id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7419 Drag select blacks out graphics asarnow@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description In ChimeraX 1.3 and now in this 1.4 release, I have an issue where control-click dragging to select causes the 3D viewer frame to black out. Everything else functions normally, including the select itself, although it is very difficult to use since the structure can't be seen. The select box *is* visible, but it's magenta instead of green. Afterwards things go back to normal if something was box selected, but if nothing was boxed then the 3D viewer remains blacked out until an interaction like moving the models/camera takes place. I'm on a 2021 M1 MacBook Pro with macOS 12.4. I was wondering if others have experienced this and if it's an M1 issue as this is the only machine I've seen exhibit the problem. Log: > set bgColor white > lighting soft > graphics silhouettes true > alias speed clipper set contourSensitivity 1.0 > alias licorice car style protein modeh default arrows f xsect oval width 1 > thick 1 > alias cylinders cartoon style protein modeh tube rad 2 sides 24 > alias cartoon_default car style protein modeh default arrows t xsect oval > width 2 thick 0.4 UCSF 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/da/Downloads/cryosparc_P502_J119_004_volume_map.mrc Opened cryosparc_P502_J119_004_volume_map.mrc as #1, grid size 288,288,288, pixel 1.26, shown at level 0.258, step 2, values float32 > open pdb:7c2l 7c2l title: S protein of SARS-CoV-2 in complex bound with 4A8 [more info...] Chain information for 7c2l #2 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_SARS2 H I J | heavy chain of 4A8 | L M N | light chain of 4A8 | Non-standard residues in 7c2l #2 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide > ribbon > select add #2 35988 atoms, 36921 bonds, 19 pseudobonds, 4568 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.71762,-0.6803,0.14903,140.64,-0.51778,-0.66428,-0.53911,432.68,0.46576,0.30971,-0.82894,108.7 > view matrix models > #2,0.71762,-0.6803,0.14903,142.1,-0.51778,-0.66428,-0.53911,455.05,0.46576,0.30971,-0.82894,144.65 > view matrix models > #2,0.76222,-0.6308,-0.14533,164.05,-0.62613,-0.66147,-0.41281,454.35,0.16427,0.40565,-0.89915,180.36 > view matrix models > #2,0.76222,-0.6308,-0.14533,193.94,-0.62613,-0.66147,-0.41281,445.2,0.16427,0.40565,-0.89915,200.36 > view matrix models > #2,0.75785,-0.61373,-0.22135,201.16,-0.64707,-0.66367,-0.37528,443.89,0.083418,0.42764,-0.90009,208.34 > view matrix models > #2,0.99255,-0.081786,0.090339,35.329,-0.053614,-0.9588,-0.27897,397.38,0.10943,0.27205,-0.95604,238.72 > view matrix models > #2,0.99255,-0.081786,0.090339,36.635,-0.053614,-0.9588,-0.27897,392.28,0.10943,0.27205,-0.95604,237.77 > view matrix models > #2,0.97511,-0.20633,-0.081204,82.434,-0.21873,-0.95518,-0.19949,405.54,-0.036403,0.21229,-0.97653,271.85 > view matrix models > #2,0.9866,-0.09676,0.13134,34.947,-0.052623,-0.95083,-0.3052,394.05,0.15441,0.2942,-0.94319,225.79 > view matrix models > #2,0.9866,-0.09676,0.13134,26.745,-0.052623,-0.95083,-0.3052,383.77,0.15441,0.2942,-0.94319,227.06 > view matrix models > #2,0.99677,-0.05179,0.06143,26.232,-0.023254,-0.91777,-0.39642,385.23,0.07691,0.39371,-0.91601,217.51 > view matrix models > #2,0.99677,-0.05179,0.06143,32.899,-0.023254,-0.91777,-0.39642,392.14,0.07691,0.39371,-0.91601,223.09 > view matrix models > #2,0.99677,-0.05179,0.06143,32.884,-0.023254,-0.91777,-0.39642,392.15,0.07691,0.39371,-0.91601,223.32 > view matrix models > #2,0.99677,-0.05179,0.06143,32.851,-0.023254,-0.91777,-0.39642,392.32,0.07691,0.39371,-0.91601,223.53 > view matrix models > #2,0.99677,-0.05179,0.06143,32.875,-0.023254,-0.91777,-0.39642,385.87,0.07691,0.39371,-0.91601,236.75 > view matrix models > #2,0.93614,0.30092,0.1819,-34.967,0.34883,-0.85986,-0.37276,318.98,0.044241,0.41241,-0.90993,237.45 > view matrix models > #2,0.93701,0.29519,0.18675,-34.705,0.34789,-0.83673,-0.42291,321.4,0.031417,0.46124,-0.88672,227.88 > view matrix models > #2,0.93701,0.29519,0.18675,-35.488,0.34789,-0.83673,-0.42291,326.56,0.031417,0.46124,-0.88672,230.34 > view matrix models > #2,0.86858,0.42544,0.2541,-56.758,0.49478,-0.77307,-0.39693,290.96,0.027568,0.47049,-0.88198,228.69 > view matrix models > #2,0.86858,0.42544,0.2541,-57.753,0.49478,-0.77307,-0.39693,298.96,0.027568,0.47049,-0.88198,228.78 > view matrix models > #2,0.78756,0.54814,0.28159,-70.872,0.6162,-0.69574,-0.36912,264.42,-0.0064174,0.46422,-0.8857,235.26 > fitmap #2/A-C inMap #1 Fit molecule 7c2l (#2) to map cryosparc_P502_J119_004_volume_map.mrc (#1) using 24910 atoms average map value = 0.2634, steps = 224 shifted from previous position = 12.2 rotated from previous position = 11.3 degrees atoms outside contour = 13486, contour level = 0.25755 Position of 7c2l (#2) relative to cryosparc_P502_J119_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation 0.70320972 0.61194990 0.36195781 -78.57162253 0.69949782 -0.68661755 -0.19813940 213.71189935 0.12727519 0.39252224 -0.91089372 234.35174082 Axis 0.92063952 0.36578995 0.13645726 Axis point 0.00000000 101.95823201 140.88291766 Rotation angle (degrees) 161.28936710 Shift along axis 37.81652043 > volume #1 level 0.4952 > view matrix models > #2,0.71295,0.67906,0.17487,-68.145,0.69514,-0.65167,-0.30349,221.5,-0.092133,0.33794,-0.93665,278.83 > view matrix models > #2,-0.4388,0.82656,0.35249,50.39,0.8975,0.4224,0.12677,-49.031,-0.044103,0.37198,-0.92719,264.77 > view matrix models > #2,-0.4388,0.82656,0.35249,58.389,0.8975,0.4224,0.12677,-45.163,-0.044103,0.37198,-0.92719,264.63 > view matrix models > #2,-0.4388,0.82656,0.35249,59.171,0.8975,0.4224,0.12677,-45.098,-0.044103,0.37198,-0.92719,264.6 > fitmap #2/A-C inMap #1 Fit molecule 7c2l (#2) to map cryosparc_P502_J119_004_volume_map.mrc (#1) using 24910 atoms average map value = 0.3122, steps = 144 shifted from previous position = 4.91 rotated from previous position = 13.6 degrees atoms outside contour = 19703, contour level = 0.49518 Position of 7c2l (#2) relative to cryosparc_P502_J119_004_volume_map.mrc (#1) coordinates: Matrix rotation and translation -0.33225250 0.86832404 0.36826853 38.10694171 0.93132412 0.24029092 0.27367085 -41.13171866 0.14914339 0.43390517 -0.88852834 221.36523818 Axis 0.57498590 0.78631012 0.22606992 Axis point 43.54828532 0.00000000 115.91298057 Rotation angle (degrees) 171.99048214 Shift along axis 39.61268839 > volume #1 level 0.4067 > vop flip #1 Opened cryosparc_P502_J119_004_volume_map.mrc z flip as #3, grid size 288,288,288, pixel 1.26, shown at step 1, values float32 > view matrix models > #2,0.27854,-0.91013,-0.30673,344.55,0.95145,0.21794,0.21735,-33.065,-0.13097,-0.35238,0.92665,170.59 > view matrix models > #2,0.27854,-0.91013,-0.30673,334.7,0.95145,0.21794,0.21735,-32.5,-0.13097,-0.35238,0.92665,131.39 > view matrix models > #2,-0.63436,-0.70619,-0.31445,432.17,0.76269,-0.50543,-0.40354,198.93,0.12605,-0.49582,0.85923,127.69 > view matrix models > #2,-0.63436,-0.70619,-0.31445,438.74,0.76269,-0.50543,-0.40354,203.19,0.12605,-0.49582,0.85923,120.74 > view matrix models > #2,-0.61634,-0.71994,-0.31908,439.11,0.77623,-0.48718,-0.40015,197.62,0.13264,-0.49431,0.85911,119.54 > view matrix models > #2,-0.61638,-0.71679,-0.32601,439.44,0.78019,-0.49978,-0.3762,196.23,0.10672,-0.48623,0.86729,120.85 > view matrix models > #2,-0.66904,-0.67425,-0.3127,437.97,0.73689,-0.54693,-0.39731,213.37,0.096856,-0.49624,0.86276,124.59 > view matrix models > #2,-0.66904,-0.67425,-0.3127,440.34,0.73689,-0.54693,-0.39731,211,0.096856,-0.49624,0.86276,124.09 > view matrix models > #2,0.97036,-0.15496,-0.18545,96.749,0.20772,0.92701,0.31226,-58.537,0.12352,-0.34152,0.93172,84.601 > view matrix models > #2,0.97036,-0.15496,-0.18545,82.727,0.20772,0.92701,0.31226,-57.043,0.12352,-0.34152,0.93172,84.103 > view matrix models > #2,0.95274,-0.21699,-0.21263,99.501,0.27517,0.91296,0.3013,-62.972,0.12874,-0.34556,0.92952,84.33 > view matrix models > #2,0.95541,-0.27338,-0.11158,96.232,0.29483,0.90406,0.30944,-65.288,0.016279,-0.32854,0.94435,95.764 > view matrix models > #2,0.95885,-0.25769,-0.11913,93.95,0.2836,0.85015,0.44363,-71.148,-0.013044,-0.45917,0.88825,129.82 > select up 35988 atoms, 36921 bonds, 19 pseudobonds, 4568 residues, 2 models selected > select up 35988 atoms, 36921 bonds, 19 pseudobonds, 4568 residues, 6 models selected > select clear Drag select of 61 residues > select up 910 atoms, 924 bonds, 125 residues, 1 model selected > select up 3394 atoms, 3475 bonds, 448 residues, 1 model selected > select up 35988 atoms, 36921 bonds, 4568 residues, 1 model selected > fitmap #2/A-C inMap #3 Fit molecule 7c2l (#2) to map cryosparc_P502_J119_004_volume_map.mrc z flip (#3) using 24910 atoms average map value = 0.5485, steps = 120 shifted from previous position = 7.47 rotated from previous position = 8.14 degrees atoms outside contour = 7331, contour level = 0.4067 Position of 7c2l (#2) relative to cryosparc_P502_J119_004_volume_map.mrc z flip (#3) coordinates: Matrix rotation and translation 0.98109307 -0.19351658 -0.00279454 63.18497752 0.17003260 0.85495714 0.49003800 -55.81814705 -0.09244126 -0.48124803 0.87169662 143.02112560 Axis -0.93306613 0.08611914 0.34924359 Axis point 0.00000000 257.19630339 187.60387694 Rotation angle (degrees) 31.36450730 Shift along axis -13.81356176 > select clear > volume #3 level 0.07212 > open /Users/da/Downloads/cryosparc_P502_J121_class_00_00062_volume.mrc Opened cryosparc_P502_J121_class_00_00062_volume.mrc as #4, grid size 288,288,288, pixel 1.26, shown at level 0.29, step 2, values float32 > vop flip #4 Opened cryosparc_P502_J121_class_00_00062_volume.mrc z flip as #5, grid size 288,288,288, pixel 1.26, shown at step 1, values float32 > volume #5 level 0.05872 > volume #5 level 0.2632 > volume #5 level 0.2648 > volume #5 level 0.2698 > volume #5 level 0.06869 > volume #5 level 0.02714 > volume #5 level 0.06537 > volume #3 level 0.3033 > volume #3 level 0.5046 > volume #3 level 0.2489 > volume #3 level 0.4475 > volume #3 level 0.2353 > volume #3 level 0.3523 > volume #3 level 0.4176 > volume #3 level 0.5155 > volume #3 level 0.4475 > volume #3 level 0.2653 > open pdb:7c2l 7c2l title: S protein of SARS-CoV-2 in complex bound with 4A8 [more info...] Chain information for 7c2l #6 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_SARS2 H I J | heavy chain of 4A8 | L M N | light chain of 4A8 | Non-standard residues in 7c2l #6 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide > ribbon > mmaker #6/A to #1/A No 'to' model specified > mmaker #6/A to #2/A Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7c2l, chain A (#2) with 7c2l, chain A (#6), sequence alignment score = 6252.9 RMSD between 1031 pruned atom pairs is 0.000 angstroms; (across all 1031 pairs: 0.000) > mmaker #6 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7c2l, chain B (#2) with 7c2l, chain B (#6), sequence alignment score = 6291.9 RMSD between 1055 pruned atom pairs is 0.000 angstroms; (across all 1055 pairs: 0.000) > select #6/M 1688 atoms, 1727 bonds, 219 residues, 1 model selected > select #6/N 1688 atoms, 1727 bonds, 219 residues, 1 model selected > select #6/L 1688 atoms, 1727 bonds, 219 residues, 1 model selected > select #6/I,M 3394 atoms, 3475 bonds, 448 residues, 1 model selected > ui hideFloating toggle > select ~sel & #6 32594 atoms, 33446 bonds, 19 pseudobonds, 4120 residues, 2 models selected > delete sel > fitmap #6 inMap #3 Fit molecule 7c2l (#6) to map cryosparc_P502_J119_004_volume_map.mrc z flip (#3) using 3394 atoms average map value = 0.3096, steps = 68 shifted from previous position = 1.5 rotated from previous position = 2.22 degrees atoms outside contour = 1163, contour level = 0.26525 Position of 7c2l (#6) relative to cryosparc_P502_J119_004_volume_map.mrc z flip (#3) coordinates: Matrix rotation and translation 0.97392177 -0.22670452 0.00902517 71.24812260 0.19502773 0.85683881 0.47727501 -61.27045637 -0.11593352 -0.46306837 0.87870764 141.79956856 Axis -0.90580313 0.12036876 0.40624138 Axis point 0.00000000 265.24806933 204.32993708 Rotation angle (degrees) 31.26962767 Shift along axis -14.30696858 > open pdb:7c2l 7c2l title: S protein of SARS-CoV-2 in complex bound with 4A8 [more info...] Chain information for 7c2l #7 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_SARS2 H I J | heavy chain of 4A8 | L M N | light chain of 4A8 | Non-standard residues in 7c2l #7 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide > ribbon > mmaker #7 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7c2l, chain B (#2) with 7c2l, chain B (#7), sequence alignment score = 6291.9 RMSD between 1055 pruned atom pairs is 0.000 angstroms; (across all 1055 pairs: 0.000) > volume #3 level 0.0966 > volume #3 level 0.1075 > volume #3 level 0.05036 > volume #3 level 0.015 > volume #3 level 0.0286 > volume #3 level 0.03404 > volume #3 level 0.05852 > volume #3 level 0.09116 > select #7/J 1706 atoms, 1748 bonds, 229 residues, 1 model selected > select #7/J,N 3394 atoms, 3475 bonds, 448 residues, 1 model selected > select ~sel & #7 32594 atoms, 33446 bonds, 19 pseudobonds, 4120 residues, 2 models selected > delete sel > color #6 red > color #7 blue > color #2 bychain > hide #!2 models > show #!2 models > volume #3 level 0.2244 > volume #3 level 0.05308 > open pdb:7c2l 7c2l title: S protein of SARS-CoV-2 in complex bound with 4A8 [more info...] Chain information for 7c2l #8 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_SARS2 H I J | heavy chain of 4A8 | L M N | light chain of 4A8 | Non-standard residues in 7c2l #8 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > hide > ribbon > mmaker #8 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7c2l, chain B (#2) with 7c2l, chain B (#8), sequence alignment score = 6291.9 RMSD between 1055 pruned atom pairs is 0.000 angstroms; (across all 1055 pairs: 0.000) > select clear Drag select of 156 residues > select clear > hide #!2 models > hide #!7 models > show #!7 models > hide #!6 models > show #!6 models > hide #!8 models > show #!8 models Drag select of 164 residues > select up 1507 atoms, 1540 bonds, 200 residues, 1 model selected > select up 3394 atoms, 3475 bonds, 448 residues, 1 model selected > select ~sel & #8 32594 atoms, 33446 bonds, 19 pseudobonds, 4120 residues, 2 models selected > delete sel > show #!2 models > select clear [Repeated 1 time(s)] > volume #3 level 0.1401 > volume #3 level 0.05852 > vop gaussian #3 sDev 3 Opened cryosparc_P502_J119_004_volume_map.mrc z flip gaussian as #9, grid size 288,288,288, pixel 1.26, shown at step 1, values float32 > select clear Drag select of 853 residues, 2 pseudobonds, 9 cryosparc_P502_J119_004_volume_map.mrc z flip gaussian > select clear [Repeated 1 time(s)] > lighting simple > select clear [Repeated 1 time(s)] > lighting soft OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 20 days 6:10 Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: HP 23f: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Graphics fixed all ChimeraX