id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19428 Crash on Mac waking from sleep zrizvi@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-arm64-arm-64bit ChimeraX Version: 1.10.dev202503130118 (2025-03-13 01:18:56 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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""deploymentId"" : 240000011 } ], ""experiments"" : [ { ""treatmentId"" : ""28060e10-d4e5-4163-aa2b-d8bd088d5cbf"", ""experimentId"" : ""6685b283afc7c17197d69eec"", ""deploymentId"" : 400000012 }, { ""treatmentId"" : ""f18344bb-554f-48ae-8449-e108a8813a55"", ""experimentId"" : ""6685b5584477001000e8c6c9"", ""deploymentId"" : 400000009 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1200_final_volume_series > (5)/J1200_class_00_final_volume.mrc"" Opened J1200_class_00_final_volume.mrc as #1, grid size 192,192,192, pixel 2.28, shown at level 0.0447, step 1, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1200_final_volume_series > (5)/J1200_class_01_final_volume.mrc"" Opened J1200_class_01_final_volume.mrc as #2, grid size 192,192,192, pixel 2.28, shown at level 0.0435, step 1, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1200_final_volume_series > (5)/J1200_class_02_final_volume.mrc"" Opened J1200_class_02_final_volume.mrc as #3, grid size 192,192,192, pixel 2.28, shown at level 0.0428, step 1, values float32 > surface dust #1 size 22.8 > surface dust #2 size 22.8 > surface dust #3 size 22.8 > volume #1 level 0.06013 > volume #2 level 0.05754 > volume #3 level 0.08757 > tile 3 models tiled > volume #1 level 0.07212 > volume #2 level 0.07157 > volume #3 level 0.09006 > select add #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.41841,0.90777,0.029918,109.67,-0.89346,0.40544,0.19324,271.02,0.16328,-0.10758,0.9807,-9.3401 > view matrix models > #2,-0.94347,0.32584,0.060744,519.71,-0.29316,-0.90584,0.30578,392.28,0.15466,0.27069,0.95016,-80.322 > ui mousemode right translate > volume #2 level 0.09184 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.50371,-0.858,0.10053,680.2,0.84388,-0.46383,0.26967,56.593,-0.18475,0.22067,0.95769,2.3273 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.50371,-0.858,0.10053,598.04,0.84388,-0.46383,0.26967,61.367,-0.18475,0.22067,0.95769,-11.724 > ui mousemode right translate > select subtract #2 Nothing selected > select add #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.12379,0.97329,0.19335,162.7,-0.98238,0.092707,0.1623,354.17,0.14004,-0.21004,0.96761,-12.745 > ui mousemode right translate > select subtract #3 Nothing selected > graphics silhouettes true > lighting shadows true > lighting soft > set bgColor white > movie record > turn y 2 180 > wait 180 > movie encode /Users/zrizvi/Desktop/movie4.mp4 Movie saved to /Users/zrizvi/Desktop/movie4.mp4 > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo lab/with > snrnp ab initio.cxs"" includeMaps true > set bgColor white > ui mousemode right ""rotate selected models"" > ui mousemode right translate ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo > lab/alphafold and cryo structures-IMPO .cxs"" Opened cryosparc_P391_J1119_006_volume_map (1).mrc as #3, grid size 400,400,400, pixel 0.731, shown at level 0.0347, step 1, values float32 Opened 7os1 map 20 as #7, grid size 32,32,40, pixel 6.67, shown at step 1, values float32 Opened cryosparc_P391_J1144_010_volume_map (3).mrc as #8, grid size 500,500,500, pixel 0.731, shown at level 0.0185, step 1, values float32 Opened combination of 8d7z and 7os1 map 15 as #6, grid size 46,48,51, pixel 5, shown at level 0.0562, step 1, values float32 Opened snrnp_fullmask.mrc as #9, grid size 500,500,500, pixel 0.731, shown at level 0.0562, step 1, values float32 Opened combination map 15 as #11, grid size 39,43,47, pixel 5, shown at level 0.0543, step 1, values float32 Opened snrnp_halfmask.mrc as #12, grid size 500,500,500, pixel 0.731, shown at level 0.0543, step 1, values float32 Opened cryosparc_P391_J1237_008_volume_map (1).mrc as #13, grid size 500,500,500, pixel 0.731, shown at level 0.0201, step 1, values float32 Opened cryosparc_P391_J1238_010_volume_map (1).mrc as #14, grid size 500,500,500, pixel 0.731, shown at level 0.0267, step 1, values float32 Opened cryosparc_P391_J1238_010_volume_map (1).mrc z flip as #16, grid size 500,500,500, pixel 0.731, shown at level 0.0267, step 1, values float32 Opened emdb 13045 as #17, grid size 336,336,336, pixel 0.832, shown at level 0.3, step 2, values float32 Log from Mon Nov 24 16:39:31 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > set bgColor transparent Log from Tue Oct 28 15:23:27 2025UCSF ChimeraX version: 1.10.dev202503130118 (2025-03-13) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo > lab/alphafold and cryo structures .cxs"" Opened cryosparc_P391_J1119_006_volume_map (1).mrc as #3, grid size 400,400,400, pixel 0.731, shown at level 0.0347, step 1, values float32 Opened combination map 20 as #6, grid size 41,40,47, pixel 6.67, shown at step 1, values float32 Opened 7os1 map 20 as #7, grid size 32,32,40, pixel 6.67, shown at step 1, values float32 Log from Wed Oct 1 15:41:12 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 7OS1 7os1 title: Cryo-EM structure of Brr2 in complex with Fbp21 [more info...] Chain information for 7os1 #1 --- Chain | Description | UniProt B | U5 small nuclear ribonucleoprotein 200 kDa helicase | U520_HUMAN 395-2129 F | WW domain-binding protein 4 | WBP4_HUMAN 198-376 > open 8d7z 8d7z title: Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 [more info...] Chain information for 8d7z #2 --- Chain | Description | UniProt A | DNA damage-binding protein 1 | DDB1_HUMAN 1-1140 B | Protein cereblon | CRBN_HUMAN 1-442 C | DNA-binding protein Ikaros | IKZF1_HUMAN 112-196 Non-standard residues in 8d7z #2 --- QFC — Mezigdomide ZN — zinc ion > hide #!1 models Drag select of 7 residues > select up 197 atoms, 201 bonds, 25 residues, 1 model selected > delete sel Drag select of 91 residues Drag select of 1 residues > select clear Drag select of 64 residues > select up 438 atoms, 441 bonds, 82 residues, 1 model selected > select up 5201 atoms, 5288 bonds, 771 residues, 1 model selected > select down 438 atoms, 441 bonds, 82 residues, 1 model selected > select clear Drag select of 306 residues > delete sel > close #2.2 > show #!1 models > hide #!1 models > open > /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_01_final_volume.mrc Opened J1123_class_01_final_volume.mrc as #3, grid size 100,100,100, pixel 2.92, shown at level 0.0422, step 1, values float32 > open > /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_00_final_volume.mrc Opened J1123_class_00_final_volume.mrc as #4, grid size 100,100,100, pixel 2.92, shown at level 0.0558, step 1, values float32 > open > /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_02_final_volume.mrc Opened J1123_class_02_final_volume.mrc as #5, grid size 100,100,100, pixel 2.92, shown at level 0.0456, step 1, values float32 > open > /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_03_final_volume.mrc Opened J1123_class_03_final_volume.mrc as #6, grid size 100,100,100, pixel 2.92, shown at level 0.0546, step 1, values float32 > open > /Users/zrizvi/Downloads/cryosparc_P391_J1123_final_volume_series/J1123_class_04_final_volume.mrc Opened J1123_class_04_final_volume.mrc as #7, grid size 100,100,100, pixel 2.92, shown at level 0.0428, step 1, values float32 > hide #!2 models > tile 5 models tiled > surface dust #3 size 29.2 > surface dust #4 size 29.2 > surface dust #5 size 29.2 > surface dust #6 size 29.2 > surface dust #7 size 29.2 > volume #3 level 0.05418 > hide #!3 models > volume #4 level 0.05357 > volume #5 level 0.04557 > volume #6 level 0.04763 > volume #7 level 0.1039 > hide #!4 models > hide #!5 models > hide #!7 models > volume #6 level 0.2244 > volume #6 level 0.04238 > hide #!6 models > close #5 > close #7 > close #6 > close #4 > close #3 > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1119_006_volume_map (1).mrc"" Opened cryosparc_P391_J1119_006_volume_map (1).mrc as #3, grid size 400,400,400, pixel 0.731, shown at level 0.0159, step 2, values float32 > show #!2 models > hide #!2 models > volume #3 step 1 > volume #3 level 0.03852 > show #!2 models > select add #2 9342 atoms, 9526 bonds, 4 pseudobonds, 1211 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,6.7476,0,1,0,108.36,0,0,1,-22.1 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.9497,0.11121,-0.29275,275.19,0.093635,0.99289,0.073432,89.183,0.29884,0.042326,-0.95337,148.15 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.9497,0.11121,-0.29275,273.09,0.093635,0.99289,0.073432,-1.5292,0.29884,0.042326,-0.95337,187.79 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.9497,0.11121,-0.29275,287.69,0.093635,0.99289,0.073432,-2.0098,0.29884,0.042326,-0.95337,182.62 > fitmap #2 inMap #3 Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3) using 9342 atoms average map value = 0.04026, steps = 124 shifted from previous position = 3.47 rotated from previous position = 11.4 degrees atoms outside contour = 5239, contour level = 0.03852 Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc (#3) coordinates: Matrix rotation and translation -0.95787247 -0.03864922 -0.28458139 308.30186913 -0.08594556 0.98406832 0.15563705 9.61657894 0.27403228 0.17353895 -0.94593369 166.53499515 Axis 0.03191650 -0.99592723 -0.08432251 Axis point 142.42454596 0.00000000 105.04054862 Rotation angle (degrees) 163.71299329 Shift along axis -13.78014654 > ui mousemode right translate > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.99729,-0.0097977,-0.07291,286.65,-0.0036854,0.9965,-0.083501,23.711,0.073473,-0.083006,-0.99384,229.02 > ui mousemode right translate > volume #3 level 0.01737 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.99476,0.023476,-0.099488,285.14,0.001435,0.97638,0.21605,-7.2578,0.10221,0.21477,-0.9713,186.28 > fitmap #2 inMap #3 Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3) using 9342 atoms average map value = 0.04026, steps = 132 shifted from previous position = 1.79 rotated from previous position = 11.7 degrees atoms outside contour = 2693, contour level = 0.017368 Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc (#3) coordinates: Matrix rotation and translation -0.95791826 -0.03877668 -0.28440985 308.30181643 -0.08600393 0.98408520 0.15549804 9.63216933 0.27385383 0.17341478 -0.94600813 166.58249595 Axis 0.03196311 -0.99593166 -0.08425250 Axis point 142.42933789 0.00000000 105.04932851 Rotation angle (degrees) 163.72355585 Shift along axis -13.77368768 > fitmap #2 inMap #3 Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3) using 9342 atoms average map value = 0.04026, steps = 44 shifted from previous position = 0.0119 rotated from previous position = 0.0153 degrees atoms outside contour = 2693, contour level = 0.017368 Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc (#3) coordinates: Matrix rotation and translation -0.95788952 -0.03875907 -0.28450904 308.30854641 -0.08607154 0.98404269 0.15572950 9.61715719 0.27393311 0.17365979 -0.94594023 166.54413567 Axis 0.03197672 -0.99592072 -0.08437664 Axis point 142.43117293 0.00000000 105.03855146 Rotation angle (degrees) 163.71802371 Shift along axis -13.77166550 > fitmap #2 inMap #3 Fit molecule 8d7z (#2) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3) using 9342 atoms average map value = 0.04026, steps = 44 shifted from previous position = 0.0117 rotated from previous position = 0.00577 degrees atoms outside contour = 2695, contour level = 0.017368 Position of 8d7z (#2) relative to cryosparc_P391_J1119_006_volume_map (1).mrc (#3) coordinates: Matrix rotation and translation -0.95791248 -0.03880891 -0.28442493 308.30559032 -0.08610228 0.98404251 0.15571360 9.62558690 0.27384315 0.17364963 -0.94596815 166.54919827 Axis 0.03199694 -0.99592072 -0.08436887 Axis point 142.43342255 0.00000000 105.03337294 Rotation angle (degrees) 163.72324049 Shift along axis -13.77305300 > select subtract #2 Nothing selected > ui mousemode right translate > volume #3 level 0.03474 > show #!1 models > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.76275,-0.33241,0.55471,210.58,0.54034,0.14368,0.82909,-85.862,-0.3553,0.93212,0.070024,64.667 > view matrix models > #1,-0.64861,-0.3233,0.68904,173.27,0.67287,0.17957,0.71764,-92.767,-0.35574,0.9291,0.10107,60.513 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.64861,-0.3233,0.68904,174.58,0.67287,0.17957,0.71764,-102.41,-0.35574,0.9291,0.10107,105.2 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.42681,-0.15092,0.89166,90.223,0.70947,0.55553,0.43363,-115.28,-0.56079,0.81769,-0.13003,183.33 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.42681,-0.15092,0.89166,87.219,0.70947,0.55553,0.43363,-104.36,-0.56079,0.81769,-0.13003,189.02 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.42681,-0.15092,0.89166,77.841,0.70947,0.55553,0.43363,-107.39,-0.56079,0.81769,-0.13003,192.33 > ui mousemode right translate > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.4752,-0.17501,0.8623,92.242,0.66584,0.56913,0.48244,-110.29,-0.57519,0.80341,-0.15392,199.81 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.4752,-0.17501,0.8623,79.426,0.66584,0.56913,0.48244,-122.16,-0.57519,0.80341,-0.15392,200.01 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.4752,-0.17501,0.8623,75.342,0.66584,0.56913,0.48244,-111.02,-0.57519,0.80341,-0.15392,195.68 > ui mousemode right translate > select subtract #1 Nothing selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 2 atomic models, 1 maps. > hide #!2 models > fitmap #1 inMap #3 Fit molecule 7os1 (#1) to map cryosparc_P391_J1119_006_volume_map (1).mrc (#3) using 14054 atoms average map value = 0.008903, steps = 2000 shifted from previous position = 7.69 rotated from previous position = 22.3 degrees atoms outside contour = 12497, contour level = 0.034742 Position of 7os1 (#1) relative to cryosparc_P391_J1119_006_volume_map (1).mrc (#3) coordinates: Matrix rotation and translation -0.62261579 -0.16535463 0.76485778 112.64603008 0.37840411 0.79192285 0.47923744 -106.36242327 -0.68495249 0.58780613 -0.43049280 277.53222150 Axis 0.06994379 0.93401912 0.35030864 Axis point 130.50602909 0.00000000 130.11272413 Rotation angle (degrees) 129.09387669 Shift along axis 5.75628873 > show #!2 models > hide #!3 models > hide #!2 models > color #!1 bychain > rainbow #!1 > show #!2 models > open > /Users/zrizvi/Downloads/fold_2025_10_01_14_30/fold_2025_10_01_14_30_model_0.cif Chain information for fold_2025_10_01_14_30_model_0.cif #4 --- Chain | Description A | . B | . C | . > mmaker #4 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 8d7z, chain A (#2) with fold_2025_10_01_14_30_model_0.cif, chain A (#4), sequence alignment score = 5128.5 RMSD between 782 pruned atom pairs is 0.703 angstroms; (across all 826 pairs: 1.841) > hide #!1 models > hide #!2 models Drag select of 201 residues > select up 1708 atoms, 1736 bonds, 219 residues, 1 model selected > select up 26102 atoms, 26594 bonds, 3276 residues, 1 model selected > select down 1708 atoms, 1736 bonds, 219 residues, 1 model selected > select clear Drag select of 351 residues > delete sel Drag select of 19 residues > select up 408 atoms, 413 bonds, 53 residues, 1 model selected > delete sle Missing or invalid ""atoms"" argument: invalid atoms specifier > delete sel > color #!4 bychain > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > ui tool show ""Show Sequence Viewer"" [Repeated 1 time(s)] > sequence chain #4/C Alignment identifier is 4/C > select #4/C:35 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/C:35-43 65 atoms, 65 bonds, 9 residues, 1 model selected > select #4/C:93 4 atoms, 3 bonds, 1 residue, 1 model selected > select #4/C:93-289 1568 atoms, 1585 bonds, 197 residues, 1 model selected > select #4/C:2136 9 atoms, 8 bonds, 1 residue, 1 model selected > select #4/C:1897-2136 1894 atoms, 1927 bonds, 240 residues, 1 model selected > select clear > select #4/a 6475 atoms, 6591 bonds, 2 pseudobonds, 824 residues, 2 models selected > delete sel > select #4/b 3135 atoms, 3209 bonds, 389 residues, 1 model selected > select #4/b 3135 atoms, 3209 bonds, 389 residues, 1 model selected > delete sel > mmaker #4 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 7os1, chain B (#1) with fold_2025_10_01_14_30_model_0.cif, chain C (#4), sequence alignment score = 8690 RMSD between 1278 pruned atom pairs is 1.099 angstroms; (across all 1720 pairs: 2.058) > show #!1 models > select clear > select #4/C:35-155 971 atoms, 978 bonds, 1 pseudobond, 120 residues, 2 models selected > select clear Drag select of 435 residues > show #!2 models > hide #!4 models > select add #4 18614 atoms, 17227 bonds, 1 pseudobond, 2318 residues, 3 models selected > select subtract #4 1711 atoms, 217 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.62262,-0.16535,0.76486,115.18,0.3784,0.79192,0.47924,-109.02,-0.68495,0.58781,-0.43049,289.31 > ui mousemode right translate > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > select add #2 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected > combine sel Remapping chain ID 'B' in 8d7z #2 to 'D' > select subtract #2 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > select subtract #1 Nothing selected > hide #!1 models > hide #!2 models > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected > select subtract #5 Nothing selected > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected > select subtract #5 Nothing selected > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected > select clear > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected > molmap map sel 20 Missing or invalid ""atoms"" argument: invalid atoms specifier > molmap sel 20 Opened combination map 20 as #6, grid size 41,40,47, pixel 6.67, shown at level 0.0439, step 1, values float32 > volume #6 style image > select subtract #5 Nothing selected > hide #!5 models > color #6 #d6d6d6ff models > volume #6 level 0,0 level 0.2577,0.8 level 0.5978,1 > volume #6 level 0,0 level 0.2181,0.9176 level 0.5978,1 > hide #!6 models > show #!1 models > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > molmap sel 20 Opened 7os1 map 20 as #7, grid size 32,32,40, pixel 6.67, shown at level 0.042, step 1, values float32 > volume #7 style image maximumIntensityProjection true > volume #7 maximumIntensityProjection false > select subtract #1 Nothing selected > hide #!1 models > color #7 darkgrey models > volume #7 level 0,0 level 0.263,0.8 level 0.3416,1 > volume #7 level 0,0 level 0.2195,0.9559 level 0.3416,1 > volume #6 level 0,0 level 0.2137,0.9176 level 0.5978,1 > volume #7 level 0,0 level 0.2353,0.9853 level 0.3416,1 > show #!1 models > hide #!7 models Drag select of 248 residues > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B Alignment identifier is 1/B > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo > lab/alphafold and cryo structures .cxs"" includeMaps true ——— End of log from Wed Oct 1 15:41:12 2025 ——— > view name session-start opened ChimeraX session > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > select subtract #1 Nothing selected > hide #!1 models > show #!1 models > show #!2 models > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1144_010_volume_map (3).mrc"" Opened cryosparc_P391_J1144_010_volume_map (3).mrc as #8, grid size 500,500,500, pixel 0.731, shown at level 0.00574, step 2, values float32 > ~tile > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right translate > hide #!2 models > show #!2 models > hide #!1 models > select subtract #1 Nothing selected > select add #2 9342 atoms, 9526 bonds, 4 pseudobonds, 1211 residues, 2 models selected > select subtract #2 Nothing selected > select add #2 9342 atoms, 9526 bonds, 4 pseudobonds, 1211 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.62262,-0.16535,0.76486,81.218,0.3784,0.79192,0.47924,35.418,-0.68495,0.58781,-0.43049,356.36 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.52947,-0.46913,-0.70681,131.84,-0.0018161,0.83255,-0.55395,192.27,0.84832,0.29459,0.43996,100.47 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.52947,-0.46913,-0.70681,163.98,-0.0018161,0.83255,-0.55395,99.716,0.84832,0.29459,0.43996,60.267 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #2,0.52947,-0.46913,-0.70681,153.85,-0.0018161,0.83255,-0.55395,115.19,0.84832,0.29459,0.43996,14.033 > ui mousemode right translate > fitmap #2 inMap #8 Fit molecule 8d7z (#2) to map cryosparc_P391_J1144_010_volume_map (3).mrc (#8) using 9342 atoms average map value = 0.02757, steps = 604 shifted from previous position = 8.82 rotated from previous position = 35.9 degrees atoms outside contour = 2104, contour level = 0.0057392 Position of 8d7z (#2) relative to cryosparc_P391_J1144_010_volume_map (3).mrc (#8) coordinates: Matrix rotation and translation -0.94498524 -0.13700654 -0.29703890 358.50627603 -0.15015795 0.98842154 0.02180467 62.42466926 0.29061226 0.06520784 -0.95461639 195.04032059 Axis 0.07363977 -0.99703526 -0.02231328 Axis point 166.88663288 0.00000000 124.13833462 Rotation angle (degrees) 162.86049384 Shift along axis -40.19126691 > volume #8 step 1 > volume #8 level 0.0185 > select subtract #2 Nothing selected > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > show #!1 models > select subtract #1 Nothing selected > hide #!8 models > show #!8 models > hide #!2 models > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.78755,-0.062423,-0.61309,107.31,-0.49475,-0.65719,-0.56862,362.63,-0.36742,0.75113,-0.54845,240.32 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.78755,-0.062423,-0.61309,153.92,-0.49475,-0.65719,-0.56862,461.83,-0.36742,0.75113,-0.54845,237.4 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.82415,-0.46278,-0.32651,159.31,-0.55854,-0.56858,-0.60395,464.32,0.093848,0.68012,-0.72707,208.27 > ui mousemode right ""translate selected models"" > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.41398,-0.8695,-0.26942,262.77,-0.71075,-0.12384,-0.69246,439.9,0.56873,0.47815,-0.66927,159.44 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.41398,-0.8695,-0.26942,253.58,-0.71075,-0.12384,-0.69246,438.33,0.56873,0.47815,-0.66927,166.04 > ui mousemode right zoom > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.041288,0.98751,0.15205,8.4958,0.88517,0.10674,-0.45287,146.71,-0.46344,0.11589,-0.87852,391.04 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.10446,0.99297,0.055625,1.5307,0.78977,-0.048827,-0.61146,204.43,-0.60444,0.1078,-0.78932,398.76 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.10446,0.99297,0.055625,-5.241,0.78977,-0.048827,-0.61146,195.76,-0.60444,0.1078,-0.78932,394.65 > select subtract #1 Nothing selected > show #!2 models > hide #!8 models > show #!8 models > show #!4 models > hide #!2 models > hide #!1 models > hide #!8 models > hide #!4 models > show #!5 models > show #!8 models > hide #!8 models > hide #!5 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!8 models > show #!4 models > hide #!4 models > show #!5 models > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 3 models selected > view matrix models > #5,-0.62262,-0.16535,0.76486,84.031,0.3784,0.79192,0.47924,-27.256,-0.68495,0.58781,-0.43049,397.84 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.23307,-0.039665,-0.97165,220.35,-0.92806,0.2894,-0.23442,371.82,0.29049,0.95639,0.030638,112.82 > view matrix models > #5,-0.25444,0.32243,-0.91176,254.57,-0.59917,0.68749,0.41032,162.86,0.75912,0.6507,0.018267,67.658 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.25444,0.32243,-0.91176,288.43,-0.59917,0.68749,0.41032,124.14,0.75912,0.6507,0.018267,-7.2692 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.205,0.26166,-0.94314,291.85,-0.40157,0.85628,0.32485,86.787,0.89259,0.44533,-0.070459,7.112 > fitmap #5 inMap #8 Fit molecule combination (#5) to map cryosparc_P391_J1144_010_volume_map (3).mrc (#8) using 23396 atoms average map value = 0.01806, steps = 224 shifted from previous position = 3.14 rotated from previous position = 4.36 degrees atoms outside contour = 14277, contour level = 0.018501 Position of combination (#5) relative to cryosparc_P391_J1144_010_volume_map (3).mrc (#8) coordinates: Matrix rotation and translation -0.64099015 -0.20317454 0.74017007 166.33811566 0.23370661 0.86687742 0.44034618 -48.45752700 -0.73110385 0.45524020 -0.50817666 342.92513809 Axis 0.00970396 0.95858454 0.28464279 Axis point 163.39250809 0.00000000 138.21080909 Rotation angle (degrees) 129.87722940 Shift along axis 52.77467107 > ui mousemode right translate > select subtract #5 Nothing selected > show #!1 models > show #!2 models > hide #!8 models > hide #!5 models > show #!5 models > hide #!1 models > hide #!2 models > hide #!5 models > show #!1 models > show #!2 models > show #!8 models > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > fitmap #1 inMap #8 Fit molecule 7os1 (#1) to map cryosparc_P391_J1144_010_volume_map (3).mrc (#8) using 14054 atoms average map value = 0.01454, steps = 296 shifted from previous position = 19.8 rotated from previous position = 17 degrees atoms outside contour = 9546, contour level = 0.018501 Position of 7os1 (#1) relative to cryosparc_P391_J1144_010_volume_map (3).mrc (#8) coordinates: Matrix rotation and translation 0.71641153 -0.50828522 0.47791281 64.65020261 0.40829833 -0.25000248 -0.87794717 316.84320098 0.56572696 0.82410248 0.02842735 12.66524064 Axis 0.87954354 -0.04537845 0.47364961 Axis point 0.00000000 164.61195793 129.02594166 Rotation angle (degrees) 104.63034271 Shift along axis 48.48370216 > select subtract #1 Nothing selected > hide #!8 models > show #!8 models > close #5 > close #6 > select add #1 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > select add #2 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected > combine sel Remapping chain ID 'B' in 8d7z #2 to 'D' > select subtract #2 14054 atoms, 14346 bonds, 1 pseudobond, 1746 residues, 2 models selected > hide #!1 models > hide #!2 models > select subtract #1 Nothing selected > rename #5 ""combination of 8d7z and 7os1"" > hide #!8 models > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected > select subtract #5 Nothing selected > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 4 models selected > molmap map sel 15 Missing or invalid ""atoms"" argument: invalid atoms specifier > molmap sel 15 Opened combination of 8d7z and 7os1 map 15 as #6, grid size 46,48,51, pixel 5, shown at level 0.0562, step 1, values float32 > vop resample #6 ongrid #8 Opened combination of 8d7z and 7os1 map 15 resampled as #9, grid size 500,500,500, pixel 0.731, shown at step 1, values float32 > save snrnp fullmask.mrc #9 Cannot determine format for 'snrnp' > save snrnp_fullmask.mrc #9 > hide #!9 models > select subtract #5 Nothing selected > split #5 Split combination of 8d7z and 7os1 (#5) into 5 models Chain information for combination of 8d7z and 7os1 A #5.1 --- Chain | Description A | No description available Chain information for combination of 8d7z and 7os1 B #5.2 --- Chain | Description B | No description available Chain information for combination of 8d7z and 7os1 D #5.4 --- Chain | Description D | No description available Chain information for combination of 8d7z and 7os1 F #5.5 --- Chain | Description F | No description available > select add #5.1 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select add #5.2 20184 atoms, 20590 bonds, 2546 residues, 2 models selected > select add #5.3 20189 atoms, 20593 bonds, 2548 residues, 3 models selected > select add #5.4 23176 atoms, 23653 bonds, 4 pseudobonds, 2931 residues, 5 models selected > select subtract #5.4 20189 atoms, 20593 bonds, 2548 residues, 3 models selected > select subtract #5.3 20184 atoms, 20590 bonds, 2546 residues, 2 models selected > select subtract #5.1 13834 atoms, 14127 bonds, 1720 residues, 1 model selected > select add #5.4 16821 atoms, 17187 bonds, 4 pseudobonds, 2103 residues, 3 models selected > combine sel > select subtract #5.2 2987 atoms, 3060 bonds, 4 pseudobonds, 383 residues, 2 models selected > select add #5.3 2992 atoms, 3063 bonds, 4 pseudobonds, 385 residues, 3 models selected > select subtract #5.3 2987 atoms, 3060 bonds, 4 pseudobonds, 383 residues, 2 models selected > select subtract #5.4 Nothing selected > hide #!5 models > show #!5 models > hide #5.1 models > show #5.1 models > hide #!5 models > select add #10 16821 atoms, 17187 bonds, 4 pseudobonds, 2103 residues, 2 models selected > molmap sel 15 Opened combination map 15 as #11, grid size 39,43,47, pixel 5, shown at level 0.0543, step 1, values float32 > vop resample #11 ongrid #8 Opened combination map 15 resampled as #12, grid size 500,500,500, pixel 0.731, shown at step 1, values float32 > save snrnp_halfmask.mrc #12 > show #!9 models > select subtract #10 Nothing selected > hide #!10 models > hide #!12 models > hide #!9 models > show #!12 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo > lab/alphafold and cryo structures .cxs"" includeMaps true ——— End of log from Tue Oct 28 15:23:27 2025 ——— > view name session-start opened ChimeraX session > hide #!12 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > show #!8 models > show #!9 models > hide #!9 models > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!12 models > hide #!12 models > hide #!8 models > show #!10 models > hide #!10 models > show #!9 models > hide #!9 models > show #!6 models > hide #!6 models > hide #!5 models > show #!5 models > select add #5.1 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select add #5.2 20184 atoms, 20590 bonds, 2546 residues, 2 models selected > select subtract #5.2 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select add #5.3 6355 atoms, 6466 bonds, 828 residues, 2 models selected > select subtract #5.3 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select add #5.4 9337 atoms, 9523 bonds, 4 pseudobonds, 1209 residues, 3 models selected > select subtract #5.4 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select add #5.4 9337 atoms, 9523 bonds, 4 pseudobonds, 1209 residues, 3 models selected > select subtract #5.4 6350 atoms, 6463 bonds, 826 residues, 1 model selected > color #5.1 darkgrey > select add #5.4 9337 atoms, 9523 bonds, 4 pseudobonds, 1209 residues, 3 models selected > select subtract #5.1 2987 atoms, 3060 bonds, 4 pseudobonds, 383 residues, 2 models selected > color #5.4 #ff8ad8ff > select subtract #5.4 Nothing selected > set bgColor white > set bgColor #ffffff00 > graphics silhouettes true > lighting shadows true > lighting soft Cell requested for row 9 is out of bounds for table with 17 rows! Resizing table model. > hide #!5.4 models > hide #5.1 models > show #5.1 models > ui tool show ""Show Sequence Viewer"" > select add #5.1 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select subtract #5.1 Nothing selected > select add #5.1 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select subtract #5.1 Nothing selected > select add #5.2 13834 atoms, 14127 bonds, 1720 residues, 1 model selected > select subtract #5.2 Nothing selected > ui tool show ""Show Sequence Viewer"" > sequence chain #5.2/B Alignment identifier is 5.2/B > select #5.2/B:635 5 atoms, 4 bonds, 1 residue, 1 model selected > select #5.2/B:635-1014 3032 atoms, 3087 bonds, 380 residues, 1 model selected > select #5.2/B:406 11 atoms, 10 bonds, 1 residue, 1 model selected > select #5.2/B:406-456 417 atoms, 427 bonds, 51 residues, 1 model selected > select > #5.2/B:410-415,418-422,463-473,482-494,508-523,532-536,544-563,572-583,589-599,616-643,657-665,677-681,696-715,729-745,748-754,760-767,773-778,790-803,813-819,845-856,875-884,892-908,912-920,923-932,939-946,949-967,982-991,994-1005,1010-1025,1030-1042,1054-1069,1074-1102,1104-1121,1127-1132,1136-1146,1151-1179,1308-1312,1314-1322,1329-1342,1355-1371,1382-1402,1411-1422,1428-1438,1442-1447,1456-1461,1464-1482,1496-1505,1515-1519,1534-1554,1565-1583,1593-1604,1606-1614,1625-1638,1649-1651,1680-1689,1710-1719,1732-1742,1747-1756,1758-1764,1767-1772,1777-1799,1813-1822,1825-1836,1841-1856,1863-1875,1886-1900,1905-1934,1936-1952,1958-1963,1967-1978,1981-1987,1989-1997,2000-2014 7408 atoms, 7457 bonds, 917 residues, 1 model selected > select clear Drag select of 32 residues > select add #5.1 6620 atoms, 6463 bonds, 858 residues, 2 models selected > show #!5.4 models > select add #5.2 20184 atoms, 20590 bonds, 2546 residues, 2 models selected > select subtract #5.2 6350 atoms, 6463 bonds, 826 residues, 1 model selected > select subtract #5.1 Nothing selected > select add #5.2 13834 atoms, 14127 bonds, 1720 residues, 1 model selected > select subtract #5.2 Nothing selected > show #!4 models > hide #!5 models > mmaker #4 to #5.2 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 combination of 8d7z and 7os1 B, chain B (#5.2) with fold_2025_10_01_14_30_model_0.cif, chain C (#4), sequence alignment score = 8641.7 RMSD between 1278 pruned atom pairs is 1.099 angstroms; (across all 1720 pairs: 2.058) > show #!5 models > hide #5.1 models > show #5.1 models > hide #!5.4 models > hide #5.1 models > show #5.1 models > hide #!5 models > ui tool show ""Show Sequence Viewer"" > sequence chain #4/C Destroying pre-existing alignment with identifier 4/C Alignment identifier is 4/C Drag select of 24 residues > show #!5 models > show #!5.4 models > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1237_008_volume_map (1).mrc"" Opened cryosparc_P391_J1237_008_volume_map (1).mrc as #13, grid size 500,500,500, pixel 0.731, shown at level 0.00814, step 2, values float32 > open ""/Users/zrizvi/Downloads/cryosparc_P391_J1238_010_volume_map (1).mrc"" Opened cryosparc_P391_J1238_010_volume_map (1).mrc as #14, grid size 500,500,500, pixel 0.731, shown at level 0.00594, step 2, values float32 > volume #13 step 1 > volume #14 step 1 > volume #13 level 0.01572 > volume #14 level 0.02668 > hide #!14 models > select add #13 198 atoms, 24 residues, 3 models selected > select clear > hide #!13 models > hide #!4 models > show #!13 models > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > select add #13 2 models selected > view matrix models > #13,-0.40708,0.64359,0.64813,21.263,0.76667,-0.14495,0.62547,-26.92,0.49649,0.75152,-0.43442,11.391 > volume #13 level 0.02141 > select subtract #13 Nothing selected > ui mousemode right ""translate selected models"" > select add #13 2 models selected > view matrix models > #13,-0.40708,0.64359,0.64813,-31.181,0.76667,-0.14495,0.62547,-2.5381,0.49649,0.75152,-0.43442,181.75 > view matrix models > #13,-0.41621,-0.14575,0.89751,82.455,0.87303,0.21182,0.43925,-60.274,-0.25413,0.96638,0.039083,197.78 > view matrix models > #13,-0.41621,-0.14575,0.89751,82.358,0.87303,0.21182,0.43925,-117.18,-0.25413,0.96638,0.039083,81.064 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #13,-0.41621,-0.14575,0.89751,60.201,0.87303,0.21182,0.43925,-86.461,-0.25413,0.96638,0.039083,66.029 > ui mousemode right translate > show #!6 models > hide #!5 models > hide #!6 models > show #!5 models > select add #5 23396 atoms, 23872 bonds, 5 pseudobonds, 2957 residues, 10 models selected > combine sel > hide #!5 models > select subtract #5 2 models selected > fitmap #15 inMap #13 Fit molecule combination (#15) to map cryosparc_P391_J1237_008_volume_map (1).mrc (#13) using 23396 atoms average map value = 0.01863, steps = 160 shifted from previous position = 7.09 rotated from previous position = 8.2 degrees atoms outside contour = 14763, contour level = 0.021405 Position of combination (#15) relative to cryosparc_P391_J1237_008_volume_map (1).mrc (#13) coordinates: Matrix rotation and translation 0.90723292 -0.41836122 -0.04361567 126.05050383 -0.17516036 -0.28148482 -0.94344324 397.35514291 0.38242291 0.86356250 -0.32865259 87.87025567 Axis 0.96506864 -0.22753468 0.12988643 Axis point 0.00000000 183.98793041 181.54924620 Rotation angle (degrees) 110.57616654 Shift along axis 42.64846573 > select clear > volume #13 level 0.02899 > fitmap #15 inMap #13 Fit molecule combination (#15) to map cryosparc_P391_J1237_008_volume_map (1).mrc (#13) using 23396 atoms average map value = 0.01863, steps = 60 shifted from previous position = 0.0153 rotated from previous position = 0.0178 degrees atoms outside contour = 16676, contour level = 0.028988 Position of combination (#15) relative to cryosparc_P391_J1237_008_volume_map (1).mrc (#13) coordinates: Matrix rotation and translation 0.90720498 -0.41845121 -0.04333255 126.00945335 -0.17497904 -0.28165974 -0.94342468 397.34395821 0.38257216 0.86346186 -0.32874331 87.88937865 Axis 0.96506180 -0.22747658 0.13003898 Axis point 0.00000000 183.97407112 181.52330203 Rotation angle (degrees) 110.58515031 Shift along axis 42.64951029 > color #13 darkgrey models > graphics silhouettes false > lighting shadows true intensity 0.5 > lighting soft > graphics silhouettes true > color #13 #a9a9a996 models > show #!14 models > show #!12 models > hide #!12 models > hide #!13 models > show #!13 models > hide #!14 models > show #!14 models > hide #!15 models > select add #14 2 models selected > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #14,-0.27306,0.17368,0.94619,-4.7228,0.95941,0.12132,0.2546,-44.149,-0.070576,0.9773,-0.19976,61.475 > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.27306,0.17368,0.94619,-54.719,0.95941,0.12132,0.2546,-67.195,-0.070576,0.9773,-0.19976,66.438 > ui mousemode right translate > select subtract #14 Nothing selected > hide #!14 models > volume #13 level 0.01509 > show #!14 models > select add #14 2 models selected > vop flip #14 Opened cryosparc_P391_J1238_010_volume_map (1).mrc z flip as #16, grid size 500,500,500, pixel 0.731, shown at step 1, values float32 > select subtract #14 Nothing selected > select add #16 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.33284,-0.26172,0.90594,39.593,0.44786,0.80157,0.39611,-131.94,-0.82985,0.53757,-0.14958,257.12 > view matrix models > #16,-0.39732,-0.27458,0.87564,57.562,0.50217,0.73359,0.45789,-139.47,-0.76809,0.62165,-0.15358,232.98 > select subtract #16 Nothing selected > hide #!13 models > show #!13 models > show #!15 models > hide #!15 models > ui mousemode right translate > hide #!16 models > show #!16 models > ui mousemode right ""rotate selected models"" > select add #16 2 models selected > view matrix models > #16,0.10865,0.049021,-0.99287,251.16,0.71835,-0.69427,0.044327,154.05,-0.68715,-0.71804,-0.11064,451.25 > view matrix models > #16,0.10865,0.049021,-0.99287,246.14,0.71835,-0.69427,0.044327,164.76,-0.68715,-0.71804,-0.11064,485.85 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #16,-0.39734,-0.011001,-0.9176,324.24,0.71547,-0.62987,-0.30226,215.34,-0.57465,-0.77662,0.25815,412.8 > view matrix models > #16,-0.39734,-0.011001,-0.9176,332.46,0.71547,-0.62987,-0.30226,227.31,-0.57465,-0.77662,0.25815,406.72 > ui mousemode right translate > fitmap #16 inMap #13 Fit map cryosparc_P391_J1238_010_volume_map (1).mrc z flip in map cryosparc_P391_J1237_008_volume_map (1).mrc using 576297 points correlation = 0.6701, correlation about mean = 0.1934, overlap = 1306 steps = 156, shift = 16, angle = 7.69 degrees Position of cryosparc_P391_J1238_010_volume_map (1).mrc z flip (#16) relative to cryosparc_P391_J1237_008_volume_map (1).mrc (#13) coordinates: Matrix rotation and translation 0.94125601 -0.33768525 -0.00240969 72.29113111 -0.33024548 -0.92196215 0.20229613 368.64395968 -0.07053407 -0.18961666 -0.97932143 382.05012944 Axis -0.98505407 0.17122735 0.01869949 Axis point 0.00000000 210.08914741 172.90339257 Rotation angle (degrees) 168.52562910 Shift along axis -0.94460007 > select clear > hide #!13 models > show #!13 models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo > lab/alphafold and cryo structures-IMPO .cxs"" includeMaps true > show #!14 models > hide #!14 models > show #!15 models > hide #!13 models > color #16 #b2b2ffc6 models > color #16 #b2b2ffc7 models > show #!13 models > hide #!15 models > hide #!16 models > show #!16 models > show #!15 models > hide #!16 models > show #!16 models > hide #!16 models > volume #13 level 0.02014 > movie record > turn y 2 180 > wait 180 > movie encode /Users/zrizvi/Desktop/movie5.mp4 Movie saved to /Users/zrizvi/Desktop/movie5.mp4 > oepn EMD:13045 Unknown command: oepn EMD:13045 > oepn EMDB:13045 Unknown command: oepn EMDB:13045 > oepn EMDB13045 Unknown command: oepn EMDB13045 > oepn EMDB-13045 Unknown command: oepn EMDB-13045 > oepn EMDB:13045 Unknown command: oepn EMDB:13045 > open EMDB:13045 Opened emdb 13045 as #17, grid size 336,336,336, pixel 0.832, shown at level 0.3, step 2, values float32, fit PDB 7os1 > hide #!15 models > hide #!13 models > show #!13 models > show #!15 models > hide #!13 models > select add #17 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #17,1,0,0,9.4039,0,1,0,54.781,0,0,1,92.25 > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.20156,0.90274,-0.38004,115.82,0.94344,0.074664,-0.32302,91.706,-0.26322,-0.42366,-0.86673,461.35 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.20156,0.90274,-0.38004,114.96,0.94344,0.074664,-0.32302,110.81,-0.26322,-0.42366,-0.86673,428.1 > ui mousemode right translate > ui mousemode right ""rotate selected models"" > view matrix models > #17,-0.22962,0.94469,-0.23416,91.821,0.85556,0.081231,-0.51128,150.18,-0.46399,-0.31774,-0.8269,436.59 > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.22962,0.94469,-0.23416,84.856,0.85556,0.081231,-0.51128,153.26,-0.46399,-0.31774,-0.8269,449.23 > ui mousemode right translate > select add #5.1 6350 atoms, 6463 bonds, 826 residues, 3 models selected > select subtract #5.1 2 models selected > select subtract #17 Nothing selected > hide #!15 models > show #!5 models > hide #!5.5 models > hide #!5.4 models > hide #5.1 models > hide #5.2 models > show #5.2 models > hide #5.3 models > show #5.3 models > hide #5.3 models > show #!15 models > mmaker #5.2 to #15 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 combination, chain B (#15) with combination of 8d7z and 7os1 B, chain B (#5.2), sequence alignment score = 8944.7 RMSD between 1720 pruned atom pairs is 0.000 angstroms; (across all 1720 pairs: 0.000) > hide #!15 models > select add #17 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #17,-0.22962,0.94469,-0.23416,84.537,0.85556,0.081231,-0.51128,152.65,-0.46399,-0.31774,-0.8269,448.64 > ui mousemode right ""rotate selected models"" > view matrix models > #17,0.16974,0.98005,-0.10336,3.9864,0.81406,-0.19855,-0.54579,200.75,-0.55542,0.0085042,-0.83152,418.96 > ui mousemode right ""translate selected models"" > view matrix models > #17,0.16974,0.98005,-0.10336,0.11539,0.81406,-0.19855,-0.54579,200.21,-0.55542,0.0085042,-0.83152,421.5 Must specify one map, got 0 > fitmap #5.2 inMap #17 Fit molecule combination of 8d7z and 7os1 B (#5.2) to map emdb 13045 (#17) using 13834 atoms average map value = 0.6118, steps = 160 shifted from previous position = 9.89 rotated from previous position = 15.8 degrees atoms outside contour = 2903, contour level = 0.3 Position of combination of 8d7z and 7os1 B (#5.2) relative to emdb 13045 (#17) coordinates: Matrix rotation and translation 0.99999996 -0.00006778 0.00028701 -0.02237487 0.00006789 0.99999993 -0.00037564 0.02489738 -0.00028698 0.00037566 0.99999989 -0.01357518 Axis 0.78657896 0.60093128 0.14203919 Axis point 0.00000000 34.43194076 73.57719080 Rotation angle (degrees) 0.02736328 Shift along axis -0.00456619 > select clear > show #!15 models > mmaker #15 to #5.2 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 combination of 8d7z and 7os1 B, chain B (#5.2) with combination, chain B (#15), sequence alignment score = 8944.7 RMSD between 1720 pruned atom pairs is 0.000 angstroms; (across all 1720 pairs: 0.000) > hide #5.2 models > color #17 #ffb2b2a3 models > show #!14 models > hide #!14 models > show #!13 models > hide #!15 models > color #17 #ffb2b2ff models > save ""/Users/zrizvi/Scripps Research Dropbox/Zeba Rizvi/SNRNP-Woo > lab/alphafold and cryo structures-IMPO .cxs"" includeMaps true ——— End of log from Mon Nov 24 16:39:31 2025 ——— > view name session-start opened ChimeraX session OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac16,1 Model Number: MW2V3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 3 days, 20 hours, 29 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.2.0 autocommand: 2.2.2 babel: 2.17.0 backports.tarfile: 1.2.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.2.0 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.1 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.19.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.1 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.13 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.dev202503130118 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 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.5.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.7 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.15 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.7 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-ProfileGrids: 1.0.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 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: 1.44 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 coverage: 7.6.12 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.13 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.17.0 fonttools: 4.56.0 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 inflect: 7.3.1 iniconfig: 2.0.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jaraco.collections: 5.1.0 jaraco.context: 5.3.0 jaraco.functools: 4.0.1 jaraco.text: 3.12.1 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 more-itertools: 10.3.0 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.6 platformdirs: 4.2.2 pluggy: 1.5.0 prompt_toolkit: 3.0.50 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.1 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.0.0 python-dateutil: 2.9.0.post0 pytz: 2025.1 pyzmq: 26.3.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 Send2Trash: 1.8.3 SEQCROW: 1.8.21 setuptools: 75.8.2 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2025.1 urllib3: 2.3.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel: 0.43.0 wheel-filename: 1.4.2 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect closed normal Window Toolkit duplicate all ChimeraX