color (#!1 & sel) lime > color (#!1 & sel) byhetero > ui tool show Matchmaker > ui mousemode right ""pick blobs"" [Repeated 1 time(s)] > select clear > open 7z13 Summary of feedback from opening 7z13 fetched from pdb --- note | Fetching compressed mmCIF 7z13 from http://files.rcsb.org/download/7z13.cif 7z13 title: S. cerevisiae CMGE dimer nucleating origin DNA melting [more info...] Chain information for 7z13 #2 --- Chain | Description | UniProt 2 a | DNA replication licensing factor MCM2 | A0A6A5Q1S9_YEASX 3 b | DNA replication licensing factor MCM3 | MCM3_YEAST 4 c | DNA replication licensing factor MCM4 | MCM4_YEAST 5 d | DNA helicase | A0A6A5PUY8_YEASX 6 e | DNA replication licensing factor MCM6 | MCM6_YEAST 7 f | DNA replication licensing factor MCM7 | A0A6A5Q4N0_YEASX A | DNA (53-MER) | B | DNA (53-MER) | C J | DNA replication complex GINS protein PSF3 | PSF3_YEAST D K | DNA replication complex GINS protein SLD5 | SLD5_YEAST E L | Cell division control protein 45 | CDC45_YEAST F M | DNA polymerase epsilon subunit B | DPB2_YEAST H O | DNA replication complex GINS protein PSF1 | A0A6A5Q203_YEASX I P | DNA replication complex GINS protein PSF2 | A0A6A5PX40_YEASX N Q | DNA polymerase epsilon catalytic subunit A | DPOE_YEAST Non-standard residues in 7z13 #2 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > select #2/L 4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/A#2/B 2173 atoms, 2436 bonds, 71 pseudobonds, 106 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #1/2 5613 atoms, 5717 bonds, 9 pseudobonds, 706 residues, 3 models selected > select #2/2 5263 atoms, 5352 bonds, 5 pseudobonds, 662 residues, 3 models selected > select #2/a 5263 atoms, 5352 bonds, 5 pseudobonds, 662 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/b 4990 atoms, 5077 bonds, 6 pseudobonds, 635 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/c 4878 atoms, 4950 bonds, 7 pseudobonds, 611 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/e 5000 atoms, 5080 bonds, 8 pseudobonds, 631 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/f 5214 atoms, 5294 bonds, 9 pseudobonds, 661 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/O 1697 atoms, 1719 bonds, 208 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/P 1581 atoms, 1613 bonds, 1 pseudobond, 189 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/J 1398 atoms, 1431 bonds, 2 pseudobonds, 173 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/K 1990 atoms, 2032 bonds, 242 residues, 1 model selected > delete atoms sel > delete bonds sel > select #2/M 4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/Q 6115 atoms, 6250 bonds, 11 pseudobonds, 758 residues, 3 models selected > select #2/N 6115 atoms, 6250 bonds, 11 pseudobonds, 758 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/d 5483 atoms, 5563 bonds, 11 pseudobonds, 693 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > hide atoms > show cartoons > ui tool show Matchmaker Traceback (most recent call last): File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/options/options.py"", line 50, in data[0] == pself.attr_name and (setattr(pself, ""value"", pself.get_attribute()) File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/options/options.py"", line 342, in set_value self.__button_group.button(self.values.index(value)).setChecked(True) AttributeError: 'NoneType' object has no attribute 'setChecked' Error processing trigger ""setting changed"": AttributeError: 'NoneType' object has no attribute 'setChecked' File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/options/options.py"", line 342, in set_value self.__button_group.button(self.values.index(value)).setChecked(True) See log for complete Python traceback. > matchmaker #!2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7pfo, chain B (#1) with 7z13, chain Q (#2), sequence alignment score = 3162.8 RMSD between 142 pruned atom pairs is 1.199 angstroms; (across all 612 pairs: 22.863) > select #1/2#2/2 10876 atoms, 11069 bonds, 14 pseudobonds, 1368 residues, 6 models selected > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > select #2/E 4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected > ui tool show Matchmaker Traceback (most recent call last): File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/triggerset.py"", line 134, in invoke return self._func(self._name, data) File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/options/options.py"", line 50, in data[0] == pself.attr_name and (setattr(pself, ""value"", pself.get_attribute()) File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/options/options.py"", line 342, in set_value self.__button_group.button(self.values.index(value)).setChecked(True) AttributeError: 'NoneType' object has no attribute 'setChecked' Error processing trigger ""setting changed"": AttributeError: 'NoneType' object has no attribute 'setChecked' File ""/Applications/ChimeraX-1.5-rc2022.10.24.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/options/options.py"", line 342, in set_value self.__button_group.button(self.values.index(value)).setChecked(True) See log for complete Python traceback. > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > select ~sel 100115 atoms, 101930 bonds, 131 pseudobonds, 12552 residues, 20 models selected > hide (#!1-2 & sel) target a > cartoon hide (#!1-2 & sel) > select /D:84 16 atoms, 14 bonds, 2 residues, 2 models selected > select /H:84 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/F#2/C 2944 atoms, 3011 bonds, 3 pseudobonds, 367 residues, 4 models selected > show sel cartoons > select /H:84 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select /H:164 8 atoms, 7 bonds, 1 residue, 1 model selected > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > ui dockable false ""Side View"" > ui dockable true ""Side View"" > show sel surfaces > hide sel surfaces > style sel sphere Changed 34 atom styles > show sel atoms > style sel ball Changed 34 atom styles > style sel stick Changed 34 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel ladder > nucleotides sel tube/slab shape box > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel sphere Changed 34 atom styles > style sel stick Changed 34 atom styles > hide sel atoms > select #2/F 4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected > select #2/F 4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected > show sel cartoons > hide sel cartoons > select #2/E 4599 atoms, 4685 bonds, 3 pseudobonds, 566 residues, 2 models selected > show sel cartoons > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > select #1/C 4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected > show sel cartoons > select #2/F 4396 atoms, 4492 bonds, 3 pseudobonds, 551 residues, 2 models selected > show sel cartoons > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > show sel atoms > select #1/D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/H:166 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 7 atom styles > select clear > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > select #1/D:152 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #1/D:153 14 atoms, 12 bonds, 2 residues, 2 models selected > select add #1/D:154 23 atoms, 20 bonds, 3 residues, 2 models selected > select add #1/D:171 32 atoms, 28 bonds, 4 residues, 2 models selected > style sel stick Changed 32 atom styles > show sel atoms > select add #1/D:155 40 atoms, 35 bonds, 5 residues, 2 models selected > select subtract #1/D:155 32 atoms, 28 bonds, 4 residues, 2 models selected > select add #1/D:156 44 atoms, 40 bonds, 5 residues, 2 models selected > select add #1/D:155 52 atoms, 47 bonds, 6 residues, 2 models selected > show sel atoms > style sel stick Changed 52 atom styles > style sel sphere Changed 52 atom styles > style sel stick Changed 52 atom styles > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues [Repeated 1 time(s)]Coulombic values for 7pfo_D SES surface #1.13: minimum, -16.05, mean -0.36, maximum 13.70 Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09, maximum 13.14 To also show corresponding color key, enter the above coulombic command and add key true > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > select /H:152 6 atoms, 5 bonds, 1 residue, 1 model selected > select /H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > mlp sel Map values for surface ""7z13_H SES surface"": minimum -29.07, mean -3.46, maximum 24.75 To also show corresponding color key, enter the above mlp command and add key true > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > mlp sel Map values for surface ""7pfo_D SES surface"": minimum -25.17, mean -3.532, maximum 22.99 Map values for surface ""7z13_H SES surface"": minimum -29.07, mean -3.46, maximum 24.75 To also show corresponding color key, enter the above mlp command and add key true > select /H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel cartoons > surface style #!2.4 mesh > surface style #2 dot > surface style #2 mesh > transparency (#!2 & sel) 50 > hide sel surfaces > show sel surfaces > surface hidePatches (#!2 & sel) > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > surface style #2#!1.13 mesh > surface style #2#1.13 dot > surface style #2#1.13 mesh > transparency (#!1-2 & sel) 50 > show sel cartoons > select /H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > select #1/D#2/H 3303 atoms, 3357 bonds, 403 residues, 2 models selected > surface style #2#1.13 solid > transparency (#!1-2 & sel) 30 > transparency (#!1-2 & sel) 70 > transparency (#!1-2 & sel) 60 > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > select #1/E#2/I 3012 atoms, 3075 bonds, 1 pseudobond, 365 residues, 3 models selected > show sel cartoons > select /H:161-164 34 atoms, 34 bonds, 4 residues, 1 model selected > select /H:164 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/D 1606 atoms, 1638 bonds, 195 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms [Repeated 1 time(s)] > select #1/E 1431 atoms, 1462 bonds, 176 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > hide sel surfaces > select #1/C 4347 atoms, 4439 bonds, 1 pseudobond, 534 residues, 2 models selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select #1/A 4204 atoms, 4314 bonds, 528 residues, 1 model selected > hide sel surfaces > hide sel cartoons > hide sel atoms > select /H:164 8 atoms, 7 bonds, 1 residue, 1 model selected > coulombic sel Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09, maximum 13.14 To also show corresponding color key, enter the above coulombic command and add key true > select /H:207 9 atoms, 8 bonds, 1 residue, 1 model selected > coulombic sel Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09, maximum 13.14 To also show corresponding color key, enter the above coulombic command and add key true > select /H:207,164 17 atoms, 15 bonds, 2 residues, 1 model selected > select /H:207,164,/E:50 Expected an objects specifier or a keyword > select /H:207,164 17 atoms, 15 bonds, 2 residues, 1 model selected > /E:50 Unknown command: /E:50 > select /H:207,164,/E:50 Expected an objects specifier or a keyword > select /E:50 17 atoms, 15 bonds, 2 residues, 2 models selected > select /H:207,164, Expected an objects specifier or a keyword > select /H:207,164 17 atoms, 15 bonds, 2 residues, 1 model selected > select #2/E:50 9 atoms, 8 bonds, 1 residue, 1 model selected > select /H:207,164 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #2/E:50 26 atoms, 23 bonds, 3 residues, 2 models selected > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for 7z13_E SES surface #2.5: minimum, -21.23, mean -2.59, maximum 15.49 Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09, maximum 13.14 To also show corresponding color key, enter the above coulombic command and add key true > transparency (#!2 & sel) 50 > show sel atoms > style sel stick Changed 26 atom styles > style sel sphere Changed 26 atom styles > style sel ball Changed 26 atom styles > style sel stick Changed 26 atom styles > style sel ball Changed 26 atom styles > select /F 5942 atoms, 6072 bonds, 4 pseudobonds, 745 residues, 4 models selected > hide (#!1-2 & sel) target a > hide sel cartoons > show sel cartoons > select #1/A 4204 atoms, 4314 bonds, 528 residues, 1 model selected > select #1/F 1546 atoms, 1580 bonds, 1 pseudobond, 194 residues, 2 models selected > hide sel cartoons > select #2/F:19 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/H:176 14 atoms, 13 bonds, 2 residues, 1 model selected > ui tool show Distances > show sel atoms > style sel stick Changed 14 atom styles > select #2/H:176 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:176 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:176 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/F:34 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/H:174 17 atoms, 15 bonds, 2 residues, 1 model selected > style sel stick Changed 17 atom styles > style sel stick Changed 17 atom styles > show sel atoms > select clear > select #2/H:176 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/H:175 16 atoms, 14 bonds, 2 residues, 2 models selected > select add #2/H:174 24 atoms, 21 bonds, 3 residues, 2 models selected > select add #2/H:173 33 atoms, 29 bonds, 4 residues, 2 models selected > show sel atoms > style sel stick Changed 33 atom styles > select #2/F:35 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #2/F:31 14 atoms, 12 bonds, 2 residues, 1 model selected > select add #2/F:26 20 atoms, 17 bonds, 3 residues, 1 model selected > style sel stick Changed 20 atom styles > show sel atoms > select #2/H:173@CA 1 atom, 1 residue, 1 model selected > select #2/H:174 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #2/H:173 17 atoms, 15 bonds, 2 residues, 2 models selected > select add #2/H:175 26 atoms, 23 bonds, 3 residues, 2 models selected > select add #2/F:35 32 atoms, 28 bonds, 4 residues, 2 models selected > select add #2/F:34 41 atoms, 36 bonds, 5 residues, 2 models selected > select add #2/F:33 49 atoms, 43 bonds, 6 residues, 2 models selected > select add #2/F:32 55 atoms, 48 bonds, 7 residues, 2 models selected > select add #2/F:31 63 atoms, 55 bonds, 8 residues, 2 models selected > show sel surfaces > hide sel surfaces > hbonds sel reveal true 10 hydrogen bonds found > select /H:207,164 17 atoms, 15 bonds, 2 residues, 1 model selected > select #2/E:50@CE 1 atom, 1 residue, 1 model selected > select /H:207,164 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #2/E:50@CE 18 atoms, 15 bonds, 3 residues, 2 models selected > hbonds sel reveal true 1 hydrogen bonds found > hide sel surfaces [Repeated 2 time(s)] > hide sel cartoons > show sel cartoons > select add #2/E:50@CG 19 atoms, 15 bonds, 3 residues, 3 models selected > hide sel surfaces > select subtract #2/E:50 17 atoms, 15 bonds, 2 residues, 3 models selected > select add #2/E:50 26 atoms, 23 bonds, 3 residues, 2 models selected > hide sel surfaces > hbonds sel reveal true 3 hydrogen bonds found > select /H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > hbonds sel reveal true 1 hydrogen bonds found > mlp sel Map values for surface ""7z13_H SES surface"": minimum -29.07, mean -3.46, maximum 24.75 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for 7z13_H SES surface #2.4: minimum, -18.77, mean -2.09, maximum 13.14 To also show corresponding color key, enter the above coulombic command and add key true > ui tool show ""Show Sequence Viewer"" > sequence chain #2/H Alignment identifier is 2/H > select #2/H:162-167,173-176,179-182,188-192,205-206 181 atoms, 180 bonds, 21 residues, 1 model selected > select #2/H:165 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:165-171 55 atoms, 54 bonds, 7 residues, 1 model selected > select #2/H:172 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/H:172-173 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/H:108-109 16 atoms, 15 bonds, 2 residues, 1 model selected > select #2/H:108-111 30 atoms, 29 bonds, 4 residues, 1 model selected > select #2/H:160 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/H:160-161 15 atoms, 14 bonds, 2 residues, 1 model selected > select #2/H:155 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/H:155 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/H:161 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:161 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel @< 5 1740 atoms, 69 bonds, 220 residues, 2 models selected > select #2/H:162 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/H:162 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/H:161 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:161 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel @< 5 1740 atoms, 69 bonds, 220 residues, 2 models selected > select #2/H:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel @< 3 1710 atoms, 26 bonds, 211 residues, 2 models selected > select sel @< 3 3614 atoms, 3371 bonds, 1 pseudobond, 496 residues, 3 models selected > select sel @< 3 30572 atoms, 4185 bonds, 1 pseudobond, 3830 residues, 3 models selected > select sel @< 3 39108 atoms, 39333 bonds, 17 pseudobonds, 5175 residues, 7 models selected > select sel @< 3 61563 atoms, 42144 bonds, 19 pseudobonds, 7843 residues, 7 models selected > select #2/H:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:156-157 14 atoms, 14 bonds, 2 residues, 1 model selected > select #2/H:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #2/H:156-157 14 atoms, 14 bonds, 2 residues, 1 model selected > select #2/H:156 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel @< 3 1715 atoms, 27 bonds, 213 residues, 2 models selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel @< 5 1752 atoms, 95 bonds, 1 pseudobond, 221 residues, 3 models selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel :< 5 1804 atoms, 224 bonds, 1 pseudobond, 221 residues, 3 models selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select sel :< 0 1697 atoms, 6 bonds, 208 residues, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/H:167 7 atoms, 6 bonds, 1 residue, 1 model selected OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: MGN63ZE/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0 (22A380) Kernel Version: Darwin 22.1.0 Time since boot: 1 day, 21 hours, 43 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.0.8 Babel: 2.10.3 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.4 ChimeraX-AtomicLibrary: 8.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5rc202210241843 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 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: 2.7.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.2 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.3 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.1.1 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 5.0.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 4.11.2 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.3 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 prompt-toolkit: 3.0.31 psutil: 5.9.1 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2022.5 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.2.1 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.5.1 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.12 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.10.0 }}} " defect feedback normal Core chimera-programmers all ChimeraX