id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10418 Crash destroying MatchMaker tool chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-64bit ChimeraX Version: 1.5 (2022-11-24 00:03:27 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. > open ""/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"" Log from Mon Jan 1 16:54:24 2024UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"" Log from Mon Jan 1 11:44:25 2024UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"" Log from Mon Jan 1 11:35:17 2024UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6msj 6msj title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome [more info...] Chain information for 6msj #1 --- Chain | Description | UniProt A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN B | Rpt2, NP_002793.2 (26SHA chain B) | PRS4_HUMAN C | 26S proteasome regulatory subunit 8 | PRS8_HUMAN D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN E | 26S proteasome regulatory subunit 10B | A0A087X2I1_HUMAN F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN G | Proteasome subunit alpha type-6 | PSA6_HUMAN H h | Proteasome subunit alpha type-2 | PSA2_HUMAN I i | Proteasome subunit alpha type-4 | PSA4_HUMAN J j | Proteasome subunit alpha type-7 | PSA7_HUMAN K k | Proteasome subunit alpha type-5 | PSA5_HUMAN L l | Proteasome subunit alpha type-1 | PSA1_HUMAN M m | Proteasome subunit alpha type-3 | PSA3_HUMAN N n | Proteasome subunit beta type-6 | PSB6_HUMAN O o | Proteasome subunit beta type-7 | PSB7_HUMAN P p | Proteasome subunit beta type-3 | PSB3_HUMAN Q q | Proteasome subunit beta type-2 | PSB2_HUMAN R r | Proteasome subunit beta type-5 | PSB5_HUMAN S s | Proteasome subunit beta type-1 | PSB1_HUMAN T t | Proteasome subunit beta type-4 | PSB4_HUMAN U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN g | Proteasome subunit alpha type-6 | PSA6_HUMAN v | substrate | Non-standard residues in 6msj #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion ZN — zinc ion > hide atoms > show cartoons > set bgColor white > lighting soft > 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 > split #1 Split 6msj (#1) into 47 models Chain information for 6msj A #1.1 --- Chain | Description A | No description available Chain information for 6msj B #1.2 --- Chain | Description B | No description available Chain information for 6msj C #1.3 --- Chain | Description C | No description available Chain information for 6msj D #1.4 --- Chain | Description D | No description available Chain information for 6msj E #1.5 --- Chain | Description E | No description available Chain information for 6msj F #1.6 --- Chain | Description F | No description available Chain information for 6msj G #1.7 --- Chain | Description G | No description available Chain information for 6msj H #1.8 --- Chain | Description H | No description available Chain information for 6msj I #1.9 --- Chain | Description I | No description available Chain information for 6msj J #1.10 --- Chain | Description J | No description available Chain information for 6msj K #1.11 --- Chain | Description K | No description available Chain information for 6msj L #1.12 --- Chain | Description L | No description available Chain information for 6msj M #1.13 --- Chain | Description M | No description available Chain information for 6msj N #1.14 --- Chain | Description N | No description available Chain information for 6msj O #1.15 --- Chain | Description O | No description available Chain information for 6msj P #1.16 --- Chain | Description P | No description available Chain information for 6msj Q #1.17 --- Chain | Description Q | No description available Chain information for 6msj R #1.18 --- Chain | Description R | No description available Chain information for 6msj S #1.19 --- Chain | Description S | No description available Chain information for 6msj T #1.20 --- Chain | Description T | No description available Chain information for 6msj U #1.21 --- Chain | Description U | No description available Chain information for 6msj V #1.22 --- Chain | Description V | No description available Chain information for 6msj W #1.23 --- Chain | Description W | No description available Chain information for 6msj X #1.24 --- Chain | Description X | No description available Chain information for 6msj Y #1.25 --- Chain | Description Y | No description available Chain information for 6msj Z #1.26 --- Chain | Description Z | No description available Chain information for 6msj a #1.27 --- Chain | Description a | No description available Chain information for 6msj b #1.28 --- Chain | Description b | No description available Chain information for 6msj c #1.29 --- Chain | Description c | No description available Chain information for 6msj d #1.30 --- Chain | Description d | No description available Chain information for 6msj e #1.31 --- Chain | Description e | No description available Chain information for 6msj f #1.32 --- Chain | Description f | No description available Chain information for 6msj g #1.33 --- Chain | Description g | No description available Chain information for 6msj h #1.34 --- Chain | Description h | No description available Chain information for 6msj i #1.35 --- Chain | Description i | No description available Chain information for 6msj j #1.36 --- Chain | Description j | No description available Chain information for 6msj k #1.37 --- Chain | Description k | No description available Chain information for 6msj l #1.38 --- Chain | Description l | No description available Chain information for 6msj m #1.39 --- Chain | Description m | No description available Chain information for 6msj n #1.40 --- Chain | Description n | No description available Chain information for 6msj o #1.41 --- Chain | Description o | No description available Chain information for 6msj p #1.42 --- Chain | Description p | No description available Chain information for 6msj q #1.43 --- Chain | Description q | No description available Chain information for 6msj r #1.44 --- Chain | Description r | No description available Chain information for 6msj s #1.45 --- Chain | Description s | No description available Chain information for 6msj t #1.46 --- Chain | Description t | No description available Chain information for 6msj v #1.47 --- Chain | Description v | No description available > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > hide #!1.4 models > hide #1.5 models > hide #!1.6 models > hide #1.7 models > hide #1.8 models > hide #1.9 models > show #1.8 models > show #1.9 models > show #1.7 models > hide #1.32 models > hide #1.33 models > show #1.33 models > hide #1.23 models > hide #1.24 models > hide #1.25 models > ui mousemode right ""translate selected models"" Drag select of 2193 residues > hide #!1.21 models > hide #1.22 models > hide #1.26 models > hide #1.27 models > hide #1.28 models > hide #!1.29 models > hide #1.30 models > hide #!1.31 models > select add #1.15 19040 atoms, 1670 bonds, 2413 residues, 10 models selected > select subtract #1.15 17397 atoms, 2193 residues, 9 models selected > select add #1 105316 atoms, 107125 bonds, 18 pseudobonds, 13534 residues, 58 models selected > select subtract #1 Nothing selected > show #!1.1 models > show #!1.2 models > hide #1.47 models > show #1.47 models > hide #1.47 models > show #1.47 models > hide #1.47 models > hide #!1.1 models > hide #!1.2 models > show #1.47 models > hide #1.47 models > show #1.47 models > hide #1.47 models > show #!1.1 models > select add #1.1 3261 atoms, 3317 bonds, 3 pseudobonds, 415 residues, 2 models selected Alignment identifier is 1.1/A > select #1.1/A:431 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1.1/A:431-433 27 atoms, 27 bonds, 3 residues, 1 model selected > select add #1.1 3261 atoms, 3317 bonds, 3 pseudobonds, 415 residues, 2 models selected > select subtract #1.1 Nothing selected > hide #!1.1 models > show #!1.2 models Destroying pre-existing alignment with identifier 1.1/A Alignment identifier is 1.1/A Alignment identifier is 1.2/B Alignment identifier is 1.3/C Alignment identifier is 1.4/D Alignment identifier is 1.5/E Alignment identifier is 1.6/F Alignment identifier is 1.7/G Alignment identifier is 1.8/H Alignment identifier is 1.9/I Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 6 Alignment identifier is 7 Alignment identifier is 8 Alignment identifier is 9 Alignment identifier is 10 Alignment identifier is 11 Alignment identifier is 1.21/U Alignment identifier is 1.22/V Alignment identifier is 1.23/W Alignment identifier is 1.24/X Alignment identifier is 1.25/Y Alignment identifier is 1.26/Z Alignment identifier is 1.27/a Alignment identifier is 1.28/b Alignment identifier is 1.29/c Alignment identifier is 1.30/d Alignment identifier is 1.31/e Alignment identifier is 1.32/f Alignment identifier is 1.33/g Alignment identifier is 1.34/h Alignment identifier is 1.35/i Alignment identifier is 1.47/v > select add #1.2 3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected Alignment identifier is 1.2/B > select #1.2/B:438 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1.2/B:438-440 28 atoms, 28 bonds, 3 residues, 1 model selected > select #1.2/B:438 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1.2/B:438-440 28 atoms, 28 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 28 atom styles > color sel byhetero > select #1.2/B:306-351 368 atoms, 370 bonds, 46 residues, 1 model selected > select #1.2/B:307-351 359 atoms, 361 bonds, 45 residues, 1 model selected > select add #1.2 3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected > select subtract #1.2 Nothing selected > show #!1.3 models > select add #1.3 3137 atoms, 3179 bonds, 2 pseudobonds, 398 residues, 2 models selected Alignment identifier is 1.3/C > select subtract #1.3 Nothing selected > hide #!1.3 models > show #!1.4 models > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected Alignment identifier is 1.4/D > select subtract #1.4 Nothing selected > hide #!1.4 models > show #!1.3 models > select add #1.3 3137 atoms, 3179 bonds, 2 pseudobonds, 398 residues, 2 models selected Alignment identifier is 1.3/C > select subtract #1.3 Nothing selected > hide #!1.3 models > show #!1.4 models > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected Alignment identifier is 1.4/D > select #1.4/D:416 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1.4/D:416-418 33 atoms, 34 bonds, 3 residues, 1 model selected > show sel atoms > style sel stick Changed 33 atom styles > color sel byhetero > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected > select subtract #1.4 Nothing selected > hide #!1.4 models > show #!1.1 models > select add #1.1 3261 atoms, 3317 bonds, 3 pseudobonds, 415 residues, 2 models selected Alignment identifier is 1.1/A > select subtract #1.1 Nothing selected > show #!1.4 models > show #1.5 models > select add #1.5 3124 atoms, 3174 bonds, 390 residues, 1 model selected Alignment identifier is 1.5/E > select subtract #1.5 Nothing selected > hide #1.5 models > show #!1.6 models Alignment identifier is 1.1/A Alignment identifier is 1.2/B Alignment identifier is 1.3/C Alignment identifier is 1.4/D Alignment identifier is 1.5/E Alignment identifier is 1.6/F Alignment identifier is 1.7/G Alignment identifier is 1.8/H Alignment identifier is 1.9/I Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 6 Alignment identifier is 7 Alignment identifier is 8 Alignment identifier is 9 Alignment identifier is 10 Alignment identifier is 11 Alignment identifier is 1.21/U Alignment identifier is 1.22/V Alignment identifier is 1.23/W Alignment identifier is 1.24/X Alignment identifier is 1.25/Y Alignment identifier is 1.26/Z Alignment identifier is 1.27/a Alignment identifier is 1.28/b Alignment identifier is 1.29/c Alignment identifier is 1.30/d Alignment identifier is 1.31/e Alignment identifier is 1.32/f Alignment identifier is 1.33/g Alignment identifier is 1.34/h Alignment identifier is 1.35/i Alignment identifier is 1.47/v > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected Alignment identifier is 1.4/D > select #1.4/D:416 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1.4/D:416-418 33 atoms, 34 bonds, 3 residues, 1 model selected > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected > select subtract #1.4 Nothing selected > hide #!1.4 models > show #!1.4 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > hide #!1.2 models > show #!1.2 models > show #1.5 models > select add #1.5 3124 atoms, 3174 bonds, 390 residues, 1 model selected Alignment identifier is 1.5/E > select subtract #1.5 Nothing selected > hide #1.5 models > hide #!1.2 models > show #!1.2 models > hide #!1.4 models > show #!1.4 models > hide #!1.6 models > show #!1.6 models > hide #!1.2 models > show #!1.2 models > hide #!1.4 models > show #!1.4 models > hide #!1.6 models > show #!1.6 models > select add #1.6 3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected Alignment identifier is 1.6/F > select subtract #1.6 Nothing selected > hide #!1.6 models > show #!1.6 models > hide #!1.6 models > show #!1.6 models > hide #!1.6 models > show #!1.21 models > hide #!1.21 models > show #1.22 models > hide #1.22 models > show #1.23 models > hide #1.23 models > show #1.23 models > hide #1.23 models > show #1.24 models > hide #1.24 models > show #1.25 models > hide #1.25 models > show #1.26 models > hide #1.26 models > show #1.26 models > hide #1.26 models > show #1.27 models > hide #1.27 models > show #1.28 models > hide #1.28 models > show #!1.29 models > hide #!1.29 models > show #1.30 models > hide #1.30 models > show #!1.31 models > hide #!1.31 models > show #1.32 models > hide #1.32 models > hide #!1.4 models > show #!1.4 models > hide #!1.4 models > show #!1.4 models > hide #!1.4 models > show #!1.4 models > hide #!1.4 models > hide #1.10 models > show #1.10 models > hide #1.7 models > show #1.7 models > hide #1.8 models > hide #1.9 models > show #1.9 models > select add #1.9 1908 atoms, 1938 bonds, 248 residues, 1 model selected Alignment identifier is 1.9/I > select #1.9/I:4 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1.9/I 1908 atoms, 1938 bonds, 248 residues, 1 model selected > select subtract #1.9 Nothing selected > select add #1.10 1739 atoms, 1763 bonds, 239 residues, 1 model selected Alignment identifier is 1.10/J > select #1.10/J:2-3 18 atoms, 18 bonds, 2 residues, 1 model selected > select #1.10/J 1739 atoms, 1763 bonds, 239 residues, 1 model selected > select #1.10/J:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1.10/J 1739 atoms, 1763 bonds, 239 residues, 1 model selected > select subtract #1.10 Nothing selected > color #1.9 white > color #1.9 #1f92eaff > color #1.9 #66ffffff > color #1.9 #8fc9f5ff > color #1.9 #66ffffff > color #1.9 #8fc9f5ff > hide #1.10 models > show #1.10 models > color #1.10 #66ffffff > select add #1.2 3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected Alignment identifier is 1.2/B > select #1.2/B:30 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1.2/B:30-440 3207 atoms, 3254 bonds, 411 residues, 1 model selected > select add #1.2 3239 atoms, 3287 bonds, 2 pseudobonds, 413 residues, 2 models selected > select subtract #1.2 Nothing selected > save /Users/jiale/Desktop/image1.png supersample 3 > hide #!1.2 models > show #!1.4 models > show #1.8 models > select add #1.9 1908 atoms, 1938 bonds, 248 residues, 1 model selected > select subtract #1.9 Nothing selected > select add #1.9 1908 atoms, 1938 bonds, 248 residues, 1 model selected > select subtract #1.9 Nothing selected > select add #1.8 1723 atoms, 1759 bonds, 230 residues, 1 model selected Alignment identifier is 1.8/H > select #1.8/H:5-6 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1.8/H 1723 atoms, 1759 bonds, 230 residues, 1 model selected > color #1.8 #33ccffff > color #1.7 #c7e4faff > color #1.13 #306db1ff > select subtract #1.8 Nothing selected > hide #1.15 models > hide #1.13 models > hide #1.19 models > show #1.19 models > hide #1.12 models > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected Alignment identifier is 1.4/D > select #1.4/D:39-40 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1.4/D:39-418 3040 atoms, 3090 bonds, 380 residues, 1 model selected > select add #1.4 3072 atoms, 3123 bonds, 2 pseudobonds, 382 residues, 2 models selected > select subtract #1.4 Nothing selected > save /Users/jiale/Desktop/image2.png supersample 3 > save ""/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"" ——— End of log from Mon Jan 1 11:35:17 2024 ——— opened ChimeraX session > color #1.7 #ccffccff > color #1.8 #99ff99ff > color #1.8 #33ff33ff > save /Users/jiale/Desktop/image1.png supersample 3 > color #1.9 #99ff99ff > color #1.10 #66cc66ff > hide #!1.4 models > show #!1.2 models > hide #1.14 models > show #1.14 models > hide #1.17 models > hide #1.8 models > color #1.10 #00cc00ff > save /Users/jiale/Desktop/image2.png supersample 3 > save /Users/jiale/Desktop/image3.png supersample 3 > save ""/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"" ——— End of log from Mon Jan 1 11:44:25 2024 ——— opened ChimeraX session > show #1.8 models > show #1.12 models > show #1.13 models > show #!1.3 models > show #!1.4 models > show #1.5 models > show #!1.6 models > show #!1.1 models > show #1.15 models > show #1.17 models > show #!1.21 models > show #1.22 models > hide #1.22 models > show #1.22 models > show #1.23 models > show #1.24 models > show #1.25 models > show #1.26 models > show #1.27 models > show #!1.29 models > show #1.28 models > show #1.30 models > show #!1.31 models > show #1.32 models > color #1.11 #006600ff > color #1.12 #66ffffff > select #1.6/F:436 9 atoms, 8 bonds, 1 residue, 1 model selected > view orient > view sel > select clear > select #1.6/F:436 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1.6/F:437 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 92 atoms, 93 bonds, 11 residues, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 92 atoms, 93 bonds, 11 residues, 1 model selected > select down 12 atoms, 12 bonds, 1 residue, 1 model selected > select up 92 atoms, 93 bonds, 11 residues, 1 model selected > show sel atoms > style sel stick Changed 92 atom styles > color sel byhetero > select clear > ui tool show ""Side View"" > select #1.12/L:10 7 atoms, 6 bonds, 1 residue, 1 model selected > view sel > select clear > ui tool show ""Side View"" > select #1.5/E:389 7 atoms, 6 bonds, 1 residue, 1 model selected > view sel > select clear > hide #!1 models > open 6msh Summary of feedback from opening 6msh fetched from pdb --- note | Fetching compressed mmCIF 6msh from http://files.rcsb.org/download/6msh.cif 6msh title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome [more info...] Chain information for 6msh #2 --- Chain | Description | UniProt A | 26S proteasome regulatory subunit 7 | PRS7_HUMAN B | 26S proteasome regulatory subunit 4 | PRS4_HUMAN C | 26S proteasome regulatory subunit 8 | PRS8_HUMAN D | 26S proteasome regulatory subunit 6B | PRS6B_HUMAN E | 26S proteasome regulatory subunit 10B | A0A087X2I1_HUMAN F | 26S proteasome regulatory subunit 6A | PRS6A_HUMAN G g | Proteasome subunit alpha type-6 | PSA6_HUMAN H h | Proteasome subunit alpha type-2 | PSA2_HUMAN I i | Proteasome subunit alpha type-4 | PSA4_HUMAN J j | Proteasome subunit alpha type-7 | PSA7_HUMAN K k | Proteasome subunit alpha type-5 | PSA5_HUMAN L l | Proteasome subunit alpha type-1 | PSA1_HUMAN M m | Proteasome subunit alpha type-3 | PSA3_HUMAN N n | Proteasome subunit beta type-6 | PSB6_HUMAN O o | Proteasome subunit beta type-7 | PSB7_HUMAN P p | Proteasome subunit beta type-3 | PSB3_HUMAN Q q | Proteasome subunit beta type-2 | PSB2_HUMAN R r | Proteasome subunit beta type-5 | PSB5_HUMAN S s | Proteasome subunit beta type-1 | PSB1_HUMAN T t | Proteasome subunit beta type-4 | PSB4_HUMAN U | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN V | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN W | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN X | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN Y | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN Z | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN a | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN b | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN c | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN d | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN e | 26S proteasome complex subunit SEM1 | SEM1_HUMAN f | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN v | substrate | Non-standard residues in 6msh #2 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate ZN — zinc ion > hide #!2 atoms > show #!2 cartoons > split #2 Split 6msh (#2) into 47 models Chain information for 6msh A #2.1 --- Chain | Description A | No description available Chain information for 6msh B #2.2 --- Chain | Description B | No description available Chain information for 6msh C #2.3 --- Chain | Description C | No description available Chain information for 6msh D #2.4 --- Chain | Description D | No description available Chain information for 6msh E #2.5 --- Chain | Description E | No description available Chain information for 6msh F #2.6 --- Chain | Description F | No description available Chain information for 6msh G #2.7 --- Chain | Description G | No description available Chain information for 6msh H #2.8 --- Chain | Description H | No description available Chain information for 6msh I #2.9 --- Chain | Description I | No description available Chain information for 6msh J #2.10 --- Chain | Description J | No description available Chain information for 6msh K #2.11 --- Chain | Description K | No description available Chain information for 6msh L #2.12 --- Chain | Description L | No description available Chain information for 6msh M #2.13 --- Chain | Description M | No description available Chain information for 6msh N #2.14 --- Chain | Description N | No description available Chain information for 6msh O #2.15 --- Chain | Description O | No description available Chain information for 6msh P #2.16 --- Chain | Description P | No description available Chain information for 6msh Q #2.17 --- Chain | Description Q | No description available Chain information for 6msh R #2.18 --- Chain | Description R | No description available Chain information for 6msh S #2.19 --- Chain | Description S | No description available Chain information for 6msh T #2.20 --- Chain | Description T | No description available Chain information for 6msh U #2.21 --- Chain | Description U | No description available Chain information for 6msh V #2.22 --- Chain | Description V | No description available Chain information for 6msh W #2.23 --- Chain | Description W | No description available Chain information for 6msh X #2.24 --- Chain | Description X | No description available Chain information for 6msh Y #2.25 --- Chain | Description Y | No description available Chain information for 6msh Z #2.26 --- Chain | Description Z | No description available Chain information for 6msh a #2.27 --- Chain | Description a | No description available Chain information for 6msh b #2.28 --- Chain | Description b | No description available Chain information for 6msh c #2.29 --- Chain | Description c | No description available Chain information for 6msh d #2.30 --- Chain | Description d | No description available Chain information for 6msh e #2.31 --- Chain | Description e | No description available Chain information for 6msh f #2.32 --- Chain | Description f | No description available Chain information for 6msh g #2.33 --- Chain | Description g | No description available Chain information for 6msh h #2.34 --- Chain | Description h | No description available Chain information for 6msh i #2.35 --- Chain | Description i | No description available Chain information for 6msh j #2.36 --- Chain | Description j | No description available Chain information for 6msh k #2.37 --- Chain | Description k | No description available Chain information for 6msh l #2.38 --- Chain | Description l | No description available Chain information for 6msh m #2.39 --- Chain | Description m | No description available Chain information for 6msh n #2.40 --- Chain | Description n | No description available Chain information for 6msh o #2.41 --- Chain | Description o | No description available Chain information for 6msh p #2.42 --- Chain | Description p | No description available Chain information for 6msh q #2.43 --- Chain | Description q | No description available Chain information for 6msh r #2.44 --- Chain | Description r | No description available Chain information for 6msh s #2.45 --- Chain | Description s | No description available Chain information for 6msh t #2.46 --- Chain | Description t | No description available Chain information for 6msh v #2.47 --- Chain | Description v | No description available > hide #!2.6 models > show #!2.6 models > hide #2.13 models > show #2.13 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > show #!2 models > show #!1 models > open 5gjr Summary of feedback from opening 5gjr fetched from pdb --- note | Fetching compressed mmCIF 5gjr from http://files.rcsb.org/download/5gjr.cif 5gjr title: An atomic structure of the human 26S proteasome [more info...] Chain information for 5gjr #3 --- Chain | Description | UniProt 0 M | 26S protease regulatory subunit 6A | PRS6A_HUMAN 1 N | 26S proteasome non-ATPase regulatory subunit 1 | PSMD1_HUMAN 2 O | 26S proteasome non-ATPase regulatory subunit 13 | PSD13_HUMAN 3 P | 26S proteasome non-ATPase regulatory subunit 12 | PSD12_HUMAN 4 Q | 26S proteasome non-ATPase regulatory subunit 11 | PSD11_HUMAN 5 R | 26S proteasome non-ATPase regulatory subunit 6 | PSMD6_HUMAN 6 S | 26S proteasome non-ATPase regulatory subunit 3 | PSMD3_HUMAN 7 T | 26S proteasome non-ATPase regulatory subunit 8 | PSMD8_HUMAN 8 U | 26S proteasome non-ATPase regulatory subunit 7 | PSMD7_HUMAN 9 V | 26S proteasome non-ATPase regulatory subunit 14 | PSDE_HUMAN AA W | 26S proteasome non-ATPase regulatory subunit 4 | PSMD4_HUMAN AB Y | 26S proteasome complex subunit DSS1 | DSS1_HUMAN AC Z | 26S proteasome non-ATPase regulatory subunit 2 | PSMD2_HUMAN B h | Proteasome subunit alpha type-6 | PSA6_HUMAN C i | Proteasome subunit alpha type-2 | PSA2_HUMAN D j | Proteasome subunit alpha type-4 | PSA4_HUMAN E k | Proteasome subunit alpha type-7 | PSA7_HUMAN F l | Proteasome subunit alpha type-5 | PSA5_HUMAN G m | Proteasome subunit alpha type-1 | PSA1_HUMAN H v | 26S protease regulatory subunit 7 | PRS7_HUMAN I w | 26S protease regulatory subunit 4 | PRS4_HUMAN J x | 26S protease regulatory subunit 8 | PRS8_HUMAN K y | 26S protease regulatory subunit 6B | PRS6B_HUMAN L z | 26S protease regulatory subunit 10B | PRS10_HUMAN X n | Proteasome subunit alpha type-3 | PSA3_HUMAN a o | Proteasome subunit beta type-6 | PSB6_HUMAN b p | Proteasome subunit beta type-7 | PSB7_HUMAN c q | Proteasome subunit beta type-3 | PSB3_HUMAN d r | Proteasome subunit beta type-2 | PSB2_HUMAN e s | Proteasome subunit beta type-5 | PSB5_HUMAN f t | Proteasome subunit beta type-1 | PSB1_HUMAN g u | Proteasome subunit beta type-4 | PSB4_HUMAN Non-standard residues in 5gjr #3 --- ADP — adenosine-5'-diphosphate > hide #!2 models > hide #!1 models > hide #!3 atoms > show #!3 cartoons > hide #!3 models > show #!1 models > color #1.11 #339933ff > color #1.12 #006600ff > color #1.13 #006600ff > color #1.12 #00cc00ff > color #1.11 #66cc00ff > color #1.12 #339933ff > select #1.1/A:415 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 137 atoms, 138 bonds, 17 residues, 1 model selected > select up 3229 atoms, 3284 bonds, 413 residues, 1 model selected > color sel bynucleotide Alignment identifier is 1.1/A > select #1.1/A:21 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1.1/A:21-433 3229 atoms, 3284 bonds, 413 residues, 1 model selected > select #1.13/M:198 12 atoms, 12 bonds, 1 residue, 1 model selected > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > hide #!1.4 models > hide #1.5 models > hide #!1.6 models > hide #1.7 models > show #1.7 models > select add #1.13 1856 atoms, 1892 bonds, 240 residues, 1 model selected > select subtract #1.13 Nothing selected > hide #1.14 models > hide #1.15 models > hide #1.16 models > hide #1.17 models > hide #1.18 models > hide #1.19 models > hide #1.20 models > hide #!1.21 models > hide #1.22 models > hide #1.23 models > hide #1.24 models > hide #1.25 models > hide #1.26 models > hide #1.27 models > hide #1.28 models > hide #!1.29 models > hide #1.30 models > hide #!1.31 models > hide #1.32 models > hide #1.33 models > hide #1.34 models > hide #1.35 models > hide #1.36 models > hide #!1.37 models > hide #1.38 models > hide #1.39 models > hide #1.40 models > show #1.40 models > hide #1.46 models > hide #1.45 models > hide #1.44 models > hide #1.43 models > hide #1.42 models > hide #1.41 models > hide #1.40 models > show #!1.2 models > hide #!1.2 models > show #!1.4 models > hide #!1.4 models > show #!1.6 models > select add #1.6 3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected > hide sel atoms Alignment identifier is 1.6/F > select #1.6/F:436 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1.6/F:436-438 33 atoms, 34 bonds, 3 residues, 1 model selected > select #1.6/F:437-438 24 atoms, 25 bonds, 2 residues, 1 model selected > select #1.6/F:437-439 30 atoms, 31 bonds, 3 residues, 1 model selected > style sel stick Changed 30 atom styles > show sel atoms > select add #1.6 3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected > select subtract #1.6 Nothing selected > select #1.6/F:25-27 26 atoms, 25 bonds, 3 residues, 1 model selected > select #1.6/F 3098 atoms, 3137 bonds, 1 pseudobond, 395 residues, 2 models selected > hide #1.7 models > hide #1.8 models > hide #1.9 models > hide #1.10 models > hide #!1.11 models > show #!1.11 models > hide #1.13 models > select subtract #1.6 Nothing selected > hide #!1.11 models > show #!1.11 models > hide #1.12 models > show #1.12 models > save /Users/jiale/Desktop/image1.png supersample 3 > hide #!1.6 models > hide #!1.11 models > hide #1.12 models > show #1.12 models > show #1.13 models > color #1.13 #8efa00ff > show #!1.11 models > show #1.10 models > hide #1.10 models > show #1.7 models > show #!1.1 models > show #!1.2 models > show #!1.3 models > show #!1.4 models > show #1.5 models > show #!1.6 models > hide #!1.1 models > hide #!1.2 models > hide #!1.3 models > hide #!1.4 models > hide #1.5 models > hide #!1.6 models > save /Users/jiale/Desktop/image2.png supersample 3 > save ""/Users/jiale/Desktop/Figures/26S HbYX motif.cxs"" ——— End of log from Mon Jan 1 16:54:24 2024 ——— opened ChimeraX session > close #2 > close #3 > select add #1.13 1856 atoms, 1892 bonds, 240 residues, 1 model selected Alignment identifier is 1.13/M > style sel stick Changed 1856 atom styles > show sel atoms > color sel byhetero > select clear > select #1.12/L:20 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 99 atoms, 100 bonds, 12 residues, 1 model selected > select up 1850 atoms, 1885 bonds, 238 residues, 1 model selected > show sel atoms > style sel stick Changed 1850 atom styles > color sel byhetero > select clear > open > ""/Users/jiale/Desktop/Ptsm_paper_pdb_deposition/Adolf_Du_Proteasome_Assembly_Submission/Maps_Models/Adolf_Du_Model1_ > PDB-8QYJ.pdb"" Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available > select add #2 19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 2 models selected > style sel stick Changed 19402 atom styles > hide sel cartoons > show sel atoms > hide sel atoms > show sel cartoons > select add #1 124718 atoms, 126873 bonds, 26 pseudobonds, 16035 residues, 60 models selected > select subtract #2 105316 atoms, 107125 bonds, 18 pseudobonds, 13534 residues, 58 models selected > combine sel > select subtract #1 Nothing selected > hide #!1 models > rename #3 26S > select add #2 19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 2 models selected > select add #3 124718 atoms, 126873 bonds, 26 pseudobonds, 16035 residues, 5 models selected > select subtract #3 19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 2 models selected > select subtract #2 Nothing selected > ui tool show Matchmaker > matchmaker #!3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2) with 26S, chain M (#3), sequence alignment score = 1132 RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs: 1.111) > matchmaker #!3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2) with 26S, chain M (#3), sequence alignment score = 1132 RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs: 1.111) > hide #!3 models > show #!1 models > hide #!2 models > show #!2 models > hide #2.1 models > hide #!2 models > show #!2 models > ui tool show Matchmaker > 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 26S, chain M (#3) with Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2), sequence alignment score = 1132 RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs: 1.111) > 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 26S, chain M (#3) with Adolf_Du_Model1_ PDB-8QYJ.pdb, chain F (#2), sequence alignment score = 1132 RMSD between 226 pruned atom pairs is 0.743 angstroms; (across all 239 pairs: 1.111) > show #!3 models > hide #!1 models > hide #!3 models > split #2 Split Adolf_Du_Model1_ PDB-8QYJ.pdb (#2) into 13 models Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb A #2.1 --- Chain | Description A | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb B #2.2 --- Chain | Description B | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb C #2.3 --- Chain | Description C | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb D #2.4 --- Chain | Description D | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb E #2.5 --- Chain | Description E | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb F #2.6 --- Chain | Description F | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb G #2.7 --- Chain | Description G | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb H #2.8 --- Chain | Description H | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb I #2.9 --- Chain | Description I | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb J #2.10 --- Chain | Description J | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb K #2.11 --- Chain | Description K | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb L #2.12 --- Chain | Description L | No description available Chain information for Adolf_Du_Model1_ PDB-8QYJ.pdb M #2.13 --- Chain | Description M | No description available > hide #2.1 models > hide #!2.2 models > hide #2.3 models > show #2.3 models > show #!2.2 models > show #2.1 models > hide #2.8 models > hide #!2.9 models > hide #!2.10 models > show #!2.10 models > show #!2.9 models > hide #!2.9 models > hide #!2.11 models > hide #2.12 models > hide #2.13 models > hide #!2.7 models > show #!2.7 models > select add #2.7 1787 atoms, 1819 bonds, 1 pseudobond, 235 residues, 2 models selected > view sel > select subtract #2.7 Nothing selected > select add #2.10 1909 atoms, 1951 bonds, 2 pseudobonds, 248 residues, 2 models selected > view sel > select clear > select #2.10/J:262 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 224 atoms, 232 bonds, 28 residues, 1 model selected > select down 5 atoms, 4 bonds, 1 residue, 1 model selected > view sel > ui tool show ""Side View"" > view sel > select clear > show #!3 models > hide #!3 models > show #!3 models > close #1 > rename #2 ""Structure 1"" > hide #!3 models > color #2.2 #8fc9f5ff > color #2.3 #57adefff > color #2.4 #1f92eaff > color #2.5 #1171bbff > color #2.6 #306db1ff > color #2.7 #c7e4faff > color #2.8 #ff8f00ff > color #2.9 #ffccccff > color #2.9 #ff6666ff > color #2.10 #ffccccff > color #2.11 #f4d6ffff > color #2.12 #ffe784ff > color #2.13 #e0b403ff > ui mousemode right ""translate selected models"" > ui mousemode right zoom > show #!2.9 models > color #2.2 #33ccffff > color #2.2 #8fc9f5ff > color #2.1 #33ccffff > color #2.3 #66ffffff > color #2.5 #666fffff > select add #2.9 1933 atoms, 1974 bonds, 1 pseudobond, 243 residues, 2 models selected > select subtract #2.9 Nothing selected > show #!3 models > close #3.1 > close #3.2 > hide #!2 models > split #3 Split 26S (#3) into 47 models Chain information for 26S A #3.1 --- Chain | Description A | No description available Chain information for 26S B #3.2 --- Chain | Description B | No description available Chain information for 26S C #3.3 --- Chain | Description C | No description available Chain information for 26S D #3.4 --- Chain | Description D | No description available Chain information for 26S E #3.5 --- Chain | Description E | No description available Chain information for 26S F #3.6 --- Chain | Description F | No description available Chain information for 26S G #3.7 --- Chain | Description G | No description available Chain information for 26S H #3.8 --- Chain | Description H | No description available Chain information for 26S I #3.9 --- Chain | Description I | No description available Chain information for 26S J #3.10 --- Chain | Description J | No description available Chain information for 26S K #3.11 --- Chain | Description K | No description available Chain information for 26S L #3.12 --- Chain | Description L | No description available Chain information for 26S M #3.13 --- Chain | Description M | No description available Chain information for 26S N #3.14 --- Chain | Description N | No description available Chain information for 26S O #3.15 --- Chain | Description O | No description available Chain information for 26S P #3.16 --- Chain | Description P | No description available Chain information for 26S Q #3.17 --- Chain | Description Q | No description available Chain information for 26S R #3.18 --- Chain | Description R | No description available Chain information for 26S S #3.19 --- Chain | Description S | No description available Chain information for 26S T #3.20 --- Chain | Description T | No description available Chain information for 26S U #3.21 --- Chain | Description U | No description available Chain information for 26S V #3.22 --- Chain | Description V | No description available Chain information for 26S W #3.23 --- Chain | Description W | No description available Chain information for 26S X #3.24 --- Chain | Description X | No description available Chain information for 26S Y #3.25 --- Chain | Description Y | No description available Chain information for 26S Z #3.26 --- Chain | Description Z | No description available Chain information for 26S a #3.27 --- Chain | Description a | No description available Chain information for 26S b #3.28 --- Chain | Description b | No description available Chain information for 26S c #3.29 --- Chain | Description c | No description available Chain information for 26S d #3.30 --- Chain | Description d | No description available Chain information for 26S e #3.31 --- Chain | Description e | No description available Chain information for 26S f #3.32 --- Chain | Description f | No description available Chain information for 26S g #3.33 --- Chain | Description g | No description available Chain information for 26S h #3.34 --- Chain | Description h | No description available Chain information for 26S i #3.35 --- Chain | Description i | No description available Chain information for 26S j #3.36 --- Chain | Description j | No description available Chain information for 26S k #3.37 --- Chain | Description k | No description available Chain information for 26S l #3.38 --- Chain | Description l | No description available Chain information for 26S m #3.39 --- Chain | Description m | No description available Chain information for 26S n #3.40 --- Chain | Description n | No description available Chain information for 26S o #3.41 --- Chain | Description o | No description available Chain information for 26S p #3.42 --- Chain | Description p | No description available Chain information for 26S q #3.43 --- Chain | Description q | No description available Chain information for 26S r #3.44 --- Chain | Description r | No description available Chain information for 26S s #3.45 --- Chain | Description s | No description available Chain information for 26S t #3.46 --- Chain | Description t | No description available Chain information for 26S v #3.47 --- Chain | Description v | No description available > hide #3.1 models > hide #3.2 models > hide #3.3 models > hide #3.4 models > hide #3.5 models > hide #3.6 models > hide #3.7 models > show #3.7 models > hide #3.14 models > show #3.14 models > hide #3.15 models > show #3.15 models > hide #3.32 models > hide #3.31 models > ui mousemode right ""translate selected models"" Drag select of 2166 residues > select add #3.21 17495 atoms, 6946 bonds, 2211 residues, 11 models selected > select subtract #3.21 10667 atoms, 1339 residues, 10 models selected > select add #3.22 11584 atoms, 3929 bonds, 1454 residues, 10 models selected > select add #3.23 14977 atoms, 7680 bonds, 1872 residues, 10 models selected > select add #3.24 17978 atoms, 10733 bonds, 2251 residues, 10 models selected > hide #3.22 models > hide #3.23 models > hide #3.24 models > hide #3.25 models > hide #3.26 models > hide #3.27 models > hide #3.28 models > hide #3.29 models > hide #3.30 models > hide #3.47 models > select clear Drag select of 263 residues > hide #3.21 models > select add #3.21 6828 atoms, 6946 bonds, 872 residues, 1 model selected > select subtract #3.21 Nothing selected > color #3.7 #c7e4faff > color #3.8 #33ccffff > color #3.9 #8fc9f5ff > color #3.10 #66ffffff > color #3.11 #1f92eaff > color #3.11 #666fffff > color #3.11 #1f92eaff > color #3.12 #666fffff > color #3.13 #306db1ff > color #3.14 #f4d6ffff > select add #3.14 1430 atoms, 1454 bonds, 191 residues, 1 model selected > select subtract #3.14 Nothing selected > ui tool show ""Side View"" > hide #3.15 models > show #3.15 models > color #3.14 #9600ccff > color #3.15 #f4d6ffff > color #3.16 #efc2ffff > color #3.17 #e499ffff > color #3.18 #d35cffff > color #3.19 #c31fffff > color #3.20 #a500e0ff > color #3.33 #c7e4faff > color #3.34 #a2d2f6ff > color #3.35 #8fc9f5ff > color #3.36 #57adefff > color #3.37 #1f92eaff > color #3.38 #1171bbff > color #3.39 #306db1ff > color #3.40 #9600ccff > color #3.41 #f4d6ffff > color #3.42 #efc2ffff > color #3.43 #e499ffff > color #3.44 #d35cffff > color #3.45 #c31fffff > color #3.46 #a500e0ff > ui mousemode right zoom > show #!2 models > select add #2.9 1933 atoms, 1974 bonds, 1 pseudobond, 243 residues, 2 models selected > select subtract #2.9 Nothing selected > select add #2.9 1933 atoms, 1974 bonds, 1 pseudobond, 243 residues, 2 models selected > select add #2.4 3781 atoms, 3851 bonds, 1 pseudobond, 485 residues, 3 models selected > select add #2.5 5667 atoms, 5772 bonds, 1 pseudobond, 725 residues, 4 models selected > combine sel > rename #1 id #4 > rename #2 id #1 > rename #3 id #2 > rename #4 id #3 > rename #3 S1_5_6_pac1 > select add #1 19402 atoms, 19748 bonds, 8 pseudobonds, 2501 residues, 19 models selected > select subtract #1 Nothing selected > hide #!1 models > hide #!2 models > show #!2 models > select add #2.11 1729 atoms, 1755 bonds, 228 residues, 1 model selected > select add #2.12 3579 atoms, 3640 bonds, 466 residues, 2 models selected > show #2.4 models > hide #2.4 models > show #2.5 models > hide #2.5 models > show #2.6 models > select add #2.6 6677 atoms, 6777 bonds, 861 residues, 3 models selected > combine sel > rename #4 26S_5_6_rpt5 > select add #2 105316 atoms, 107125 bonds, 13534 residues, 48 models selected > select subtract #2 Nothing selected > hide #!2 models > color #4 #00fdffff > color #4 white > hide #4#!3 atoms > select #4/K 1729 atoms, 1755 bonds, 228 residues, 1 model selected > color sel #1f92eaff > select #4/L 1850 atoms, 1885 bonds, 238 residues, 1 model selected > color sel #666fffff > select #4/F 3098 atoms, 3137 bonds, 395 residues, 1 model selected > color sel #ccffccff > color sel #33ff33ff > color sel #ffff00ff > color sel #ffe784ff > color sel #ffeb99ff > select clear > ui tool show Matchmaker > matchmaker #4 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 S1_5_6_pac1, chain E (#3) with 26S_5_6_rpt5, chain L (#4), sequence alignment score = 1130.7 RMSD between 226 pruned atom pairs is 0.654 angstroms; (across all 236 pairs: 1.014) > matchmaker #4 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 S1_5_6_pac1, chain E (#3) with 26S_5_6_rpt5, chain L (#4), sequence alignment score = 1130.7 RMSD between 226 pruned atom pairs is 0.654 angstroms; (across all 236 pairs: 1.014) > matchmaker #4 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 S1_5_6_pac1, chain E (#3) with 26S_5_6_rpt5, chain L (#4), sequence alignment score = 1130.7 RMSD between 226 pruned atom pairs is 0.654 angstroms; (across all 236 pairs: 1.014) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 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 Pro Model Identifier: MacBookPro17,1 Model Number: MYDC2LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 4 days, 4 hours, 49 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 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 DELL P2415Q: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.1.0 Babel: 2.11.0 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: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 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-Clipper: 0.19.0 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: 1.5 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-ISOLDE: 1.5 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: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 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: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 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: 5.1.0 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: 2.8.4 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 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 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: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 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: 0.6.2 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: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal UI can't reproduce all ChimeraX