id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20321 Crash in QDockWidget::event() in Qt 6.9.2 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.4.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. 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All rights reserved. > open ""/Users/pdamke/Desktop/Chimera Sessions/05-13-2028/AcCAST_for_R35.cxs"" Opened Full_J2530_resampled_sharp.mrc as #1, grid size 512,512,512, pixel 1.65, shown at level 0.119, step 1, values float32 Opened Full_J2530_resampled_sharp.mrc gaussian as #4, grid size 512,512,512, pixel 1.65, shown at level 0.0735, step 1, values float32 Log from Mon May 4 17:36:01 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/ekello73/Desktop/AcCAST_model_grant_app > copy/04_Full_map_withSTC_noDNA.cxs"" Opened Full_J2530_resampled_sharp.mrc as #1, grid size 512,512,512, pixel 1.65, shown at level 0.135, step 1, values float32 Log from Mon May 4 16:44:14 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/tpottang/Desktop/grant_model/Full_map_withSTC_noDNA.cxs Opened 00_new_full_P59_J2530_resamples_sharp.mrc as #1, grid size 512,512,512, pixel 1.65, shown at level 0.135, step 1, values float32 Log from Mon May 4 16:32:32 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. > open /Users/tpottang/Desktop/grant_model/Full_map_no_STC.cxs Opened TightTarget_285A_J2871_sharp.mrc as #2, grid size 256,256,256, pixel 1.3, shown at level 0.0494, step 1, values float32 Opened 285A_B40_J2870_sharp.mrc as #3, grid size 256,256,256, pixel 1.3, shown at level 0.132, step 1, values float32 Opened 00_new_full_P59_J2530_resamples_sharp.mrc as #6, grid size 512,512,512, pixel 1.65, shown at level 0.135, step 1, values float32 Log from Mon May 4 16:03:19 2026UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/tpottang/Desktop/grant_model/C06_S2_AcCAST_recruitment_004.pdb Chain information for C06_S2_AcCAST_recruitment_004.pdb #1 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available A | No description available B | No description available C | No description available D E F G H | No description available > open /Users/tpottang/Desktop/grant_model/TightTarget_285A_J2871_sharp.mrc Opened TightTarget_285A_J2871_sharp.mrc as #2, grid size 256,256,256, pixel 1.3, shown at level 8.48e-05, step 1, values float32 > lighting soft > open /Users/tpottang/Desktop/grant_model/285A_B40_J2870_sharp.mrc Opened 285A_B40_J2870_sharp.mrc as #3, grid size 256,256,256, pixel 1.3, shown at level 0.0737, step 1, values float32 > volume #3 level 0.1187 > volume #2 level 0.00969 > hide > show cartoons > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > set bgColor white > color #3 grey models > color #3 #80808089 models > color #3 #80808080 models Called attribute on invalid object: 2147487593 [Repeated 21 time(s)] > color #2 #b3b3b3ff models > color #2 grey models > color #2 #8080807f models > open /Users/tpottang/Downloads/AcCAST_PD.pdb Summary of feedback from opening /Users/tpottang/Downloads/AcCAST_PD.pdb --- warnings | End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11 Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1 12 Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1 9 Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1 7 Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1 3 Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1 7 Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109 1 3 Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A 120 1 3 Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A 125 1 5 Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A 134 1 5 Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A 143 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205 1 4 Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A 232 1 11 Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A 255 1 6 Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A 258 1 3 Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A 275 1 9 Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A 293 1 3 End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340 1 16 Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A 371 1 4 Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A 384 1 3 Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A 407 1 21 Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A 429 1 11 Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A 484 1 5 134 messages similar to the above omitted End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11 Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1 12 Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1 9 Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1 7 Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1 3 Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1 7 Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109 1 3 Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A 120 1 3 Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A 125 1 5 Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A 134 1 5 Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A 143 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205 1 4 Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A 232 1 11 Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A 255 1 6 Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A 258 1 3 Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A 275 1 9 Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A 293 1 3 End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340 1 16 Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A 371 1 4 Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A 384 1 3 Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A 407 1 21 Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A 429 1 11 Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A 484 1 5 134 messages similar to the above omitted End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11 Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1 12 Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1 9 Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1 7 Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1 3 Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1 7 Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109 1 3 Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A 120 1 3 Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A 125 1 5 Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A 134 1 5 Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A 143 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205 1 4 Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A 232 1 11 Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A 255 1 6 Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A 258 1 3 Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A 275 1 9 Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A 293 1 3 End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340 1 16 Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A 371 1 4 Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A 384 1 3 Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A 407 1 21 Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A 429 1 11 Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A 484 1 5 134 messages similar to the above omitted End residue of secondary structure not found: HELIX 1 1 GLU A 14 MET A 24 1 11 Start residue of secondary structure not found: HELIX 2 2 THR A 29 GLY A 40 1 12 Start residue of secondary structure not found: HELIX 3 3 ALA A 56 ASN A 64 1 9 Start residue of secondary structure not found: HELIX 4 4 GLY A 77 ALA A 83 1 7 Start residue of secondary structure not found: HELIX 5 5 ILE A 84 LEU A 86 1 3 Start residue of secondary structure not found: HELIX 6 6 VAL A 87 TYR A 91 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 8 8 ARG A 100 GLU A 106 1 7 Start residue of secondary structure not found: HELIX 9 9 GLY A 107 CYS A 109 1 3 Start residue of secondary structure not found: HELIX 10 10 ASP A 118 GLU A 120 1 3 Start residue of secondary structure not found: HELIX 11 11 LEU A 121 SER A 125 1 5 Start residue of secondary structure not found: HELIX 12 12 GLU A 130 ASN A 134 1 5 Start residue of secondary structure not found: HELIX 13 13 LEU A 139 PHE A 143 1 5 1 messages similar to the above omitted End residue of secondary structure not found: HELIX 15 15 GLY A 202 GLY A 205 1 4 Start residue of secondary structure not found: HELIX 16 16 GLY A 222 ALA A 232 1 11 Start residue of secondary structure not found: HELIX 17 17 TRP A 250 GLU A 255 1 6 Start residue of secondary structure not found: HELIX 18 18 ILE A 256 THR A 258 1 3 Start residue of secondary structure not found: HELIX 19 19 GLU A 267 LEU A 275 1 9 Start residue of secondary structure not found: HELIX 20 20 ASN A 291 ASP A 293 1 3 End residue of secondary structure not found: HELIX 21 21 LEU A 325 ASN A 340 1 16 Start residue of secondary structure not found: HELIX 22 22 HIS A 368 VAL A 371 1 4 Start residue of secondary structure not found: HELIX 23 23 THR A 382 MET A 384 1 3 Start residue of secondary structure not found: HELIX 24 24 THR A 387 LYS A 407 1 21 Start residue of secondary structure not found: HELIX 25 25 GLN A 419 LEU A 429 1 11 Start residue of secondary structure not found: HELIX 26 26 VAL A 480 LEU A 484 1 5 134 messages similar to the above omitted Chain information for AcCAST_PD.pdb --- Chain | Description 4.1/1 | No description available 4.1/2 | No description available 4.1/3 | No description available 4.1/A | No description available 4.2/A 4.3/A 4.4/A 4.5/A | No description available 4.1/B | No description available 4.1/C | No description available 4.1/D 4.1/E 4.1/F 4.1/G 4.1/H | No description available Computing secondary structure [Repeated 3 time(s)] > ui tool show Matchmaker Called attribute on invalid object: 2147489647 [Repeated 21 time(s)] Called attribute on invalid object: 2147491725 [Repeated 21 time(s)] > hide #4.2 models > hide #4.3 models > hide #4.4 models Called attribute on invalid object: 2147494640 [Repeated 21 time(s)] > hide #4.5 models > hide #!4.1 models > show #!4.1 models > chain info #4.1 Unknown command: chain info #4.1 > info chains #4.1 chain id #4.1/2 chain_id 2 chain id #4.1/3 chain_id 3 chain id #4.1/A chain_id A chain id #4.1/B chain_id B chain id #4.1/C chain_id C chain id #4.1/D chain_id D chain id #4.1/E chain_id E chain id #4.1/F chain_id F chain id #4.1/G chain_id G chain id #4.1/H chain_id H chain id #4.1/1 chain_id 1 > show #4.2 models > show #4.3 models > show #4.4 models Called attribute on invalid object: 2147503925 [Repeated 21 time(s)] > show #4.5 models > hide #4.5 models > hide #4.4 models > hide #4.3 models > hide #4.2 models > hide #!4.1 models > hide #!4 models Called attribute on invalid object: 2147512941 [Repeated 21 time(s)] > close #4 > color /1 #decb6a > color /2 #6f6ade > color /3 #de726a > color /A #464561 > color /B #3ae080 > color /C #8a706e > color /D,F,H #df68ff > color /E,G,I #ab58b9 > hide #!1 models > show #!1 models > hide #!2 models > hide #!3 models > combine #1/E > color #4 #9c9c9cff Called attribute on invalid object: 2147523743 [Repeated 21 time(s)] > undo > hide #!1 models > show #!1 models > color #4 #9c9c9cff > undo > hide #!1 models > hide #!4 models > show #!4 models Called attribute on invalid object: 2147535116 [Repeated 21 time(s)] > select #4 25081 atoms, 26244 bonds, 2 pseudobonds, 2563 residues, 2 models selected > ~select #4/F 22960 atoms, 24091 bonds, 2 pseudobonds, 2299 residues, 2 models selected > delete sel > show #!1 models > hide #!1 models > show #!1 models > combine #1/E > select #5 25081 atoms, 26244 bonds, 2 pseudobonds, 2563 residues, 2 models selected > ~select #5/E 22960 atoms, 24091 bonds, 2 pseudobonds, 2299 residues, 2 models selected > delete sel > hide #!1 models Called attribute on invalid object: 2147551162 [Repeated 21 time(s)] > rename #4 TnsC_F Called attribute on invalid object: 2147553932 [Repeated 21 time(s)] > ~select #5/E Nothing selected > rename #5 TnsC_E > color #5 #ab58b8ff > color #5 #9f58b8ff > color #5 #9f68b8ff > color #5 #9f68d2ff > show #!1 models Called attribute on invalid object: 2147565288 [Repeated 21 time(s)] > hide #!4 models > hide #!5 models > color /1 #decb6a > color /2 #6f6ade > color /3 #de726a > color /A #464561 > color /B #3ae080 > color /C #8a706e > color /D,F,H #df68ff > color /E,G,I #9f68d2 > show #!2 models > volume #2 level 0.0385 Called attribute on invalid object: 2147572757 [Repeated 21 time(s)] > hide #!2 models > show #!3 models > volume #3 level 0.1861 > ui tool show ""Color Zone"" > color zone #3 near #1 distance 7.78 > volume #2 level 0.04941 > hide #!2 models > volume #3 level 0.1765 > hide #!1 models > volume #3 level 0.1319 Called attribute on invalid object: 2147589196 [Repeated 21 time(s)] > save /Users/tpottang/Desktop/grant_model/Recruitment_map_sharp.cxs > hide #!3 models > show #!2 models > show #!1 models > color zone #2 near #1 distance 7.78 Called attribute on invalid object: 2147599158 [Repeated 21 time(s)] > save /Users/tpottang/Desktop/grant_model/Recruitment_map_EMhancer.cxs > open > /Users/tpottang/Desktop/Coot_Session/Coot_005/Session_2/00_new_full_P59_J2530_resamples_sharp.mrc Opened 00_new_full_P59_J2530_resamples_sharp.mrc as #6, grid size 512,512,512, pixel 1.65, shown at level 0.0222, step 2, values float32 > color #6 #edededff models > color #6 grey models > color #6 #8080807d models > color #6 #7f7f7f7d models Called attribute on invalid object: 2147610054 [Repeated 21 time(s)] > volume #6 step 1 > volume #6 step 2 > hide #!2 models > volume #6 level 0.03755 > volume #6 step 1 > volume #6 level 0.06724 > ui tool show ""Fit in Map"" > fitmap #6 inMap #3 Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map 285A_B40_J2870_sharp.mrc using 218511 points correlation = 0, correlation about mean = 0, overlap = 0 steps = 24, shift = 0, angle = 0 degrees Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to 285A_B40_J2870_sharp.mrc (#3) coordinates: Matrix rotation and translation 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.00000000 0.00000000 Axis 0.00000000 0.00000000 1.00000000 Axis point 0.00000000 0.00000000 0.00000000 Rotation angle (degrees) 0.00000000 Shift along axis 0.00000000 > select add #6 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,-105.46,0,1,0,33.977,0,0,1,-242.2 > view matrix models #6,1,0,0,-256.26,0,1,0,-219.67,0,0,1,-241.72 > view matrix models #6,1,0,0,-239.48,0,1,0,-252.35,0,0,1,-231.84 > view matrix models #6,1,0,0,-244.97,0,1,0,-247.07,0,0,1,-244.65 > view matrix models > #6,0.13485,-0.98857,-0.067425,567.09,0.96307,0.11476,0.24356,-472.21,-0.23304,-0.09778,0.96754,-83.516 > view matrix models > #6,0.13485,-0.98857,-0.067425,592.22,0.96307,0.11476,0.24356,-427.62,-0.23304,-0.09778,0.96754,-77.569 > view matrix models > #6,0.13485,-0.98857,-0.067425,549.04,0.96307,0.11476,0.24356,-395.39,-0.23304,-0.09778,0.96754,-83.343 > fitmap #6 inMap #3 Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map 285A_B40_J2870_sharp.mrc using 218511 points correlation = 0.3963, correlation about mean = 0.08938, overlap = 1277 steps = 864, shift = 13.9, angle = 21.3 degrees Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to 285A_B40_J2870_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.23359617 -0.97158680 -0.03810405 689.79091582 0.94439979 -0.23603679 0.22890102 -222.63510864 -0.23139117 0.01748494 0.97270366 -140.64443760 Axis -0.10913026 0.09977232 0.98900762 Axis point 415.20437418 156.21604391 0.00000000 Rotation angle (degrees) 104.38667687 Shift along axis -236.58830450 > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > view matrix models > #6,-0.2336,-0.97159,-0.038104,693.43,0.9444,-0.23604,0.2289,-222.88,-0.23139,0.017485,0.9727,-136.61 > view matrix models > #6,-0.2336,-0.97159,-0.038104,802.76,0.9444,-0.23604,0.2289,-251.1,-0.23139,0.017485,0.9727,-61.824 > volume #6 level 0.1351 > view matrix models > #6,-0.2336,-0.97159,-0.038104,805.06,0.9444,-0.23604,0.2289,-253.75,-0.23139,0.017485,0.9727,-64.791 > view matrix models > #6,0.10892,0.98958,0.094129,-212.64,-0.95191,0.076552,0.29665,383.06,0.28636,-0.12191,0.95033,-214.48 > view matrix models > #6,0.10892,0.98958,0.094129,-209.61,-0.95191,0.076552,0.29665,355.76,0.28636,-0.12191,0.95033,-263.69 > view matrix models > #6,0.10892,0.98958,0.094129,-260.91,-0.95191,0.076552,0.29665,348.1,0.28636,-0.12191,0.95033,-283.66 > view matrix models > #6,0.10892,0.98958,0.094129,-279.85,-0.95191,0.076552,0.29665,385.97,0.28636,-0.12191,0.95033,-254.15 > view matrix models > #6,0.10892,0.98958,0.094129,-303.81,-0.95191,0.076552,0.29665,385.3,0.28636,-0.12191,0.95033,-275.96 > view matrix models > #6,-0.20776,0.9519,0.22521,-214.42,-0.91801,-0.26925,0.29116,517.03,0.33779,-0.14625,0.92979,-278.17 > view matrix models > #6,-0.20776,0.9519,0.22521,-227.67,-0.91801,-0.26925,0.29116,555.69,0.33779,-0.14625,0.92979,-287.86 > view matrix models > #6,0.87998,0.46224,-0.10942,-330.16,-0.44132,0.88078,0.17166,-67.794,0.17573,-0.10277,0.97906,-260.1 > view matrix models > #6,0.87998,0.46224,-0.10942,-330.25,-0.44132,0.88078,0.17166,-81.371,0.17573,-0.10277,0.97906,-259.34 > view matrix models > #6,0.87998,0.46224,-0.10942,-342.78,-0.44132,0.88078,0.17166,-92.159,0.17573,-0.10277,0.97906,-256.66 > fitmap #6 inMap #3 Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map 285A_B40_J2870_sharp.mrc using 90411 points correlation = 0.6254, correlation about mean = 0.2904, overlap = 2025 steps = 252, shift = 22, angle = 13.9 degrees Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to 285A_B40_J2870_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.90384918 0.30897439 -0.29595858 -226.36256515 -0.28396823 0.95062447 0.12520050 -163.18871223 0.32002922 -0.02911954 0.94696006 -341.01242842 Axis -0.17762163 -0.70899903 -0.68247413 Axis point 141.07727232 0.00000000 -577.43365398 Rotation angle (degrees) 25.74754494 Shift along axis 388.63968611 > hide #!2 models > select subtract #6 Nothing selected > show #!1 models > fitmap #6 inMap #3 Fit map 00_new_full_P59_J2530_resamples_sharp.mrc in map 285A_B40_J2870_sharp.mrc using 90411 points correlation = 0.6254, correlation about mean = 0.2905, overlap = 2025 steps = 80, shift = 0.0137, angle = 0.00252 degrees Position of 00_new_full_P59_J2530_resamples_sharp.mrc (#6) relative to 285A_B40_J2870_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.90384022 0.30896472 -0.29599606 -226.35067110 -0.28396400 0.95062852 0.12517933 -163.18151047 0.32005829 -0.02908989 0.94695115 -341.02759778 Axis -0.17755727 -0.70905222 -0.68243561 Axis point 141.17371119 0.00000000 -577.44999943 Rotation angle (degrees) 25.74845678 Shift along axis 388.62379806 > color zone #6 near #1 distance 9.88 > color zone #6 near #1 distance 9 [Repeated 2 time(s)] > color zone #6 near #1 distance 5 [Repeated 1 time(s)] > undo [Repeated 5 time(s)] > color zone #6 near #1 distance 5 > color zone #6 near #1 distance 6 > save /Users/tpottang/Desktop/grant_model/Full_map_no_STC.cxs ——— End of log from Mon May 4 16:03:19 2026 ——— > view name session-start opened ChimeraX session > open /Users/tpottang/Desktop/grant_model/AcCAST_no_STC_DNA.pdb Chain information for AcCAST_no_STC_DNA.pdb #7 --- Chain | Description 1 | No description available 2 | No description available 3 | No description available A | No description available B | No description available C | No description available D E F G H | No description available J K L M | No description available > hide > show cartoons > ui tool show Matchmaker Called attribute on invalid object: 2147487447 [Repeated 21 time(s)] > matchmaker #!7 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 C06_S2_AcCAST_recruitment_004.pdb, chain A (#1) with AcCAST_no_STC_DNA.pdb, chain A (#7), sequence alignment score = 3300.7 RMSD between 642 pruned atom pairs is 0.000 angstroms; (across all 642 pairs: 0.000) Called attribute on invalid object: 2147489148 [Repeated 21 time(s)] Called attribute on invalid object: 2147489087 [Repeated 21 time(s)] Called attribute on invalid object: 2147490786 [Repeated 21 time(s)] > save /Users/tpottang/Desktop/grant_model/AcCAST_no_STC_DNA.pdb models #7 > relModel #1 > hide #!1 models > hide #!6 models > show #!1 models > color /1 #decb6a > color /2 #6f6ade > color /3 #de726a > color /A #464561 > color /B #3ae080 > color /C #8a706e > color /D,F,H #df68ff > color /E,G,I #9f68d2 > hide #!1 models > color /1 #decb6a > color /2 #6f6ade > color /3 #de726a > color /A #464561 > color /B #3ae080 > color /C #8a706e > color /D,F,H #df68ff > color /E,G,I #9f68d2 > color /J,L #4ac4d8 > color /K,M #2d8a9e > color /1 #decb6a > color /2 #6f6ade > color /3 #de726a > color /A #464561 > color /B #3ae080 > color /C #8a706e > color /D,F,H #df68ff > color /E,G,I #9f68d2 > color /J,K #5dd4c4 > color /L,M #3a9b8e > color /1 #decb6a > color /2 #6f6ade > color /3 #de726a > color /A #464561 > color /B #3ae080 > color /C #8a706e > color /D,F,H #df68ff > color /E,G,I #9f68d2 > color /J,M #5dd4c4 > color /K,L #3a9b8e > color /J,M #3ad6d6 > color /K,L #2a9b9b > color /J,M #5dd4c4 > color /K,L #3a9b8e > show #!2 models Called attribute on invalid object: 2147503452 [Repeated 21 time(s)] > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!6 models > ui tool show ""Color Zone"" > color zone #6 near #7 distance 1.65 [Repeated 1 time(s)] > color zone #6 near #7 distance 15.88 > color zone #6 near #7 distance 10 > color zone #6 near #7 distance 9 > color zone #6 near #7 distance 8 > hide #!7 models Called attribute on invalid object: 2147520980 [Repeated 21 time(s)] > close #1-5 > rename #6 #1 No name or id option specified for renaming > rename #6 id #1 > rename #7 id #2 Called attribute on invalid object: 2147527433 [Repeated 21 time(s)] > save /Users/tpottang/Desktop/grant_model/Full_map_withSTC_noDNA.cxs ——— End of log from Mon May 4 16:32:32 2026 ——— > view name session-start opened ChimeraX session > rename #1 Full_J2530_resampled_sharp.mrc Called attribute on invalid object: 2147485600 [Repeated 21 time(s)] Called attribute on invalid object: 2147486384 [Repeated 21 time(s)] > save /Users/tpottang/Desktop/grant_model/Full_map_withSTC_noDNA.cxs > includeMaps true ——— End of log from Mon May 4 16:44:14 2026 ——— > view name session-start opened ChimeraX session > show #!2 models > hide #!1 models > show #!1 models > volume #1 level 0.1166 > volume style surface > transparency 0 > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > open 7SVW Summary of feedback from opening 7SVW fetched from pdb --- note | Fetching compressed mmCIF 7svw from http://files.rcsb.org/download/7svw.cif 7svw title: Strand-transfer complex of TnsB from ShCAST [more info...] Chain information for 7svw #3 --- Chain | Description 1 4 | STC_LE_For 2 5 | STC_LE_Rev1 3 6 | STC_LE_Rev2 A B C D | TnsB Non-standard residues in 7svw #3 --- MG — magnesium ion > show cartoons > hide cartoons > hide atoms > show cartoons > matchmaker #3 to #2/K 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 AcCAST_no_STC_DNA.pdb, chain K (#2) with 7svw, chain B (#3), sequence alignment score = 1042.1 RMSD between 206 pruned atom pairs is 1.035 angstroms; (across all 433 pairs: 15.651) > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 0.1191 > hide #!1 models > show #!1 models > ui tool show ""Map Filter"" > volume gaussian #1 sDev 1.74 Opened Full_J2530_resampled_sharp.mrc gaussian as #4, grid size 512,512,512, pixel 1.65, shown at step 1, values float32 > volume #4 level 0.06925 > volume #4 level 0.07347 > lighting soft > hide #!3 models > hide #!4 models > color #2/1 #ff6a6a > color #2/2 #fdff9a > color #2/3 #fdf09a > color #2/A #ffadff > color #2/B #98bfff > color #2/C #88f5ff > color #2/D-I #a9ff95 > color #2/J-M #ffadff > color #2/J-M #a294ff > color zone #4 near #2 distance 10 > show #!4 models > show #!3 models > hide #!2 models > hide #!4 models > color #3/2 #fdff9a > color #3/5 #fdff9a > color #3/4 #fdf09a > color #3/1 #fdf09a > color #3/A-D #a294ff > color zone #4 near #2,3 distance 4 > show #!4 models > color zone #4 near #2,3 distance 8 > hide #!4 models > show #!4 models > hide #!3 models > show #!3 models > show #!2 models > show #!1 models > hide #!3 models > hide #!4 models > combine #2/H > select add #5 39585 atoms, 41084 bonds, 2 pseudobonds, 4335 residues, 2 models selected > select subtract #5 Nothing selected > select add #5 39585 atoms, 41084 bonds, 2 pseudobonds, 4335 residues, 2 models selected > select #5/H 2121 atoms, 2153 bonds, 264 residues, 1 model selected > select ~sel & ##selected 37464 atoms, 38931 bonds, 2 pseudobonds, 4071 residues, 2 models selected > delete atoms (#!5 & sel) > delete bonds (#!5 & sel) > select add #5 2121 atoms, 2153 bonds, 264 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.80497,-0.53833,-0.24945,124.77,0.56963,0.81881,0.071159,-438.89,0.16595,-0.19938,0.96577,-218.24 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.80497,-0.53833,-0.24945,153.99,0.56963,0.81881,0.071159,-446.61,0.16595,-0.19938,0.96577,-196.92 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.14215,-0.98809,-0.058874,513.9,0.97572,0.14988,-0.15968,-246.25,0.16661,-0.034745,0.98541,-270.44 > view matrix models > #5,0.263,-0.8878,-0.37769,571.13,0.9529,0.17774,0.24575,-433.31,-0.15105,-0.42453,0.89272,54.262 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.263,-0.8878,-0.37769,566.68,0.9529,0.17774,0.24575,-423.08,-0.15105,-0.42453,0.89272,52.811 > fitmap # 5inMap #4 Missing or invalid ""atomsOrMap"" argument: invalid atom specifier > fitmap #5 inMap #4 Fit molecule copy of AcCAST_no_STC_DNA.pdb (#5) to map Full_J2530_resampled_sharp.mrc gaussian (#4) using 2121 atoms average map value = 0.0943, steps = 312 shifted from previous position = 22 rotated from previous position = 58.4 degrees atoms outside contour = 601, contour level = 0.07347 Position of copy of AcCAST_no_STC_DNA.pdb (#5) relative to Full_J2530_resampled_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.52065199 -0.74134327 0.42347568 304.13775764 0.59581209 0.67075407 0.44169778 -314.71906516 -0.61149771 0.02234110 0.79093073 341.81783214 Axis -0.24071502 0.59408530 0.76754084 Axis point 558.08074356 50.10809398 0.00000000 Rotation angle (degrees) 60.58259419 Shift along axis 2.17865005 > hide #!4 models > show #!4 models > hide #!4 models > ui mousemode right ""translate selected models"" > show #!4 models > view matrix models > #5,0.83567,-0.46943,0.28511,-143.93,0.342,0.85095,0.39865,-496.09,-0.42975,-0.23563,0.87166,89.846 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.62822,-0.7766,0.047163,169.85,0.65343,0.55955,0.50984,-560.83,-0.42233,-0.28947,0.85898,113.62 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.62822,-0.7766,0.047163,185.21,0.65343,0.55955,0.50984,-559.29,-0.42233,-0.28947,0.85898,124.57 > view matrix models > #5,0.62822,-0.7766,0.047163,184.15,0.65343,0.55955,0.50984,-569.54,-0.42233,-0.28947,0.85898,127.1 > fitmap #5 inMap #4 Fit molecule copy of AcCAST_no_STC_DNA.pdb (#5) to map Full_J2530_resampled_sharp.mrc gaussian (#4) using 2121 atoms average map value = 0.0943, steps = 288 shifted from previous position = 25 rotated from previous position = 25.5 degrees atoms outside contour = 602, contour level = 0.07347 Position of copy of AcCAST_no_STC_DNA.pdb (#5) relative to Full_J2530_resampled_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.52060272 -0.74144609 0.42335623 304.24467679 0.59675690 0.67060979 0.44064011 -314.58471788 -0.61061772 0.02324232 0.79158435 340.80420377 Axis -0.23962629 0.59360003 0.76825662 Axis point 557.31409928 50.70201870 0.00000000 Rotation angle (degrees) 60.56746204 Shift along axis 2.18256441 > close #5 > combine #2/H > hide #!4 models > hide #!2 models > select #5/G,H 4242 atoms, 4306 bonds, 528 residues, 1 model selected > select ~sel & ##selected 35343 atoms, 36778 bonds, 2 pseudobonds, 3807 residues, 2 models selected > delete atoms (#!5 & sel) > delete bonds (#!5 & sel) > show #!4 models > select add #5 4242 atoms, 4306 bonds, 528 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.79815,-0.58809,-0.13078,103.31,0.55674,0.63704,0.53312,-559,-0.23021,-0.49833,0.83587,120.15 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.79815,-0.58809,-0.13078,124.23,0.55674,0.63704,0.53312,-565.18,-0.23021,-0.49833,0.83587,138.43 > fitmap #5 inMap #4 Fit molecule copy of AcCAST_no_STC_DNA.pdb (#5) to map Full_J2530_resampled_sharp.mrc gaussian (#4) using 4242 atoms average map value = 0.0957, steps = 104 shifted from previous position = 6.87 rotated from previous position = 13.8 degrees atoms outside contour = 1097, contour level = 0.07347 Position of copy of AcCAST_no_STC_DNA.pdb (#5) relative to Full_J2530_resampled_sharp.mrc gaussian (#4) coordinates: Matrix rotation and translation 0.50679091 -0.86206353 0.00307127 570.84070822 0.84127553 0.49534152 0.21654620 -240.02366360 -0.18819791 -0.10715987 0.97626754 143.74420728 Axis -0.18557475 0.10965111 0.97649303 Axis point 509.70536604 372.31004138 0.00000000 Rotation angle (degrees) 60.71198716 Shift along axis 8.11273404 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > color zone #4 near #2,3,5 distance 8 > color zone #4 near #2,3,5 distance 15 > color zone #4 near #2,3,5 distance 20 > color zone #4 near #2,3,5 distance 15 > color zone #4 near #2,3,5 distance 10 > color #4 #fdff9a > color zone #4 near #2,3,5 distance 10 > hide #!5 models > color zone #4 near #2,3,5 distance 11 > color zone #4 near #2,3,5 distance 12 > save /Users/ekello73/Desktop/AcCAST_integration_complex.png supersample 300 > save /Users/ekello73/Desktop/AcCAST_for_R35.cxs ——— End of log from Mon May 4 17:36:01 2026 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 Pro OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,9 Model Number: MPHH3LL/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 Performance and 4 Efficiency) Memory: 16 GB System Firmware Version: 18000.101.7 OS Loader Version: 18000.101.7 Software: System Software Overview: System Version: macOS 26.4.1 (25E253) Kernel Version: Darwin 25.4.0 Time since boot: 4 days, 19 hours, 52 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: DELL U3423WE: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Web Services duplicate all ChimeraX