id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14625 silhouettes → tiny boxes xin_gu@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Hi! Thank you so much for your help in advance. I have been having this issue with my chimeraX displaying my cryoEM data. It's strange that whenever I open a density map, if I opaque it, there are a many broken little pieces (look like display artefects) on the map. Also with models, when I export, sometimes I will also see weird looking shapes near the edge of models. Are there ways to solve this? I tried to delete and then reinstall newer version of ChimeraX, it didn't help... Thank you! Log: UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/xingu/Dropbox (HMS)/Midnolin proteasome structural > paper/ChimeraX/Sessions/CryoEM/AAA_Density_PSMD14_Distances.cxs"" format > session Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J1146_deephighRes.mrc as #8, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Log from Thu Jan 11 22:17:31 2024UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models > Colored.cxs"" Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J1146_deephighRes.mrc as #8, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Log from Mon Jan 8 16:16:33 2024UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models > Colored.cxs"" Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown at level 0.14, step 2, values float32 Log from Sat Jan 6 18:38:43 2024UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. > open ""/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Atomic > Models Colored.cxs"" Log from Sat Jan 6 18:11:44 2024UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/MINDUbl_j1332_231230.pdb"" Chain information for MINDUbl_j1332_231230.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available y | No description available z | No description available > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/conf2_j268_noZFAND4_240103.pdb"" Chain information for conf2_j268_noZFAND4_240103.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available y | No description available > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/conf1B_j1146_231114.pdb"" Chain information for conf1B_j1146_231114.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available y | No description available > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/conf1A_j1144_231114.pdb"" Chain information for conf1A_j1144_231114.pdb #4 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available y | No description available > hide #!1 models > hide #!3 models > hide #!4 models > hide #!2 models > show #!2 models > show #!1 models > hide #!2 models > show #!3 models > show #!4 models > show #!2 models > show cartoons > hide atoms > set bgColor white > graphics silhouettes true > lighting soft [Repeated 1 time(s)] > select A Expected an objects specifier or a keyword > select #4/y:380-410 273 atoms, 272 bonds, 31 residues, 1 model selected > select #4/y:380-410 273 atoms, 272 bonds, 31 residues, 1 model selected > select clear > select /y 1698 atoms, 1702 bonds, 1 pseudobond, 204 residues, 5 models selected > ui tool show ""Color Actions"" > color sel light coral > select /A 12413 atoms, 12613 bonds, 3 pseudobonds, 1571 residues, 6 models selected > select /n 5368 atoms, 5433 bonds, 11 pseudobonds, 720 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /o 5260 atoms, 5324 bonds, 16 pseudobonds, 704 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /p 5063 atoms, 5135 bonds, 20 pseudobonds, 657 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /q 5520 atoms, 5620 bonds, 16 pseudobonds, 692 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /r 5728 atoms, 5840 bonds, 8 pseudobonds, 748 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /s 6388 atoms, 6500 bonds, 4 pseudobonds, 824 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /t 6436 atoms, 6556 bonds, 4 pseudobonds, 824 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select /A 12413 atoms, 12613 bonds, 3 pseudobonds, 1571 residues, 6 models selected > color sel light sky blue > select /B 12092 atoms, 12266 bonds, 4 pseudobonds, 1528 residues, 6 models selected > color sel light sky blue > select /C 11796 atoms, 11953 bonds, 3 pseudobonds, 1490 residues, 6 models selected > color sel light sky blue > select /D 12140 atoms, 12341 bonds, 3 pseudobonds, 1509 residues, 7 models selected > color sel light sky blue > select /E 10566 atoms, 10710 bonds, 15 pseudobonds, 1325 residues, 7 models selected > color sel light sky blue > select /F 11233 atoms, 11387 bonds, 7 pseudobonds, 1429 residues, 8 models selected > color sel light sky blue > select /G 7471 atoms, 7607 bonds, 954 residues, 4 models selected > color sel white smoke > select /H 7185 atoms, 7339 bonds, 921 residues, 4 models selected > color sel white smoke > select /I 8085 atoms, 8205 bonds, 1022 residues, 4 models selected > color sel white smoke > select /J 7548 atoms, 7652 bonds, 956 residues, 4 models selected > color sel white smoke > select /K 7059 atoms, 7161 bonds, 4 pseudobonds, 921 residues, 8 models selected > color sel white smoke > select /L 7472 atoms, 7608 bonds, 948 residues, 4 models selected > color sel white smoke > select /M 7654 atoms, 7794 bonds, 975 residues, 4 models selected > color sel white smoke > select /N 5948 atoms, 6052 bonds, 792 residues, 4 models selected > color sel silver > select /n Nothing selected > select /N 5948 atoms, 6052 bonds, 792 residues, 4 models selected > color sel silver > select /O 6668 atoms, 6776 bonds, 884 residues, 4 models selected > color sel silver > select /P 6364 atoms, 6480 bonds, 816 residues, 4 models selected > color sel silver > select /Q 6312 atoms, 6444 bonds, 788 residues, 4 models selected > color sel silver > select /R 6196 atoms, 6320 bonds, 796 residues, 4 models selected > color sel silver > select /S 6572 atoms, 6692 bonds, 848 residues, 4 models selected > color sel silver > select /T 6660 atoms, 6792 bonds, 852 residues, 4 models selected > color sel silver > select /U 26004 atoms, 26457 bonds, 12 pseudobonds, 3334 residues, 8 models selected > color sel lavender > select /V 14097 atoms, 14367 bonds, 2 pseudobonds, 1731 residues, 6 models selected > color sel lemon chiffon > select /W 14198 atoms, 14385 bonds, 2 pseudobonds, 1742 residues, 6 models selected > color sel lemon chiffon > select /X 13172 atoms, 13354 bonds, 2 pseudobonds, 1668 residues, 6 models selected > color sel lemon chiffon > select /Y 12504 atoms, 12736 bonds, 1518 residues, 4 models selected > color sel lemon chiffon > select /Z 9160 atoms, 9332 bonds, 1148 residues, 4 models selected > color sel lemon chiffon > select /a 12048 atoms, 12280 bonds, 1500 residues, 4 models selected > color sel lemon chiffon > select /b 5836 atoms, 5916 bonds, 764 residues, 4 models selected > color sel thistle > select /c 8890 atoms, 9054 bonds, 6 pseudobonds, 1130 residues, 8 models selected > color sel dark sea green > select /d 8453 atoms, 8625 bonds, 6 pseudobonds, 1039 residues, 8 models selected > color sel lemon chiffon > select /e 1287 atoms, 1321 bonds, 4 pseudobonds, 147 residues, 8 models selected > color sel lemon chiffon > select /f 24186 atoms, 24598 bonds, 8 pseudobonds, 3132 residues, 8 models selected > color sel light cyan > select /g Nothing selected > select /y 1698 atoms, 1702 bonds, 1 pseudobond, 204 residues, 5 models selected > color sel light coral > select /z 471 atoms, 481 bonds, 59 residues, 1 model selected > color sel tan > select clear > save ""/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Atomic > Models Colored.cxs"" ——— End of log from Sat Jan 6 18:11:44 2024 ——— opened ChimeraX session > hide #!2 models > hide #!3 models > hide #!4 models > hide #!1 models > show #!4 models > show #!1 models > hide #!4 models > show #!4 models > hide #!4 models > hide #!1 models > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/UblC_j1332/j1332_highRes_resampled.mrc"" Opened j1332_highRes_resampled.mrc as #5, grid size 440,440,440, pixel 0.825, shown at level 0.13, step 2, values float32 > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/Conf2_j268/J268_highres_resampled.mrc"" Opened J268_highres_resampled.mrc as #6, grid size 440,440,440, pixel 0.825, shown at level 0.127, step 2, values float32 > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/Conf1A_j1144/J1144_deephighRes.mrc"" Opened J1144_deephighRes.mrc as #7, grid size 440,440,440, pixel 0.825, shown at level 0.115, step 2, values float32 > hide #!6 models > hide #!7 models > show #!1 models > volume #7 level 0.14 > volume #6 level 0.14 > volume #5 level 0.14 > color zone #5 near #1 distance 4.95 > surface dust #5 size 8.25 > volume zone #5 nearAtoms #1 range 4.95 > hide #!5 models > hide #!1 models > show #!6 models > show #!2 models > color zone #6 near #2 distance 4.95 > surface dust #6 size 8.25 > volume zone #6 nearAtoms #2 range 4.95 > hide #!2 models > hide #!6 models > show #!7 models > show #!4 models > color zone #7 near #4 distance 4.95 > surface dust #7 size 8.25 > volume zone #7 nearAtoms #4 range 4.95 > hide #!4 models > show #!5 models > hide #!7 models > hide #!5 models > show #!5 models > show #!7 models > hide #!5 models > select clear > show #!5 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!5 models > show #!5 models > hide #!7 models > show #!7 models > hide #!5 models > show #!5 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!7 models > show #!7 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!7 models > show #!7 models > show #!5 models > hide #!5 models > show #!5 models > hide #!7 models > hide #!5 models > show #!7 models > hide #!7 models > show #!5 models > hide #!5 models > show #!7 models > show #!5 models > hide #!7 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > show #!7 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!5 models > show #!4 models > show #!1 models > hide #!4 models > show #!4 models > hide #!4 models > save ""/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models > Colored.cxs"" ——— End of log from Sat Jan 6 18:38:43 2024 ——— opened ChimeraX session > open ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/Conf1B_j1146/J1146_deephighRes.mrc"" Opened J1146_deephighRes.mrc as #8, grid size 440,440,440, pixel 0.825, shown at level 0.117, step 2, values float32 > hide #!1 models > show #!4 models > show #!3 models > hide #!4 models > surface dust #8 size 8.25 > color zone #8 near #3 distance 4.95 > volume zone #8 nearAtoms #3 range 4.95 > hide #!3 models > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!7 models > volume #8 level 0.14 > volume #8 level 0.08 > volume #8 level 0.4 > volume #8 level 0.08 > volume #8 level 0.04 > volume #8 level 0.3 > volume #8 level 0.2 > volume #8 level 0.14 > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!7 models > show #!7 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!7 models > save ""/Users/Chris/Desktop/Most Recent Models from Susan 010324/All Models > Colored.cxs"" ——— End of log from Mon Jan 8 16:16:33 2024 ——— opened ChimeraX session > hide #!8 models > show #!1 models > show #!2 models > show #!3 models > show #!4 models > select A/ Expected an objects specifier or a keyword > select A / Expected an objects specifier or a keyword > select / A 12413 atoms, 12613 bonds, 3 pseudobonds, 1571 residues, 6 models selected > select / H 7185 atoms, 7339 bonds, 921 residues, 4 models selected > delete atoms sel > delete bonds sel > select / I 8085 atoms, 8205 bonds, 1022 residues, 4 models selected > delete atoms sel > delete bonds sel > select / J 7548 atoms, 7652 bonds, 956 residues, 4 models selected > delete atoms sel > delete bonds sel > select / K 7059 atoms, 7161 bonds, 4 pseudobonds, 921 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / L 7472 atoms, 7608 bonds, 948 residues, 4 models selected > delete atoms sel > delete bonds sel > select / M 7654 atoms, 7794 bonds, 975 residues, 4 models selected > delete atoms sel > delete bonds sel > select / N 5948 atoms, 6052 bonds, 792 residues, 4 models selected > delete atoms sel > delete bonds sel > select / O 6668 atoms, 6776 bonds, 884 residues, 4 models selected > delete atoms sel > delete bonds sel > select / P 6364 atoms, 6480 bonds, 816 residues, 4 models selected > delete atoms sel > delete bonds sel > select / Q 6312 atoms, 6444 bonds, 788 residues, 4 models selected > delete atoms sel > delete bonds sel > select / R 6196 atoms, 6320 bonds, 796 residues, 4 models selected > delete atoms sel > delete bonds sel > select / S 6572 atoms, 6692 bonds, 848 residues, 4 models selected > delete atoms sel > delete bonds sel > select / T 6660 atoms, 6792 bonds, 852 residues, 4 models selected > delete atoms sel > delete bonds sel > select / U 26004 atoms, 26457 bonds, 12 pseudobonds, 3334 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / V 14097 atoms, 14367 bonds, 2 pseudobonds, 1731 residues, 6 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / W 14198 atoms, 14385 bonds, 2 pseudobonds, 1742 residues, 6 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / X 13172 atoms, 13354 bonds, 2 pseudobonds, 1668 residues, 6 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / Y 12504 atoms, 12736 bonds, 1518 residues, 4 models selected > delete atoms sel > delete bonds sel > select / Z 9160 atoms, 9332 bonds, 1148 residues, 4 models selected > delete atoms sel > delete bonds sel > select / a 12048 atoms, 12280 bonds, 1500 residues, 4 models selected > delete atoms sel > delete bonds sel > select / b 5836 atoms, 5916 bonds, 764 residues, 4 models selected > delete atoms sel > delete bonds sel > select / d 8453 atoms, 8625 bonds, 6 pseudobonds, 1039 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / e 1287 atoms, 1321 bonds, 4 pseudobonds, 147 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / f 24186 atoms, 24598 bonds, 8 pseudobonds, 3132 residues, 8 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > select / g Nothing selected > select / G 7471 atoms, 7607 bonds, 954 residues, 4 models selected > delete atoms sel > delete bonds sel > select / z 471 atoms, 481 bonds, 59 residues, 1 model selected > delete atoms sel > delete bonds sel > select / y 1698 atoms, 1702 bonds, 1 pseudobond, 204 residues, 5 models selected > delete atoms (#!1-4 & sel) > delete bonds (#!1-4 & sel) > hide #!3 models > hide #!2 models > select clear > save ""/Users/Chris/Desktop/Most Recent Models from Susan > 010324/AAA_Density_PSMD14_Distances.cxs"" ——— End of log from Thu Jan 11 22:17:31 2024 ——— opened ChimeraX session > hide #!1 models > show #!8 models > volume #8 color #b2b2b26d OpenGL version: 4.1 INTEL-22.1.29 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2020.61.1.0.0 (iBridge: 21.16.2057.0.0,0) OS Loader Version: 580~1053 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 37 days, 23 hours, 39 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 File attachment: Screenshot 2024-02-22 at 1.58.06 PM.png }}} [attachment:""Screenshot 2024-02-22 at 1.58.06 PM.png""] " defect closed normal Graphics nonchimerax Eric Pettersen all ChimeraX