id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18385 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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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crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/0fe51d64/coldshock_canonHiber_filt.mrc Opened coldshock_canonHiber_filt.mrc as #1, grid size 232,232,232, pixel 2.59, shown at level 0.00651, step 1, values float32 > open > /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/2f5041e5/coldshock_CDwithoutBalon_filt.mrc Opened coldshock_CDwithoutBalon_filt.mrc as #2, grid size 270,270,270, pixel 2.59, shown at level 0.00734, step 2, values float32 > open > /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/8d822ac8/coldshock_noncanonHiber_filt.mrc Opened coldshock_noncanonHiber_filt.mrc as #3, grid size 232,232,232, pixel 2.59, shown at level 0.00408, step 1, values float32 > open > /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/eb6b5fa6/coldshock_CDcolliding_filt.mrc Opened coldshock_CDcolliding_filt.mrc as #4, grid size 270,270,270, pixel 2.59, shown at level 0.00718, step 2, values float32 > open > /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/M_maps/MSR-050825/species/f27bc761/coldshock_CDwithBalon_filt.mrc Opened coldshock_CDwithBalon_filt.mrc as #5, grid size 270,270,270, pixel 2.59, shown at level 0.00736, step 2, values float32 > hide #!5 models > hide #!4 models > hide #!2 models > volume #3 level 0.003637 > volume #3 level 0.003397 > volume #3 level 0.003774 > volume #1 level 0.00402 > volume #1 level 0.006047 > volume #1 level 0.004573 > volume #1 level 0.003836 > volume #1 level 0.004481 > volume #2 level 0.0043 > volume #4 level 0.005212 > volume #4 level 0.004387 > volume #5 level 0.004957 > volume #5 level 0.003779 > volume #5 level 0.004912 > volume #1 level 0.003698 > volume #1 level 0.003513 > open 8rdv fromDatabase pdb format mmcif 8rdv title: Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon, mRNA and P-site tRNA (structure 2). [more info...] Chain information for 8rdv #6 --- Chain | Description | UniProt A4 | Small ribosomal subunit protein uS2 | A0A0M4TFJ4_9GAMM 1-269 Af | Large ribosomal subunit protein uL3 | A0A0M4T1M3_9GAMM 1-212 B | Methyl-accepting chemotaxis protein | A0A0M3V8U3_9GAMM 1-369 BQ | Small ribosomal subunit protein uS8 | A0A0M4U618_9GAMM 1-132 Ba | Large ribosomal subunit protein bL34 | A0A0M4TEZ6_9GAMM 1-44 C1 | Large ribosomal subunit protein bL9 | A0A0M3V9E8_9GAMM 1-166 CT | Small ribosomal subunit protein uS3 | A0A0M4T6V9_9GAMM 1-241 Cl | Large ribosomal subunit protein uL2 | A0A0M3V8Q0_9GAMM 1-274 D8 | 5S rRNA | Dm | Small ribosomal subunit protein uS4 | A0A0M4TE52_9GAMM 1-213 E5 | Small ribosomal subunit protein uS5 | A0A0M3V8J0_9GAMM 1-171 E9 | Large ribosomal subunit protein uL4 | A0A0M4U627_9GAMM 1-200 F | Small ribosomal subunit protein uS9 | A0A0M4T6M9_9GAMM 1-128 F7 | Large ribosomal subunit protein uL5 | A0A0M4T1L5_9GAMM 1-178 FG | Small ribosomal subunit protein bS6 | A0A0M4U628_9GAMM 1-134 GR | Large ribosomal subunit protein uL6 | A0A0M5MKV2_9GAMM 1-177 GS | Small ribosomal subunit protein uS7 | A0A0M3V8N5_9GAMM 1-157 H | Elongation factor Tu | A0A0M4U5B4_9GAMM 1-396 HK | Small ribosomal subunit protein uS14 | A0A0M3V8P8_9GAMM 1-101 IX | Large ribosomal subunit protein uL13 | A0A0M4TBP4_9GAMM 1-142 JY | Small ribosomal subunit protein uS10 | A0A0M4TE68_9GAMM 1-103 Je | Large ribosomal subunit protein uL14 | A0A0M5MJS2_9GAMM 1-122 KU | Small ribosomal subunit protein uS11 | A0A0M3V8P6_9GAMM 1-129 Kd | Large ribosomal subunit protein uL15 | A0A0M4T6V1_9GAMM 1-146 L6 | Small ribosomal subunit protein uS12 | A0A0M4U4C3_9GAMM 1-124 Lg | Large ribosomal subunit protein uL16 | A0A0M3V8J3_9GAMM 1-137 MB | Large ribosomal subunit protein bL17 | A0A0M4U611_9GAMM 1-119 MM | Small ribosomal subunit protein uS13 | A0A0M5MJL8_9GAMM 1-118 NV | Small ribosomal subunit protein bS21 | A0A0M4SY21_9GAMM 1-71 Nc | Large ribosomal subunit protein uL18 | A0A0M4TUJ2_9GAMM 1-116 OL | Small ribosomal subunit protein uS15 | A0A0M4TF29_9GAMM 1-88 Oi | Large ribosomal subunit protein bL19 | A0A0M4TV08_9GAMM 1-130 PO | Large ribosomal subunit protein bL20 | A0A0M5MJR6_9GAMM 1-118 Pj | Small ribosomal subunit protein bS16 | A0A0M4T275_9GAMM 1-89 QZ | Small ribosomal subunit protein uS17 | A0A0M4U401_9GAMM 1-91 Qb | Large ribosomal subunit protein bL21 | A0A0M5TIS3_9GAMM 1-103 R3 | Small ribosomal subunit protein bS18 | A0A0M5MK69_9GAMM 1-76 RF | Large ribosomal subunit protein uL22 | A0A0M4SWS6_9GAMM 1-109 SP | Small ribosomal subunit protein uS19 | A0A0M4TUJ8_9GAMM 1-91 Sn | Large ribosomal subunit protein uL23 | A0A0M5MJH9_9GAMM 1-116 TI | Large ribosomal subunit protein uL24 | A0A0M4TE60_9GAMM 1-105 To | Small ribosomal subunit protein bS20 | A0A0M4T3R2_9GAMM 1-88 UC | Large ribosomal subunit protein bL25 | A0A0M4U726_9GAMM 1-219 V | Heterogenous tRNA | VH | Large ribosomal subunit protein bL27 | A0A0M4TUE5_9GAMM 1-85 WD | Large ribosomal subunit protein bL28 | A0A0M4T6Y7_9GAMM 1-78 XE | Large ribosomal subunit protein uL29 | A0A0M4TBX9_9GAMM 1-65 Y | Heterogenous mRNA | YW | Large ribosomal subunit protein uL30 | A0A0M4SWR7_9GAMM 1-59 Z2 | 23S rRNA | aA | Large ribosomal subunit protein bL32 | A0A0M4SWQ6_9GAMM 1-60 bk | Large ribosomal subunit protein bL33 | A0A0M4SWV1_9GAMM 1-51 dh | Large ribosomal subunit protein bL35 | A0A0M4U4I0_9GAMM 1-65 ep | Large ribosomal subunit protein bL36 | A0A0M4U3Z5_9GAMM 1-38 fJ | Large ribosomal subunit protein bL31B | A0A0M4SX87_9GAMM 1-93 iN | 16S rRNA | 7 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #6 142059 atoms, 154016 bonds, 4467 pseudobonds, 10507 residues, 3 models selected > hide sel atoms > show sel cartoons > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,215.56,0,1,0,1.8946,0,0,1,74.466 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.95489,-0.291,-0.059171,290.09,0.29542,0.91065,0.28886,-95.856,-0.030174,-0.29331,0.95554,143.63 > view matrix models > #6,0.94197,-0.30307,0.14432,253.41,0.25615,0.92684,0.27451,-88.549,-0.21696,-0.22161,0.95069,166.48 > view matrix models > #6,0.96869,0.14338,0.20267,153.65,-0.20929,0.91075,0.35599,-14.47,-0.13354,-0.38727,0.91225,189.33 > view matrix models > #6,0.98296,0.16668,0.077495,172.08,-0.18357,0.9118,0.36732,-21.81,-0.0094369,-0.37529,0.92686,160.77 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.98296,0.16668,0.077495,46.378,-0.18357,0.9118,0.36732,0.46417,-0.0094369,-0.37529,0.92686,226.2 > view matrix models > #6,0.98296,0.16668,0.077495,24.772,-0.18357,0.9118,0.36732,73.732,-0.0094369,-0.37529,0.92686,225.79 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.99682,0.077536,0.018407,50.717,-0.079351,0.94442,0.31903,57.864,0.0073523,-0.31947,0.94757,208.06 > view matrix models > #6,0.96567,0.21901,0.1397,5.6733,-0.2174,0.97571,-0.026882,148.35,-0.14219,-0.0044106,0.98983,169.15 > view matrix models > #6,0.97204,0.18697,0.14208,9.9379,-0.18592,0.98235,-0.020733,139.94,-0.14345,-0.0062618,0.98964,169.77 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.97204,0.18697,0.14208,44.909,-0.18592,0.98235,-0.020733,134.98,-0.14345,-0.0062618,0.98964,156.38 > ui tool show ""Fit in Map"" > fitmap #6 inMap #1 Fit molecule 8rdv (#6) to map coldshock_canonHiber_filt.mrc (#1) using 142059 atoms average map value = 0.008669, steps = 100 shifted from previous position = 14 rotated from previous position = 11 degrees atoms outside contour = 3433, contour level = 0.0035132 Position of 8rdv (#6) relative to coldshock_canonHiber_filt.mrc (#1) coordinates: Matrix rotation and translation 0.99900134 0.03551027 0.02711709 92.10578523 -0.03521318 0.99931530 -0.01135620 109.53736959 -0.02750178 0.01038998 0.99956776 117.85837821 Axis 0.23645643 0.59389657 -0.76900925 Axis point 3223.96809613 -2528.42295718 0.00000000 Rotation angle (degrees) 2.63558909 Shift along axis -3.80130908 > select subtract #6 Nothing selected > fitmap #6 inMap #3 Fit molecule 8rdv (#6) to map coldshock_noncanonHiber_filt.mrc (#3) using 142059 atoms average map value = 0.005992, steps = 44 shifted from previous position = 0.078 rotated from previous position = 0.0748 degrees atoms outside contour = 20304, contour level = 0.0037738 Position of 8rdv (#6) relative to coldshock_noncanonHiber_filt.mrc (#3) coordinates: Matrix rotation and translation 0.99896294 0.03558325 0.02840567 91.76464938 -0.03527833 0.99931516 -0.01116458 109.48473981 -0.02878349 0.01015089 0.99953413 118.16990151 Axis 0.22791996 0.61150666 -0.75770185 Axis point 3180.90669206 -2496.87444205 0.00000000 Rotation angle (degrees) 2.68017736 Shift along axis -1.67191103 > show #!3 models > hide #!1 models > volume #3 level 0.002918 > color #6 grey > select add #6 142059 atoms, 154016 bonds, 4467 pseudobonds, 10507 residues, 3 models selected > select /B 2829 atoms, 2870 bonds, 1 pseudobond, 362 residues, 2 models selected > color sel #D62828 > hide #!6 models > hide #!3 models > show #!6 models > color /V #08A8C6 > color /H #FCBF49 > select clear > select add #6 142059 atoms, 154016 bonds, 4467 pseudobonds, 10507 residues, 3 models selected > select subtract /B:272 142050 atoms, 154006 bonds, 4467 pseudobonds, 10506 residues, 3 models selected > select subtract /B:273 142042 atoms, 153998 bonds, 4467 pseudobonds, 10505 residues, 3 models selected > color #6 #D3D3D3 > color /H #FCBF49 > color /V #08A8C6 > select clear > select /B 2829 atoms, 2870 bonds, 1 pseudobond, 362 residues, 2 models selected > color sel #D62828 > select clear > show #!3 models > volume #3 level 0.002371 > volume #3 level 0.004048 > open 8rdw fromDatabase pdb format mmcif 8rdw title: Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon and EF-Tu(GDP) (structure 3). [more info...] Chain information for 8rdw #7 --- Chain | Description | UniProt A4 | Small ribosomal subunit protein uS2 | A0A0M4TFJ4_9GAMM 1-269 Af | Large ribosomal subunit protein uL3 | A0A0M4T1M3_9GAMM 1-212 B | Methyl-accepting chemotaxis protein | A0A0M3V8U3_9GAMM 1-369 BQ | Small ribosomal subunit protein uS8 | A0A0M4U618_9GAMM 1-132 Ba | Large ribosomal subunit protein bL34 | A0A0M4TEZ6_9GAMM 1-44 C1 | Large ribosomal subunit protein bL9 | A0A0M3V9E8_9GAMM 1-166 CT | Small ribosomal subunit protein uS3 | A0A0M4T6V9_9GAMM 1-241 Cl | Large ribosomal subunit protein uL2 | A0A0M3V8Q0_9GAMM 1-274 D | Large ribosomal subunit protein bL12 | A0A0M4SX69_9GAMM 1-123 D8 | 5S rRNA | Dm | Small ribosomal subunit protein uS4 | A0A0M4TE52_9GAMM 1-213 E5 | Small ribosomal subunit protein uS5 | A0A0M3V8J0_9GAMM 1-171 E9 | Large ribosomal subunit protein uL4 | A0A0M4U627_9GAMM 1-200 F | Small ribosomal subunit protein uS9 | A0A0M4T6M9_9GAMM 1-128 F7 | Large ribosomal subunit protein uL5 | A0A0M4T1L5_9GAMM 1-178 FG | Small ribosomal subunit protein bS6 | A0A0M4U628_9GAMM 1-134 GR | Large ribosomal subunit protein uL6 | A0A0M5MKV2_9GAMM 1-177 GS | Small ribosomal subunit protein uS7 | A0A0M3V8N5_9GAMM 1-157 H | Elongation factor Tu | A0A0M4U5B4_9GAMM 1-396 HK | Small ribosomal subunit protein uS14 | A0A0M3V8P8_9GAMM 1-101 IX | Large ribosomal subunit protein uL13 | A0A0M4TBP4_9GAMM 1-142 JY | Small ribosomal subunit protein uS10 | A0A0M4TE68_9GAMM 1-103 Je | Large ribosomal subunit protein uL14 | A0A0M5MJS2_9GAMM 1-122 KU | Small ribosomal subunit protein uS11 | A0A0M3V8P6_9GAMM 1-129 Kd | Large ribosomal subunit protein uL15 | A0A0M4T6V1_9GAMM 1-146 L6 | Small ribosomal subunit protein uS12 | A0A0M4U4C3_9GAMM 1-124 Lg | Large ribosomal subunit protein uL16 | A0A0M3V8J3_9GAMM 1-137 MB | Large ribosomal subunit protein bL17 | A0A0M4U611_9GAMM 1-119 MM | Small ribosomal subunit protein uS13 | A0A0M5MJL8_9GAMM 1-118 NV | Small ribosomal subunit protein bS21 | A0A0M4SY21_9GAMM 1-71 Nc | Large ribosomal subunit protein uL18 | A0A0M4TUJ2_9GAMM 1-116 OL | Small ribosomal subunit protein uS15 | A0A0M4TF29_9GAMM 1-88 Oi | Large ribosomal subunit protein bL19 | A0A0M4TV08_9GAMM 1-130 PO | Large ribosomal subunit protein bL20 | A0A0M5MJR6_9GAMM 1-118 Pj | Small ribosomal subunit protein bS16 | A0A0M4T275_9GAMM 1-89 QZ | Small ribosomal subunit protein uS17 | A0A0M4U401_9GAMM 1-91 Qb | Large ribosomal subunit protein bL21 | A0A0M5TIS3_9GAMM 1-103 R3 | Small ribosomal subunit protein bS18 | A0A0M5MK69_9GAMM 1-76 RF | Large ribosomal subunit protein uL22 | A0A0M4SWS6_9GAMM 1-109 SP | Small ribosomal subunit protein uS19 | A0A0M4TUJ8_9GAMM 1-91 Sn | Large ribosomal subunit protein uL23 | A0A0M5MJH9_9GAMM 1-116 TI | Large ribosomal subunit protein uL24 | A0A0M4TE60_9GAMM 1-105 To | Small ribosomal subunit protein bS20 | A0A0M4T3R2_9GAMM 1-88 UC | Large ribosomal subunit protein bL25 | A0A0M4U726_9GAMM 1-219 VH | Large ribosomal subunit protein bL27 | A0A0M4TUE5_9GAMM 1-85 WD | Large ribosomal subunit protein bL28 | A0A0M4T6Y7_9GAMM 1-78 XE | Large ribosomal subunit protein uL29 | A0A0M4TBX9_9GAMM 1-65 YW | Large ribosomal subunit protein uL30 | A0A0M4SWR7_9GAMM 1-59 Z2 | 23S rRNA | aA | Large ribosomal subunit protein bL32 | A0A0M4SWQ6_9GAMM 1-60 bk | Large ribosomal subunit protein bL33 | A0A0M4SWV1_9GAMM 1-51 dh | Large ribosomal subunit protein bL35 | A0A0M4U4I0_9GAMM 1-65 ep | Large ribosomal subunit protein bL36 | A0A0M4U3Z5_9GAMM 1-38 fJ | Large ribosomal subunit protein bL31B | A0A0M4SX87_9GAMM 1-93 iN | 16S rRNA | Non-standard residues in 8rdw #7 --- GDP — guanosine-5'-diphosphate MG — magnesium ion 7 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select add #7 142682 atoms, 154557 bonds, 4425 pseudobonds, 10699 residues, 4 models selected > hide sel atoms > show sel cartoons > view matrix models #7,1,0,0,182.59,0,1,0,-21.711,0,0,1,18.146 > view matrix models #7,1,0,0,182.74,0,1,0,-23.828,0,0,1,8.9496 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.9131,0.10227,0.39469,99.941,-0.07888,0.99405,-0.075078,7.2713,-0.40003,0.037421,0.91574,93.967 > view matrix models > #7,0.76653,-0.37929,0.51824,191.73,0.49034,0.86678,-0.090887,-72.429,-0.41473,0.32378,0.85039,56.804 > view matrix models > #7,0.86493,0.19523,0.46237,77.967,-0.22602,0.97405,0.011516,20.957,-0.44812,-0.11446,0.88661,137.08 > view matrix models > #7,0.98502,0.14956,0.085873,140.35,-0.1571,0.98357,0.088909,-9.4113,-0.071165,-0.10107,0.99233,42.591 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.98502,0.14956,0.085873,44.567,-0.1571,0.98357,0.088909,33.149,-0.071165,-0.10107,0.99233,169.83 > view matrix models > #7,0.98502,0.14956,0.085873,26.43,-0.1571,0.98357,0.088909,99.993,-0.071165,-0.10107,0.99233,175.82 > view matrix models > #7,0.98502,0.14956,0.085873,61.355,-0.1571,0.98357,0.088909,95.57,-0.071165,-0.10107,0.99233,160.38 > view matrix models > #7,0.98502,0.14956,0.085873,61.65,-0.1571,0.98357,0.088909,95.316,-0.071165,-0.10107,0.99233,157.17 > fitmap #7 inMap #3 Fit molecule 8rdw (#7) to map coldshock_noncanonHiber_filt.mrc (#3) using 142682 atoms average map value = 0.00596, steps = 92 shifted from previous position = 21.7 rotated from previous position = 9.69 degrees atoms outside contour = 26538, contour level = 0.0040475 Position of 8rdw (#7) relative to coldshock_noncanonHiber_filt.mrc (#3) coordinates: Matrix rotation and translation 0.99916956 0.03241120 0.02469236 93.24986343 -0.03220587 0.99944366 -0.00866862 108.41335331 -0.02495958 0.00786619 0.99965751 118.03237077 Axis 0.19885295 0.59713013 -0.77710560 Axis point 3571.83042084 -2837.37460473 0.00000000 Rotation angle (degrees) 2.38278595 Shift along axis -8.44372641 > select subtract #7 Nothing selected > hide #!6 models > volume #3 level 0.004492 > volume #3 level 0.004048 > show #!6 models > hide #!7 models > ui tool show ""Surface Color"" > ui tool show ""Color Zone"" > color zone #3 near #6 distance 15.53 > color zone #3 near #6 distance 15.4 > color zone #3 near #6 distance 4.87 > color zone #3 near #6 distance 4.52 > color zone #3 near #6 distance 6.08 > hide #!3 models > show #!3 models > color zone #3 near #6 distance 9.68 > color zone #3 near #6 distance 6.93 > color zone #3 near #6 distance 47.77 > color zone #3 near #6 distance 5 > color zone #3 near #6 distance 50 > color zone #3 near #7 distance 48.67 > color zone #3 near #7 distance 30.03 > color zone #3 near #6 distance 30.03 > color zone #3 near #6 distance 15.03 > volume #3 level 0.003568 > volume #3 level 0.002439 > volume #3 level 0.002747 > volume #3 level 0.002884 > volume #3 level 0.003363 > volume #3 level 0.003124 > volume splitbyzone #3 Opened coldshock_noncanonHiber_filt.mrc 0 as #8.1, grid size 232,232,232, pixel 2.59, shown at level 0.00312, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 1 as #8.2, grid size 232,232,232, pixel 2.59, shown at level 0.00312, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 as #8.3, grid size 232,232,232, pixel 2.59, shown at level 0.00312, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 3 as #8.4, grid size 232,232,232, pixel 2.59, shown at level 0.00312, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 4 as #8.5, grid size 232,232,232, pixel 2.59, shown at level 0.00312, step 1, values float32 > ui tool show ""Fit in Map"" > hide #!8 models > show #!7 models > hide #!6 models > color #7 #D3D3D3 > select #7/B:251 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 61 atoms, 60 bonds, 8 residues, 1 model selected > select up 2871 atoms, 2914 bonds, 368 residues, 1 model selected > color sel #D62828 > select #7/H:308 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 99 atoms, 102 bonds, 12 residues, 1 model selected > select up 2918 atoms, 2968 bonds, 386 residues, 1 model selected > select up 2947 atoms, 2998 bonds, 388 residues, 1 model selected > select up 142682 atoms, 154557 bonds, 10699 residues, 1 model selected > select down 2947 atoms, 2998 bonds, 388 residues, 1 model selected > color sel #FCBF49 > fitmap #7 inMap #3 Fit molecule 8rdw (#7) to map coldshock_noncanonHiber_filt.mrc (#3) using 142682 atoms average map value = 0.00596, steps = 40 shifted from previous position = 0.026 rotated from previous position = 0.0197 degrees atoms outside contour = 10980, contour level = 0.0031235 Position of 8rdw (#7) relative to coldshock_noncanonHiber_filt.mrc (#3) coordinates: Matrix rotation and translation 0.99917339 0.03239976 0.02455170 93.27698067 -0.03220330 0.99944641 -0.00835559 108.34749174 -0.02480882 0.00755804 0.99966364 118.03603866 Axis 0.19208976 0.59581921 -0.77980831 Axis point 3590.48202106 -2844.08965597 0.00000000 Rotation angle (degrees) 2.37400788 Shift along axis -9.57241428 > show #!8 models > hide #!8 models > show #!3 models > volume #8.1 level 0.003303 > volume #3 level 0.004903 > volume #3 level 0.004048 > volume #3 level 0.00374 > color zone #3 near #7 distance 15.03 > color zone #3 near #7 distance 3 > color zone #3 near #7 distance 30 > color zone #3 near #7 distance 3 > color zone #3 near #7 distance 4 > color zone #3 near #7 distance 45 > color zone #3 near #7 distance 4 > color zone #3 near #7 distance 6 > color zone #3 near #7 distance 60 > volume splitbyzone #3 Opened coldshock_noncanonHiber_filt.mrc 0 as #9.1, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 1 as #9.2, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 as #9.3, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 3 as #9.4, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 > view matrix models > #7,0.99917,0.0324,0.024552,94.63,-0.032203,0.99945,-0.0083556,108.29,-0.024809,0.007558,0.99966,121.28 > fitmap #7 inMap #3 Fit molecule 8rdw (#7) to map coldshock_noncanonHiber_filt.mrc (#3) using 142682 atoms average map value = 0.00596, steps = 52 shifted from previous position = 3.5 rotated from previous position = 0.00828 degrees atoms outside contour = 20361, contour level = 0.0037395 Position of 8rdw (#7) relative to coldshock_noncanonHiber_filt.mrc (#3) coordinates: Matrix rotation and translation 0.99917264 0.03238693 0.02459927 93.27284194 -0.03219349 0.99944786 -0.00821955 108.32264072 -0.02485190 0.00742081 0.99966360 118.08633635 Axis 0.18882681 0.59702609 -0.77968217 Axis point 3595.01414754 -2845.16973281 0.00000000 Rotation angle (degrees) 2.37355959 Shift along axis -9.78595401 > close #1 > close #2 > close #4 > close #5 > hide #!9 models > show #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!8.1 models > show #!8.1 models > color #8.1 #D3D3D3 > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!8 models > select clear > show #!3 models > hide #!9.1 models > show #!9 models > hide #!9 models > hide #!7 models > hide #!3 models > show #!3 models > color #3 #D3D3D3 > hide #!3 models > show #!6 models > show #!3 models > show #!7 models > ui tool show ""Color Zone"" > color zone #3 near #6 distance 15.53 > color zone #3 near #6 distance 4.53 > color zone #3 near #6 distance 45.53 > color zone #3 near #6 distance 4.53 > color zone #3 near #6 distance 3.53 > color zone #3 near #6 distance 30.53 > hide #!3 models > show #!3 models > color zone #3 near #6 distance 3.53 > color zone #3 near #6 distance 15.53 > hide #!3 models > show #!3 models > hide #!7 models > show #!7 models > volume splitbyzone #3 Opened coldshock_noncanonHiber_filt.mrc 0 as #1.1, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 1 as #1.2, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 as #1.3, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 3 as #1.4, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 4 as #1.5, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 > hide #!1.1 models > show #!1.1 models > hide #!1.2 models > show #!1.2 models > hide #!1.4 models > show #!1.4 models > hide #!1.1 models > show #!1.1 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > show #!1.1 models > select add #1.1 2 models selected > color zone #1.1 near #7 distance 15.53 > select clear > color #1.1 #D3D3D3 > color #1.3 #D3D3D3 > hide #!6 models > hide #!7 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > set bgColor white > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > graphics silhouettes true > material Reflectivity: 0.8 Specular reflectivity 0.3 Specular exponent: 30 Ambient reflectivity 0.8 Transparent cast shadows: false Meshes cast shadows: false > material Reflectivity: 0.8 Specular reflectivity 0.3 Specular exponent: 30 Ambient reflectivity 0.8 Transparent cast shadows: false Meshes cast shadows: false > material dull > material Reflectivity: 0.8 Specular reflectivity 0 Specular exponent: 30 Ambient reflectivity 0.8 Transparent cast shadows: false Meshes cast shadows: false > graphics Background color: 100,100,100 > lighting Intensity: 0.5 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.5 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01) > lighting intensity 0.7 > lighting fill intensity 0.3 Expected keyword ""fillColor"", ""fillDirection"", or ""fillIntensity"" > lighting fillIntensity 0.3 > lighting Intensity: 0.7 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0.3 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 1.5 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01) > lighting ambientIntensity 0.8 > lighting depthCue true > lighting Intensity: 0.7 Direction: 0.577,-0.577,-0.577 Color: 100,100,100 Fill intensity: 0.3 Fill direction: -0.2,-0.2,-0.959 Fill color: 100,100,100 Ambient intensity: 0.8 Ambient color: 100,100,100 Depth cue: 1, start 0.5, end 1, color 100,100,100 Shadow: False (depth map size 2048, depth bias 0.005) Multishadows: 64 (max 1024, depth map size 1024, depth bias 0.01) > material Reflectivity: 0.8 Specular reflectivity 0 Specular exponent: 30 Ambient reflectivity 0.8 Transparent cast shadows: false Meshes cast shadows: false > graphics silhouettes Current silhouette settings: enabled: True width: 2 color: 0,0,0 depth jump: 0.03 > graphics silhouettes width 4 > graphics silhouettes Current silhouette settings: enabled: True width: 4 color: 0,0,0 depth jump: 0.03 > save > /Users/mariehelmke/Documents/Hiwi_Pfeffer_2025/FigurePrep_manuskript/Figure3_noncanonHiber.cxs > includeMaps true > volume #3 level 0.004082 > volume #3 level 0.005177 > volume #3 level 0.004082 > volume #3 level 0.004 > volume #3 level 0.005 > volume #3 level 0.0045 > volume #3 level 0.006 > volume #3 level 0.003 > volume #3 level 0.0035 > volume #3 level 0.0030 > volume #3 level 0.0038 > volume #3 level 0.004 > volume #3 level 0.0042 > volume #3 level 0.0040 > volume #3 level 0.0047 > volume #3 level 0.0038 > show #!6 models > volume #3 level 0.0040 > volume #3 level 0.0045 > volume #3 level 0.0035 > volume #3 level 0.0033 > volume #3 level 0.0040 > volume #3 level 0.0038 > hide #!6 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > show #!8 models > hide #!8 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9.2 models > hide #!9.3 models > hide #!9.4 models > show #!9.4 models > hide #!9.4 models > show #!9.4 models > hide #!9.4 models > show #!9.4 models > hide #!9.4 models > show #!9.4 models > hide #!9.4 models > show #!9.4 models > hide #!1.4 models > show #!1.4 models > hide #!1.4 models > hide #!1 models > volume #9.4 level 0.0038 > hide #!9.4 models > show #!9.4 models > hide #!9.4 models > show #!9.4 models > ui tool show ""Side View"" Need to color zone map before it can be split > show #!1.4 models > hide #!1.4 models > hide #!1 models > show #!1 models > hide #!1.1 models > hide #!1.3 models > hide #!9 models > show #!9 models > hide #!1.2 models > show #!1.2 models > show #!9.2 models > hide #!9.2 models > show #!8 models > hide #!8 models > hide #!3 models > show #!1.3 models > show #!1.1 models > hide #!1.1 models > hide #!1.2 models > hide #!1 models > show #!8 models > hide #!8.3 models > show #!8.3 models > hide #!8.1 models > show #!8.1 models > hide #!8.1 models > show #!8.1 models > show #!1 models > hide #!8 models > hide #!9 models > show #!1.2 models > show #!1.4 models > show #!1.1 models > hide #!1 models > show #!8 models > hide #!8 models > show #!9 models > show #!9.2 models > show #!9.3 models > show #!9.1 models > hide #!9.1 models > show #!9.1 models > hide #!9.1 models > show #!9.1 models > hide #!9.1 models > hide #!9.3 models > show #!9.3 models > hide #!8.5 models > show #!8.5 models > hide #!8.1 models > hide #!8.3 models > hide #!8.2 models > hide #!8.4 models > show #!8.4 models > hide #!8.4 models > volume #8.4 level 0.0038 > hide #!9.3 models > show #!9.3 models > hide #!8 models > show #!8 models > hide #!9.3 models > show #!9.3 models > hide #!9.3 models > show #!9.3 models > hide #!9.3 models > show #!9.1 models > show #!9.3 models > hide #!9 models > show #!8.4 models > show #!8.3 models > show #!8.2 models > show #!8.1 models > hide #!8.4 models > show #!9 models > hide #!9.1 models > hide #!9.2 models > hide #!9.3 models > hide #!9.4 models > show #!9.4 models > show #!8.4 models > hide #!8.4 models > show #!8.4 models > hide #!8.3 models > show #!8.3 models > hide #!8.1 models > show #!8.1 models > show #!3 models > hide #!8 models > hide #!9 models > hide #!9.4 models > show #!1 models > hide #!1 models > show #!8 models > hide #!3 models > hide #!8.1 models > show #!8.1 models > show #!9 models > hide #!8 models > show #!9.1 models > show #!9.2 models > show #!9.3 models > show #!9.4 models > hide #!9.3 models > show #!9.3 models > show #!7 models > hide #!7 models > show #!6 models > hide #!9 models > show #!9 models > color zone #9.3 near #6 distance 15.53 > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9.2 models > show #!9.2 models > hide #!9.2 models > show #!9.2 models > show #!7 models > hide #!6 models > hide #!9.2 models > show #!9.2 models > hide #!9.2 models > show #!9.2 models > color zone #9.3 near #6 distance 3.53 > color zone #9.3 near #6 distance 30.53 > color zone #9.3 near #6 distance 300.53 > color zone #9.3 near #6 distance 30.53 > color zone #9.3 near #6 distance 3.53 > color zone #9.3 near #6 distance 15.53 > volume splitbyzone #9.3 Opened coldshock_noncanonHiber_filt.mrc 2 0 as #2.1, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 1 as #2.2, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 2 as #2.3, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 3 as #2.4, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 4 as #2.5, grid size 232,232,232, pixel 2.59, shown at level 0.00374, step 1, values float32 > show #!9.3 models > hide #!9.3 models > show #!9.3 models > hide #!2 models > hide #!9.1 models > hide #!7 models > hide #!9.2 models > show #!8 models > hide #!8.1 models > hide #!8.3 models > hide #!8.4 models > hide #!8.5 models > hide #!9.3 models > show #!9.3 models > hide #!8.2 models > show #!8.2 models > volume all level 0.0038 > show #!9.2 models > hide #!9.2 models > show #!9.2 models > hide #!9.2 models > show #!9.2 models > hide #!9 models > hide #!8 models > show #!3 models > color zone #3 near #6 distance 15.53 > volume splitbyzone #3 Opened coldshock_noncanonHiber_filt.mrc 0 as #4.1, grid size 232,232,232, pixel 2.59, shown at level 0.0038, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 1 as #4.2, grid size 232,232,232, pixel 2.59, shown at level 0.0038, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 2 as #4.3, grid size 232,232,232, pixel 2.59, shown at level 0.0038, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 3 as #4.4, grid size 232,232,232, pixel 2.59, shown at level 0.0038, step 1, values float32 Opened coldshock_noncanonHiber_filt.mrc 4 as #4.5, grid size 232,232,232, pixel 2.59, shown at level 0.0038, step 1, values float32 > show #!2 models > hide #!2 models > hide #!4 models > show #!4 models > show #!3 models > hide #!4 models > show #!4 models > hide #!3 models > hide #!4.3 models > show #!4.3 models > hide #!4.1 models > show #!4.1 models > hide #!4.1 models > show #!4.1 models > ui tool show ""Side View"" > view name sideview_noncanonical_1 > transparency #2.2 60 > transparency #4.2 60 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: MXCV3D/A Chip: Apple M3 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: 90 Tage, 1 Stunde und 50 Minuten Graphics/Displays: Apple M3: Chipset Model: Apple M3 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 Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-ArtiaX: 0.5.0 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 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-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 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: 2.1.6 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: 2.14.2 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 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: 1.18.1 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 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: 1.41 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 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 geomdl: 5.3.1 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 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 openvr: 1.26.701 packaging: 23.2 pandas: 2.2.3 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pyarrow: 18.1.0 pycollada: 0.8 pydantic: 2.10.5 pydantic_core: 2.27.2 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 starfile: 0.5.11 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX