id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18316 Crash on Mac waking from sleep nnmanh542@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.10.1 (2025-07-24 20:15:27 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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""rollouts"" : [ { ""rolloutId"" : ""645197bf528fbf3c3af54105"", ""factorPackIds"" : { ""SIRI_VALUE_INFERENCE_PERVASIVE_ENTITY_RESOLUTION"" : ""663e65b4a1526e1ca0e288a1"" }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""6434420a89ec2e0a7a38bf5a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000011 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/annguyen/Downloads/cryosparc_P12_J230_001_volume_map (1).mrc"" Opened cryosparc_P12_J230_001_volume_map (1).mrc as #1, grid size 100,100,100, pixel 5.73, shown at level 1.38, step 1, values float32 > open ""/Users/annguyen/Downloads/cryosparc_P12_J279_001_volume_map (1).mrc"" Opened cryosparc_P12_J279_001_volume_map (1).mrc as #2, grid size 100,100,100, pixel 5.73, shown at level 1.1, step 1, values float32 > volume #1 level 0.1117 > open 7old fromDatabase pdb format mmcif 7old title: Thermophilic eukaryotic 80S ribosome at pe/E (TI)-POST state [more info...] Chain information for 7old #3 --- Chain | Description | UniProt 1 | 26S rRNA | 2 | 18S rRNA | 3 | 5S rRNA | 4 | 5.8S rRNA | 5 | pe/E tRNA | A | Putative guanine nucleotide-binding protein | G0S9U0_CHATD 1-316 B | HABP4_PAI-RBP1 domain-containing protein | G0S428_CHATD 1-302 C | Elongation factor 2 | G0S5T7_CHATD 1-845 LA | 60S ribosomal protein L2-like protein | G0S4P8_CHATD 1-254 LB | 60S ribosomal protein L3-like protein | G0RXW1_CHATD 1-392 LC | 60S ribosomal protein L4-like protein | G0SFC3_CHATD 1-365 LD | 60S ribosomal protein l5-like protein | G0SEG2_CHATD 1-304 LE | 60S ribosomal protein L6 | G0S0D6_CHATD 1-200 LF | 60S ribosomal protein l7-like protein | G0SFL0_CHATD 1-249 LG | 60S ribosomal protein L8 | G0SAJ9_CHATD 1-262 LH | 60S ribosomal protein l9-like protein | G0S0E5_CHATD 1-229 LI | 60S ribosomal protein L10-like protein | G0SEI1_CHATD 1-219 LJ | Putative ribosomal protein | G0SHQ2_CHATD 1-173 LK | 60S ribosomal protein L12-like protein | G0SGH8_CHATD 1-165 LL | 60S ribosomal protein L13 | G0S992_CHATD 1-213 LM | 60S ribosomal protein L14-like protein | G0S1R0_CHATD 1-142 LN | Ribosomal protein L15 | G0RZ88_CHATD 1-203 LO | 60S ribosomal protein L16-like protein | G0SH61_CHATD 1-204 LP | 60S ribosomal protein l17-like protein | G0SGY1_CHATD 1-187 LQ | Ribosomal protein L18-like protein | G0S9B5_CHATD 1-213 LR | Ribosomal protein L19 | G0S9T3_CHATD 1-192 LS | 60S ribosomal protein L20 | G0SCE2_CHATD 1-174 LT | 60S ribosomal protein l21-like protein | G0S0Z3_CHATD 1-160 LU | 60S ribosomal protein L22-like protein | G0SDS8_CHATD 1-127 LV | 60S ribosomal protein l23-like protein | G0SI44_CHATD 1-139 LW | 60S ribosomal protein L24-like protein | G0S1P9_CHATD 1-205 LX | 60S ribosomal protein L25-like protein | G0S507_CHATD 1-156 LY | 60S ribosomal protein L26-like protein | G0RYN9_CHATD 1-138 LZ | 60S ribosomal protein L27 | G0RZE9_CHATD 1-135 La | 60S ribosomal protein L28-like protein | Lb | 60S ribosomal protein L29 | Q2H9W4_CHAGB 1-65 Lc | 60S ribosomal protein l30-like protein | G0SEI0_CHATD 1-108 Ld | Putative 60S ribosomal protein | G0SD68_CHATD 4-123 Le | 60S ribosomal protein L32-like protein | G0S6V4_CHATD 1-131 Lf | 60S ribosomal protein l33-like protein | G0SCL3_CHATD 1-109 Lg | Ribosomal protein l34-like protein | G0SFN0_CHATD 1-119 Lh | Dolichyl-diphosphooligosaccharide--protein glycotransferase | G0S0D7_CHATD 1-126 Li | 60S ribosomal protein L36 | G0SBN1_CHATD 1-110 Lj | Ribosomal protein L37 | G0S101_CHATD 1-95 Lk | 60S ribosomal protein L38-like protein | G0SG89_CHATD 1-81 Ll | Ribosomal protein eL39 | Q2H9R2_CHAGB 1-51 Lm | Ubiquitin | G0S8G4_CHATD 3-128 Ln Lr | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 Lo | 60S ribosomal protein L44-like protein | G0SBZ6_CHATD 1-106 Lp | 60S ribosomal protein L43-like protein | G0S6B0_CHATD 1-92 Lq | Putative 60S ribosomal protein | G0SHJ6_CHATD 1-147 Ls | 60S acidic ribosomal protein P0 | G0SGP3_CHATD 1-312 SA | 40S ribosomal protein S0 | G0RYF9_CHATD 1-285 SB | 40S ribosomal protein S1 | G0S7T8_CHATD 1-255 SC | 40S ribosomal protein S2-like protein | G0SAV4_CHATD 1-263 SD | 40S ribosomal protein S3-like protein | G0S6I7_CHATD 1-254 SE | 40S ribosomal protein S4 | G0S1A6_CHATD 1-264 SF | 40S ribosomal protein s5-like protein | G0S1Z0_CHATD 1-212 SG | 40S ribosomal protein S6 | G0RY43_CHATD 1-239 SH | 40S ribosomal protein S7 | G0S8C4_CHATD 1-203 SI | 40S ribosomal protein S8 | G0RY45_CHATD 1-202 SJ | 40S ribosomal protein s9-like protein | G0S0Z4_CHATD 1-190 SK | 40S ribosomal protein s10-like protein | G0RZD8_CHATD 1-159 SL | 40S ribosomal protein S11-like protein | G0SF00_CHATD 1-161 SM | 40S ribosomal protein S12 | G0SHH9_CHATD 1-144 SN | 40S ribosomal protein S13-like protein | G0RZM9_CHATD 1-151 SO | 40S ribosomal protein S14-like protein | G0SFL1_CHATD 1-150 SP | 40S ribosomal protein s15-like protein | G0S084_CHATD 1-153 SQ | 40S ribosomal protein S16-like protein | G0SBR7_CHATD 1-143 SR | 40S ribosomal protein S17-like protein | G0S871_CHATD 1-143 SS | Putative ribosomal protein | G0S6J7_CHATD 1-156 ST | 40S ribosomal protein S19-like protein | G0SFK8_CHATD 1-153 SU | 40S ribosomal protein S20-like protein | G0S379_CHATD 1-116 SV | 40S ribosomal protein S21-like protein | G0SI21_CHATD 1-98 SW | 40S ribosomal protein S22-like protein | G0SHI0_CHATD 1-130 SX | 40S ribosomal protein s23-like protein | G0RY17_CHATD 1-145 SY | 40S ribosomal protein S24 | RS24_CHATD 1-136 SZ | 40S ribosomal protein S25 | G0S1Y9_CHATD 1-99 Sa | 40S ribosomal protein S26 | G0S2X4_CHATD 1-119 Sb | Ribosomal protein s27-like protein | G0S1S4_CHATD 1-82 Sc | 40S ribosomal protein S28-like protein | G0S9M9_CHATD 1-68 Sd | Ribosomal protein uS14 | Q2HB68_CHAGB 1-56 Se | 40S ribosomal protein S30 | Q2H4C5_CHAGB 1-62 Sf | 40S ribosomal protein S27a-like protein | G0S2X5_CHATD 1-154 Non-standard residues in 7old #3 --- B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid GDP — guanosine-5'-diphosphate MG — magnesium ion ZN — zinc ion > hide atoms > show cartoons Enter a PDB ID in the entry field Mismatch between Cocoa 'v' and Carbon '\x0' for virtual key 9 with QFlags(NoModifier) Mismatch between Cocoa 'V' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier) Mismatch between Cocoa 'v' and Carbon '\x0' for virtual key 9 with QFlags(ControlModifier) Mismatch between Cocoa 'v' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\u221a' and Carbon '\x0' for virtual key 9 with QFlags(AltModifier) Mismatch between Cocoa '\u25ca' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\u221a' and Carbon '\x0' for virtual key 9 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\u25ca' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x16' and Carbon '\x0' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > open 8bf9 fromDatabase pdb format mmcif Summary of feedback from opening 8bf9 fetched from pdb --- note | Fetching compressed mmCIF 8bf9 from http://files.rcsb.org/download/8bf9.cif 8bf9 title: Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. [more info...] Chain information for 8bf9 #4 --- Chain | Description | UniProt 5 | RNA (1766) | 8 | RNA (156-MER) | A | Translocon-associated protein subunit alpha | B | Translocon-associated protein subunit beta | W5P572_SHEEP 1-186 C | Sec61a | D | Translocon-associated protein subunit delta | W5P940_SHEEP 1-173 G | Translocon-associated protein subunit gamma | W5NYA9_SHEEP 1-185 P | Large ribosomal subunit protein uL22 | W5Q9T9_SHEEP 1-184 R | Ribosomal protein L19 | W5PLN0_SHEEP 1-196 U | RL22 protein (Fragment) | A0A6P7EJM7_SHEEP 1-128 X | Ribosomal protein L23/L25 N-terminal domain-containing protein | A0A6P3CX48_SHEEP 1-156 Y | RL26 protein (Fragment) | A0A7K9BN74_9PICI 1-134 b | Sec61b | d | Large ribosomal subunit protein eL31 | W5PUU0_SHEEP 1-125 g | Protein transport protein Sec61 subunit gamma | A0A836CVU8_SHEEP -5-75 h | Large ribosomal subunit protein uL29 | A0A6P3TAC5_SHEEP 1-123 j | Ribosomal protein L37 | W5P472_SHEEP 1-97 k | Large ribosomal subunit protein eL38 | l | 60S ribosomal protein L39 | > show cartoons > hide atoms > ui mousemode right ""translate selected models"" > select add #4 55482 atoms, 60473 bonds, 1730 pseudobonds, 3914 residues, 3 models selected > view matrix models #4,1,0,0,-430.48,0,1,0,148.55,0,0,1,-122.58 > select subtract #4 Nothing selected > select add #3 214209 atoms, 229425 bonds, 4810 pseudobonds, 17997 residues, 4 models selected > view matrix models #3,1,0,0,129.21,0,1,0,-201.06,0,0,1,-11.791 > view matrix models #3,1,0,0,-108.26,0,1,0,-180.88,0,0,1,-268.29 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.14613,-0.15801,0.97656,-97.466,-0.85875,-0.51032,0.045932,418.99,0.49111,-0.84534,-0.21027,133.56 > view matrix models > #3,0.28427,-0.25084,0.92535,-100.18,-0.87968,-0.45205,0.1477,382.48,0.38125,-0.856,-0.34917,206.26 > ui mousemode right ""move picked models"" > view matrix models > #3,0.28427,-0.25084,0.92535,-153.65,-0.87968,-0.45205,0.1477,505.59,0.38125,-0.856,-0.34917,500.54 > view matrix models > #3,0.28427,-0.25084,0.92535,-56.372,-0.87968,-0.45205,0.1477,606.9,0.38125,-0.856,-0.34917,594.17 > view matrix models > #3,0.28427,-0.25084,0.92535,-12.885,-0.87968,-0.45205,0.1477,596.31,0.38125,-0.856,-0.34917,498.5 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit molecule 7old (#3) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 214209 atoms average map value = 0.7378, steps = 196 shifted from previous position = 32.4 rotated from previous position = 36.9 degrees atoms outside contour = 55126, contour level = 0.11166 Position of 7old (#3) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation 0.47481197 0.34239392 0.81075273 -156.74890563 -0.67940501 -0.44297390 0.58496405 421.78272722 0.55943044 -0.82857741 0.02229483 347.78131290 Axis -0.80214761 0.14261879 -0.57984402 Axis point 0.00000000 323.22435899 72.43629804 Rotation angle (degrees) 118.22488875 Shift along axis -15.76901128 > color #1 #b2b2b2b7 models > view matrix models #1,1,0,0,-222.47,0,1,0,-46.584,0,0,1,-150.86 > view matrix models > #3,0.47481,0.34239,0.81075,-166.98,-0.67941,-0.44297,0.58496,433.9,0.55943,-0.82858,0.022295,352.6 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.47503,-0.030968,-0.87943,666.16,0.38634,0.89057,-0.24004,34.685,0.79063,-0.45379,-0.41108,316.06 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.47503,-0.030968,-0.87943,616.34,0.38634,0.89057,-0.24004,99.968,0.79063,-0.45379,-0.41108,177.74 > view matrix models > #3,-0.47503,-0.030968,-0.87943,427.62,0.38634,0.89057,-0.24004,-4.4885,0.79063,-0.45379,-0.41108,211.25 > fitmap #3 inMap #1 Fit molecule 7old (#3) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 214209 atoms average map value = 1.244, steps = 96 shifted from previous position = 67.4 rotated from previous position = 15.6 degrees atoms outside contour = 2514, contour level = 0.11166 Position of 7old (#3) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.61311858 -0.19110802 -0.76652680 707.61475725 0.35557936 0.79969249 -0.48379256 107.85702207 0.70544235 -0.56918332 -0.42235226 359.80518554 Axis -0.05430150 -0.93605132 0.34764821 Axis point 255.98611489 0.00000000 383.42085790 Rotation angle (degrees) 128.16215440 Shift along axis -14.29862127 > view matrix models > #3,-0.61312,-0.19111,-0.76653,515.58,0.35558,0.79969,-0.48379,58.407,0.70544,-0.56918,-0.42235,192.28 > undo > select subtract #3 Nothing selected > select add #3 214209 atoms, 229425 bonds, 4810 pseudobonds, 17997 residues, 4 models selected > select subtract #3 Nothing selected > select add #4 55482 atoms, 60473 bonds, 1730 pseudobonds, 3914 residues, 3 models selected > view matrix models #4,1,0,0,-330.9,0,1,0,125.38,0,0,1,-170.27 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.63642,0.68218,-0.35999,43.252,0.69404,0.71009,0.11864,-20.981,0.33656,-0.17434,-0.92538,476.53 > view matrix models > #4,0.65578,0.02597,-0.75451,35.734,0.57232,0.63467,0.51928,-94.691,0.49234,-0.77235,0.40134,194.25 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.65578,0.02597,-0.75451,1.5827,0.57232,0.63467,0.51928,-312.88,0.49234,-0.77235,0.40134,108.54 > view matrix models > #4,0.65578,0.02597,-0.75451,117.69,0.57232,0.63467,0.51928,-295.2,0.49234,-0.77235,0.40134,94.404 > view matrix models > #4,0.65578,0.02597,-0.75451,131.59,0.57232,0.63467,0.51928,-319.36,0.49234,-0.77235,0.40134,74.668 > fitmap #4 inMap #1 Fit molecule 8bf9 (#4) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 55482 atoms average map value = 1.003, steps = 160 shifted from previous position = 33.6 rotated from previous position = 27.7 degrees atoms outside contour = 7113, contour level = 0.11166 Position of 8bf9 (#4) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation 0.61337148 0.21051822 -0.76122106 293.92775943 0.20676955 0.88740241 0.41202344 -240.94324241 0.76224785 -0.41012077 0.50077857 -15.43390777 Axis -0.47491119 -0.88003106 -0.00216541 Axis point 227.02612225 0.00000000 316.03855197 Rotation angle (degrees) 59.94863156 Shift along axis 72.48137520 > undo > toolshed show > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.98305,0.16823,-0.072841,337.76,0.16816,0.98573,0.0071961,-125.24,0.073012,-0.0051744,-0.99732,418.27 > view matrix models > #4,-0.791,-0.29959,0.53344,248.01,-0.33169,0.94264,0.037568,39.409,-0.5141,-0.14722,-0.845,606.66 > view matrix models > #4,-0.93733,0.015697,0.3481,234.54,-0.024501,0.99354,-0.11078,-25.446,-0.34759,-0.11236,-0.93089,570.55 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.93733,0.015697,0.3481,207.6,-0.024501,0.99354,-0.11078,-28.23,-0.34759,-0.11236,-0.93089,606.33 > view matrix models > #4,-0.93733,0.015697,0.3481,211.07,-0.024501,0.99354,-0.11078,-20.698,-0.34759,-0.11236,-0.93089,612.89 > fitmap #4 inMap #1 Fit molecule 8bf9 (#4) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 55482 atoms average map value = 1.274, steps = 104 shifted from previous position = 40.8 rotated from previous position = 23.5 degrees atoms outside contour = 5888, contour level = 0.11166 Position of 8bf9 (#4) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.99984326 0.01309177 0.01191864 607.92104186 0.01430173 0.99406427 0.10785026 -80.76132776 -0.01043594 0.10800381 -0.99409570 576.19775515 Axis 0.00685881 0.99851492 0.05404546 Axis point 305.85968810 0.00000000 288.57980617 Rotation angle (degrees) 179.35862267 Shift along axis -45.33090597 > volume #1 level 0.1577 Enter a PDB ID in the entry field > open 3j7r fromDatabase pdb format mmcif Summary of feedback from opening 3j7r fetched from pdb --- warnings | Atom OP1 has no neighbors to form bonds with according to residue template for U /S4:15 Atom OP2 has no neighbors to form bonds with according to residue template for U /S4:15 3j7r title: Structure of the translating mammalian ribosome-Sec61 complex [more info...] Chain information for 3j7r #5 --- Chain | Description | UniProt 1 | Sec61 alpha subunit | A0A4X1TV07_PIG 25-466 2 | Sec61 gamma subunit | A0A480WFL1_PIG 1-68 3 | Sec61 beta subunit | 5 | 28S ribosomal RNA | 7 | 5S ribosomal RNA | 8 | 5.8S ribosomal RNA | A | Ribosomal protein uL2 | A0A480Q387_PIG 1-257 B | Ribosomal protein uL3 | A0A480L253_PIG 2-395 C | Ribosomal protein uL4 | A0A287AE76_PIG 2-368 D | Ribosomal protein uL18 | A0A287ASD0_PIG 1-297 E | Ribosomal protein eL6 | RL6_PIG 38-284 F | Ribosomal protein uL30 | A0A480W0U3_PIG 26-250 G | Ribosomal protein eL8 | A0A4X1W808_PIG 1-266 H | Ribosomal protein uL6 | I3LP78_PIG 1-192 I | Ribosomal protein uL16 | RL10_PIG 2-214 J | Ribosomal protein uL5 | RL11_PIG 1-178 L | Ribosomal protein eL13 | A0A4X1TBV3_PIG 1-211 M | Ribosomal protein eL14 | RL14_PIG 1-213 N | Ribosomal protein eL15 | A0A286ZL65_PIG 1-204 O | Ribosomal protein uL13 | A0A480L469_PIG 3-203 P | Ribosomal protein uL22 | A0A287B386_PIG 2-154 Q | Ribosomal protein eL18 | A0A4X1W0N5_PIG 1-188 R | Ribosomal protein eL19 | A0A480VXS3_PIG 2-196 S | Ribosomal protein eL20 | A0A287APR1_PIG -47-176 S2 | 18S ribosomal RNA | S4 | Messenger RNA | S5 | A/P tRNA | S6 | P/E tRNA | SA | Ribosomal protein uS2 | RSSA_PIG 1-295 SB | Ribosomal protein eS1 | B6V8C8_PIG 1-264 SC | Ribosomal protein uS5 | I3LJ87_PIG 59-276 SD | Ribosomal protein uS3 | RS3_PIG 1-243 SE | Ribosomal protein eS4 | A0A4X1W0I3_PIG 1-263 SF | Ribosomal protein uS7 | F2Z5E6_PIG 1-204 SG | Ribosomal protein eS6 | A0A480E3J4_PIG 1-249 SH | Ribosomal protein eS7 | A0A287A9Y6_PIG 1-194 SI | Ribosomal protein eS8 | A0A480YST6_PIG 1-208 SJ | Ribosomal protein uS4 | A0A480Q6G1_PIG 1-194 SK | Ribosomal protein eS10 | A0A480EHW2_PIG 1-165 SL | Ribosomal protein uS17 | A0A480QMH2_PIG 1-158 SM | Ribosomal protein eS12 | RS12_PIG 9-132 SN | Ribosomal protein uS15 | F6Q5P0_PIG 1-151 SO | Ribosomal protein uS11 | SP | Ribosomal protein uS19 | RS15_PIG 1-145 SQ | Ribosomal protein uS9 | RS16_PIG 1-146 SR | Ribosomal protein eS17 | RS17_PIG 1-135 SS | Ribosomal protein uS13 | RS18_PIG 1-152 ST | Ribosomal protein eS19 | A0A4X1SDD8_PIG 1-145 SU | Ribosomal protein uS10 | RS20_PIG 1-119 SV | Ribosomal protein eS21 | RS21_PIG 1-83 SW | Ribosomal protein uS8 | A0A480KS86_PIG 1-130 SX | Ribosomal protein uS12 | RS23_PIG 1-143 SY | Ribosomal protein eS24 | A0A4X1SJK8_PIG 1-132 SZ | Ribosomal protein es25 | A0A480V055_PIG 1-125 Sa | Ribosomal protein eS26 | RS26_PIG 1-115 Sb | Ribosomal protein eS27 | A0A287BF06_PIG 1-84 Sc | Ribosomal protein eS28 | RS28_PIG 1-69 Sd | Ribosomal protein uS14 | RS29_PIG 1-56 Se | Ribosomal protein eS30 | A0A480W155_PIG -73-59 Sf | Ribosomal protein eS31 | A0A4X1W6H9_PIG 1-156 Sg | Ribosomal protein RACK1 | RACK1_PIG 1-317 T | Ribosomal protein eL21 | RL21_PIG 1-160 U | Ribosomal protein eL22 | RL22_PIG 1-128 V | Ribosomal protein uL14 | A0A480VZZ1_PIG 1-140 W | Ribosomal protein eL24 | A0A4X1SH42_PIG 1-157 X | Ribosomal protein uL23 | A0A480KZ98_PIG 1-156 Y | Ribosomal protein uL24 | A0A4X1V977_PIG 1-145 Z | Ribosomal protein eL27 | RL27_PIG 1-136 a | Ribosomal protein uL15 | A0A4X1SN08_PIG 1-148 b | Ribosomal protein eL29 | RL29_PIG 1-160 c | Ribosomal protein eL30 | A0A4X1TXJ8_PIG 1-115 d | Ribosomal protein eL31 | RL31_PIG 1-125 e | Ribosomal protein eL32 | RL32_PIG 1-135 f | Ribosomal protein eL33 | A0A480KUB2_PIG 1-110 g | Ribosomal protein eL34 | RL34_PIG 1-117 h | Ribosomal protein uL29 | RL35_PIG 1-123 i | Ribosomal protein eL36 | A0A480QBP0_PIG 1-105 j | Ribosomal protein eL37 | A0A480UVT3_PIG 2-87 k | Ribosomal protein eL38 | F2Z568_PIG 1-70 l | Ribosomal protein eL39 | A0A4X1VIM4_PIG 1-51 m | Ribosomal protein eL40 | RL40_PIG 1-128 n | Ribosomal protein eL41 | o | Ribosomal protein eL42 | A0A480LCM6_PIG 1-106 p | Ribosomal protein eL43 | A0A480WPS5_PIG 2-92 r | Ribosomal protein eL28 | A0A480YX24_PIG 2-126 z | Ribosomal protein uL1 | A0A480NYW2_PIG 1-217 Non-standard residues in 3j7r #5 --- MG — magnesium ion ZN — zinc ion > show sel cartoons > hide sel atoms > show sel cartoons > hide sel atoms > select subtract #4 Nothing selected > select add #5 222336 atoms, 238785 bonds, 5347 pseudobonds, 18054 residues, 4 models selected > hide sel atoms > show sel cartoons > view matrix models #5,1,0,0,48.598,0,1,0,-19.462,0,0,1,-6.8603 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.94492,-0.32479,0.040421,145.62,0.32663,0.94366,-0.053117,-80.427,-0.020892,0.063394,0.99777,-18.475 > view matrix models > #5,0.79865,-0.59472,0.09199,249.51,0.60144,0.79404,-0.088186,-105.2,-0.020598,0.12576,0.99185,-34.725 > view matrix models > #5,0.54187,-0.067985,0.83771,-45.611,0.55997,0.77247,-0.29952,-25.818,-0.62675,0.6314,0.45665,147.62 > view matrix models > #5,0.093891,0.61115,-0.78593,358.59,0.9823,0.071675,0.17308,-81.891,0.16211,-0.78827,-0.5936,636.61 > view matrix models > #5,0.99544,0.079456,0.052735,11.767,0.030107,-0.78655,0.61679,305.14,0.090486,-0.61239,-0.78536,662.21 > view matrix models > #5,0.22478,0.62395,-0.74844,306.92,0.96424,-0.031759,0.26312,-73.28,0.1404,-0.78082,-0.60878,645.04 > view matrix models > #5,0.22979,0.62416,-0.74674,304.95,0.96318,-0.035781,0.26648,-72.802,0.13961,-0.78048,-0.6094,645.35 > view matrix models > #5,-0.010133,-0.90075,-0.43422,719.49,0.83432,-0.24698,0.49287,-41.52,-0.55119,-0.35728,0.75401,323.35 > view matrix models > #5,-0.29233,-0.8772,0.38088,555.73,0.863,-0.070368,0.50029,-102.46,-0.41205,0.47494,0.77759,38.346 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.29233,-0.8772,0.38088,514.24,0.863,-0.070368,0.50029,-83.627,-0.41205,0.47494,0.77759,86.547 > view matrix models > #5,-0.29233,-0.8772,0.38088,400.87,0.863,-0.070368,0.50029,-127.27,-0.41205,0.47494,0.77759,-141.45 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.28815,0.025296,0.95725,-26.751,0.80021,0.55543,0.2262,-209.29,-0.52597,0.83118,-0.18029,67.138 > fitmap #5 inMap #1 Fit molecule 3j7r (#5) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 222336 atoms average map value = 1.202, steps = 220 shifted from previous position = 111 rotated from previous position = 31.5 degrees atoms outside contour = 15579, contour level = 0.15768 Position of 3j7r (#5) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.44298016 -0.45570532 0.77207593 321.80419538 0.67521627 0.39695181 0.62170110 -197.80941071 -0.58978943 0.79671948 0.13185787 191.79400298 Axis 0.09838873 0.76558934 0.63576145 Axis point 249.52586229 0.00000000 49.82519700 Rotation angle (degrees) 117.19918293 Shift along axis 2.15636446 > hide #!4 models > show #!4 models > hide #!5 models > select #4/D 943 atoms, 957 bonds, 2 pseudobonds, 145 residues, 2 models selected > select #3/Lm 419 atoms, 424 bonds, 4 pseudobonds, 53 residues, 2 models selected > select #4/G 1055 atoms, 1070 bonds, 158 residues, 1 model selected > hide #!4 models > show #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!3 models > volume #1 level 0.07485 > volume #1 level 0.1301 > volume #1 level 0.1945 > volume #1 level 0.1301 > hide #!4 models > show #!5 models > ui tool show ""Side View"" > show #!2 models > hide #!2 models > show #!3 models Mismatch between Cocoa 'c' and Carbon '\x0' for virtual key 8 with QFlags(NoModifier) Mismatch between Cocoa 'C' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier) Mismatch between Cocoa 'c' and Carbon '\x0' for virtual key 8 with QFlags(ControlModifier) Mismatch between Cocoa 'c' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\u00e7' and Carbon '\x0' for virtual key 8 with QFlags(AltModifier) Mismatch between Cocoa '\u00c7' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\u00e7' and Carbon '\x0' for virtual key 8 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\u00c7' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x3' and Carbon '\x0' for virtual key 8 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > clip off > show #!4 models > hide #!5 models Enter a PDB ID in the entry field > open 7kai fromDatabase pdb format mmcif 7kai title: Cryo-EM structure of the Sec complex from S. cerevisiae, wild-type, class with Sec62, conformation 1 (C1) [more info...] Chain information for 7kai #6 --- Chain | Description | UniProt A | Protein transport protein SEC61 | SC61A_YEAST 1-480 B | Protein transport protein SBH1 | SC6B1_YEAST 1-82 C | Protein transport protein SSS1 | SC61G_YEAST 1-80 D | Protein translocation protein SEC63 | SEC63_YEAST 2-663 E | Translocation protein SEC66 | SEC66_YEAST 1-206 F | Translocation protein SEC72 | SEC72_YEAST 1-193 G | Protein transport protein Sec62 | > select add #4 55482 atoms, 60473 bonds, 1730 pseudobonds, 3914 residues, 3 models selected > select subtract #4 Nothing selected > hide #!4 models > hide #!3 models > show #!6 cartoons > hide #!6 atoms > ui mousemode right ""translate selected models"" > select add #6 10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected > view matrix models #6,1,0,0,81.654,0,1,0,171.06,0,0,1,-24.225 > view matrix models #6,1,0,0,74.929,0,1,0,182.3,0,0,1,-29.163 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.61854,0.10391,-0.77886,227.87,0.61958,-0.67411,0.40212,297.63,-0.48325,-0.73129,-0.48134,373.09 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.61854,0.10391,-0.77886,99.303,0.61958,-0.67411,0.40212,281.31,-0.48325,-0.73129,-0.48134,279.3 > view matrix models > #6,0.61854,0.10391,-0.77886,64.859,0.61958,-0.67411,0.40212,283.66,-0.48325,-0.73129,-0.48134,298.65 > view matrix models > #6,0.61854,0.10391,-0.77886,74.869,0.61958,-0.67411,0.40212,280.8,-0.48325,-0.73129,-0.48134,314.77 > view matrix models > #6,0.61854,0.10391,-0.77886,68.405,0.61958,-0.67411,0.40212,285.62,-0.48325,-0.73129,-0.48134,326.43 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.17002,-0.71875,-0.67416,252.35,0.26651,-0.62509,0.73365,283.66,-0.94872,-0.3044,0.085275,247.52 > view matrix models > #6,0.074982,-0.90403,-0.42083,259.91,0.048092,-0.41825,0.90706,258.87,-0.99602,-0.088252,0.012116,230.73 > view matrix models > #6,-0.15483,-0.94919,-0.27397,280.81,0.0010143,-0.27747,0.96073,235.85,-0.98794,0.14847,0.043923,187.22 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.15483,-0.94919,-0.27397,277.89,0.0010143,-0.27747,0.96073,236.43,-0.98794,0.14847,0.043923,182.39 > view matrix models > #6,-0.15483,-0.94919,-0.27397,270.1,0.0010143,-0.27747,0.96073,238.94,-0.98794,0.14847,0.043923,195.63 > fitmap #6 inMap #1 Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 10718 atoms average map value = 1.233, steps = 128 shifted from previous position = 59.9 rotated from previous position = 35.7 degrees atoms outside contour = 301, contour level = 0.13007 Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.10816285 -0.93883714 0.32693364 409.66306876 -0.02786266 0.33159671 0.94300969 148.09376535 -0.99374265 0.09288937 -0.06202495 406.02238554 Axis -0.46820539 0.72736499 0.50172093 Axis point 404.63507264 0.00000000 -52.82122007 Rotation angle (degrees) 114.79012046 Shift along axis 119.62169244 > undo > show #!5 models > select subtract #6 Nothing selected > show #!4 models > hide #!4 models > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > select add #6 10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected > view matrix models > #6,-0.15483,-0.94919,-0.27397,313.18,0.0010143,-0.27747,0.96073,207.82,-0.98794,0.14847,0.043923,131.47 > view matrix models > #6,-0.15483,-0.94919,-0.27397,313.32,0.0010143,-0.27747,0.96073,207.01,-0.98794,0.14847,0.043923,131.06 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.14061,-0.92385,-0.356,318.9,0.40707,-0.38171,0.82981,180.97,-0.90251,-0.028238,0.42974,90.93 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.14061,-0.92385,-0.356,307.64,0.40707,-0.38171,0.82981,210.98,-0.90251,-0.028238,0.42974,137.86 > view matrix models > #6,-0.14061,-0.92385,-0.356,282.89,0.40707,-0.38171,0.82981,199.96,-0.90251,-0.028238,0.42974,127.32 > view matrix models > #6,-0.14061,-0.92385,-0.356,282.72,0.40707,-0.38171,0.82981,200.35,-0.90251,-0.028238,0.42974,127.17 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.25681,-0.90113,-0.34931,295.72,0.42003,-0.42958,0.7994,210.38,-0.87042,0.058569,0.48882,100 > view matrix models > #6,-0.28634,-0.84898,-0.44412,305.49,0.36901,-0.52549,0.76661,238.09,-0.88422,0.055622,0.46375,106.16 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.28634,-0.84898,-0.44412,302.73,0.36901,-0.52549,0.76661,245.36,-0.88422,0.055622,0.46375,117.19 > view matrix models > #6,-0.28634,-0.84898,-0.44412,298.19,0.36901,-0.52549,0.76661,242.95,-0.88422,0.055622,0.46375,114.52 > view matrix models > #6,-0.28634,-0.84898,-0.44412,299.18,0.36901,-0.52549,0.76661,245.86,-0.88422,0.055622,0.46375,116.45 > view matrix models > #6,-0.28634,-0.84898,-0.44412,298.13,0.36901,-0.52549,0.76661,245.47,-0.88422,0.055622,0.46375,113.14 > fitmap #6 inMap #1 Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 10718 atoms average map value = 1.243, steps = 124 shifted from previous position = 79.8 rotated from previous position = 25 degrees atoms outside contour = 206, contour level = 0.13007 Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.44566880 -0.88524978 -0.13308688 525.60779991 0.62690477 -0.41475890 0.65951909 183.49975684 -0.63903811 0.21049429 0.73981243 204.55973898 Axis -0.27105708 0.30542114 0.91282309 Axis point 248.72625582 218.26555113 0.00000000 Rotation angle (degrees) 124.07707591 Shift along axis 100.30183906 > undo > hide #!5 models > view matrix models > #6,-0.28634,-0.84898,-0.44412,298.8,0.36901,-0.52549,0.76661,246.79,-0.88422,0.055622,0.46375,116.85 > view matrix models > #6,-0.28634,-0.84898,-0.44412,300.74,0.36901,-0.52549,0.76661,250.37,-0.88422,0.055622,0.46375,116.98 > view matrix models > #6,-0.28634,-0.84898,-0.44412,295.03,0.36901,-0.52549,0.76661,248.6,-0.88422,0.055622,0.46375,122.82 > view matrix models > #6,-0.28634,-0.84898,-0.44412,295.39,0.36901,-0.52549,0.76661,247.22,-0.88422,0.055622,0.46375,119.89 > fitmap #6 inMap #1 Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 10718 atoms average map value = 1.252, steps = 132 shifted from previous position = 69.6 rotated from previous position = 14 degrees atoms outside contour = 128, contour level = 0.13007 Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.50210231 -0.77701432 -0.37966038 551.57406813 0.29122789 -0.56528942 0.77177339 252.46983545 -0.81429698 0.27694151 0.51012137 250.18376402 Axis -0.39430287 0.34633674 0.85122036 Axis point 287.36516646 196.41254098 0.00000000 Rotation angle (degrees) 141.13578337 Shift along axis 82.91385494 > undo > view matrix models > #6,-0.28634,-0.84898,-0.44412,291.09,0.36901,-0.52549,0.76661,250.51,-0.88422,0.055622,0.46375,128.28 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.65713,-0.73207,-0.17963,290.61,0.29854,-0.47157,0.82976,243.52,-0.69214,0.49163,0.52843,20.445 > view matrix models > #6,-0.54642,-0.76733,-0.3356,301.86,0.21282,-0.51477,0.83049,263.27,-0.81002,0.38237,0.44459,67.727 > fitmap #6 inMap #1 Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 10718 atoms average map value = 1.283, steps = 132 shifted from previous position = 73.9 rotated from previous position = 43.2 degrees atoms outside contour = 145, contour level = 0.13007 Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.56048648 -0.77324597 -0.29655616 522.99378216 0.71208631 -0.63279811 0.30413748 258.45120363 -0.42283327 -0.04070863 0.90529267 195.50461904 Axis -0.22538111 0.08253094 0.97076877 Axis point 224.09082246 251.30323054 0.00000000 Rotation angle (degrees) 130.09043809 Shift along axis 93.24708045 > undo > volume #1 level 0.07485 > fitmap #6 inMap #1 Fit molecule 7kai (#6) to map cryosparc_P12_J230_001_volume_map (1).mrc (#1) using 10718 atoms average map value = 1.269, steps = 116 shifted from previous position = 77.5 rotated from previous position = 9.05 degrees atoms outside contour = 157, contour level = 0.074854 Position of 7kai (#6) relative to cryosparc_P12_J230_001_volume_map (1).mrc (#1) coordinates: Matrix rotation and translation -0.67920128 -0.72835307 -0.09048420 536.37887288 0.42277926 -0.48903191 0.76295836 218.05786119 -0.59995274 0.47994746 0.64008369 169.44235071 Axis -0.21934487 0.39485867 0.89217401 Axis point 254.00802490 186.84176094 0.00000000 Rotation angle (degrees) 139.82474868 Shift along axis 119.62214637 > undo > show #!5 models > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.28634,-0.84898,-0.44412,273.5,0.36901,-0.52549,0.76661,231.44,-0.88422,0.055622,0.46375,24.349 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.79561,-0.51975,0.31124,189.7,0.46231,-0.18888,0.86637,149.36,-0.39151,0.83318,0.39056,-163.62 > view matrix models > #6,-0.33373,-0.88323,-0.32943,269.67,0.45285,-0.45671,0.76573,207.91,-0.82677,0.10636,0.55239,-5.1508 > volume #1 level 0.489 > view matrix models > #6,-0.21804,-0.82307,-0.52441,270.56,0.47699,-0.55867,0.67851,233.03,-0.85143,-0.1022,0.51441,37.268 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.21804,-0.82307,-0.52441,283.38,0.47699,-0.55867,0.67851,247.89,-0.85143,-0.1022,0.51441,130.88 > view matrix models > #6,-0.21804,-0.82307,-0.52441,294.76,0.47699,-0.55867,0.67851,245.27,-0.85143,-0.1022,0.51441,121.54 > view matrix models > #6,-0.21804,-0.82307,-0.52441,295.18,0.47699,-0.55867,0.67851,245.43,-0.85143,-0.1022,0.51441,126.7 > view matrix models > #6,-0.21804,-0.82307,-0.52441,295.43,0.47699,-0.55867,0.67851,245.08,-0.85143,-0.1022,0.51441,127.46 > view matrix models > #6,-0.21804,-0.82307,-0.52441,295.72,0.47699,-0.55867,0.67851,245.21,-0.85143,-0.1022,0.51441,128.06 > volume #1 level 0.07485 > hide #!5 models > show #!5 models > hide #!6 models > select subtract #6 Nothing selected > show #!4 models > hide #!5 models > volume #1 level 0.1669 > hide #!4 models > hide #!1 models > show #!6 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > ui mousemode right ""rotate selected models"" > select add #6 10718 atoms, 10924 bonds, 6 pseudobonds, 1399 residues, 2 models selected > view matrix models > #6,-0.0055515,-0.95806,-0.28652,250.94,0.41205,-0.26326,0.8723,180.15,-0.91114,-0.11322,0.39623,155.82 > undo > show #!5 models > hide #!6 models > select subtract #6 Nothing selected ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10.1 (2025-07-24) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M2 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: Mac14,7 Model Number: Z16U000NJD/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 44 days, 19 hours, 36 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P3223QE: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.6.1 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.19 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.4 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.7 ChimeraX-AtomicLibrary: 14.1.19 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: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 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 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10.1 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: 2.5.1 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 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: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 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: 2.7.10 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: 1.1.3 ChimeraX-ProfileGrids: 1.1.3 ChimeraX-PubChem: 2.2 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: 2.17.1 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: 1.45.2 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: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.10.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.15 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.59.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.14.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.8.1 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.3.2 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.10.0 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.11.0 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 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: 4.3.8 pluggy: 1.6.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 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: 3.2.3 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: 8.4.1 pytest-cov: 6.2.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 27.0.0 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 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 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: 2025.3.13 tinyarray: 1.2.4 tornado: 6.5.1 traitlets: 5.14.3 typing_extensions: 4.14.1 tzdata: 2025.2 urllib3: 2.5.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal Window Toolkit duplicate all ChimeraX