id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8226 Unsupported scale factor (0.000000) detected on Display0 kelvin.lau@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.6.1-arm64-arm-64bit ChimeraX Version: 1.6.dev202212061854 (2022-12-06 18:54:31 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00000001002cc580 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 284 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2022-12-23 15:38:46.00 +0100"",""app_version"":""1.6.0"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.6.1 (21G217)"",""incident_id"":""75277C2A-7508-466A-B610-F8FBAE481D1D"",""name"":""ChimeraX""} { ""uptime"" : 1100000, ""procLaunch"" : ""2022-12-22 09:49:40.3289 +0100"", ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,4"", ""procStartAbsTime"" : 26871231372981, ""coalitionID"" : 247878, ""osVersion"" : { ""train"" : ""macOS 12.6.1"", ""build"" : ""21G217"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2022-12-23 15:35:20.3367 +0100"", ""incident"" : ""75277C2A-7508-466A-B610-F8FBAE481D1D"", ""bug_type"" : ""309"", ""pid"" : 4804, ""procExitAbsTime"" : 28030116930814, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D91302BD-DBCE-5C53-8136-7D7F3BF49D6F"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""F0D674B1-5FA4-E9D0-6B9C-8D1ED9987542"", ""wakeTime"" : 22773, ""sleepWakeUUID"" : ""078C4E2B-E764-4E06-892C-46AF3304BEDD"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/kelvinlau/Downloads/cryosparc_P6_J81_004_volume_map_sharp.mrc Opened cryosparc_P6_J81_004_volume_map_sharp.mrc as #1, grid size 250,250,250, pixel 1.66, shown at level 0.0934, step 1, values float32 > volume #1 level 0.1699 > surface dust #1 size 16.6 > open > /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb Chain information for SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb #2 --- Chain | Description A | No description available > open > /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb Chain information for SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb #3 --- Chain | Description A | No description available > close #3 > select add #2 9282 atoms, 9503 bonds, 1191 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,238.29,0,1,0,160.08,0,0,1,63.535 > view matrix models #2,1,0,0,268.35,0,1,0,103.19,0,0,1,165.1 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.50961,-0.10696,0.85373,262.71,-0.22592,0.94079,0.25272,100.6,-0.83022,-0.32166,0.45528,155.62 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.50961,-0.10696,0.85373,196.11,-0.22592,0.94079,0.25272,230.53,-0.83022,-0.32166,0.45528,200.66 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.49784,-0.19129,0.84591,196.02,-0.15047,0.94153,0.30147,231.4,-0.85412,-0.27737,0.43994,200.36 > view matrix models > #2,0.13946,0.46657,0.87342,191.49,-0.35554,0.84682,-0.39559,229.07,-0.9242,-0.25537,0.28399,199.53 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.13946,0.46657,0.87342,199.37,-0.35554,0.84682,-0.39559,235.61,-0.9242,-0.25537,0.28399,205.47 > ui mousemode right select > fitmap #2 inMap #1 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) to map cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) using 9282 atoms average map value = 0.086, steps = 84 shifted from previous position = 8.12 rotated from previous position = 6.55 degrees atoms outside contour = 7068, contour level = 0.16994 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) relative to cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.20825569 0.51136147 0.83374997 206.39416826 -0.42245097 0.81585364 -0.39486454 231.44674363 -0.88213647 -0.26998570 0.38593131 202.15824498 Axis 0.06379456 0.87656343 -0.47703963 Axis point 276.81499655 0.00000000 24.47113983 Rotation angle (degrees) 78.16931126 Shift along axis 119.60708187 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.20826,0.51136,0.83375,89.2,-0.42245,0.81585,-0.39486,239.57,-0.88214,-0.26999,0.38593,203.41 > select clear > select add #2 9282 atoms, 9503 bonds, 1191 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.2559,0.43621,0.86269,89.795,-0.31797,0.88073,-0.35101,240.75,-0.91291,-0.18449,0.36408,203.01 > view matrix models > #2,-0.4747,0.87397,0.10415,81.061,-0.72608,-0.32197,-0.60757,236.66,-0.49747,-0.36403,0.7874,207.94 > view matrix models > #2,0.62893,0.43037,0.64748,94.135,-0.4547,0.87914,-0.14268,239.16,-0.63063,-0.20467,0.74861,206.3 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.62893,0.43037,0.64748,211.11,-0.4547,0.87914,-0.14268,225.04,-0.63063,-0.20467,0.74861,218.81 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.771,0.063459,0.63366,212.96,-0.25069,0.94493,0.2104,227.37,-0.58541,-0.32107,0.74445,219.4 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.771,0.063459,0.63366,208.02,-0.25069,0.94493,0.2104,227.33,-0.58541,-0.32107,0.74445,214.53 > hide #2 models > show #2 models > hide #2 models > show #2 models > view matrix models > #2,0.771,0.063459,0.63366,204.85,-0.25069,0.94493,0.2104,227.07,-0.58541,-0.32107,0.74445,202.91 > view matrix models > #2,0.771,0.063459,0.63366,204.6,-0.25069,0.94493,0.2104,226.89,-0.58541,-0.32107,0.74445,202.1 > fitmap #2 inMap #1 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) to map cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) using 9282 atoms average map value = 0.09942, steps = 128 shifted from previous position = 13.4 rotated from previous position = 12.4 degrees atoms outside contour = 6548, contour level = 0.16994 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#2) relative to cryosparc_P6_J81_004_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.78888549 -0.13060681 0.60050108 201.64318990 -0.04479087 0.96233622 0.26814695 215.28574743 -0.61290575 -0.23843420 0.75332308 197.44056504 Axis -0.38444217 0.92084902 0.06512533 Axis point 418.32043794 0.00000000 -274.24590614 Rotation angle (degrees) 41.21239498 Shift along axis 133.58390578 > hide #2 models > open /Users/kelvinlau/Downloads/cryosparc_P6_J103_003_volume_map_sharp.mrc Opened cryosparc_P6_J103_003_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 1.38, shown at level 0.105, step 2, values float32 > surface dust #3 size 13.8 > volume #3 step 1 > surface dust #3 size 13.8 > volume #3 level 0.1602 > volume #3 level 0.2099 > open > /Users/kelvinlau/Downloads/30BRBD_819d3.result/30BRBD_819d3_unrelaxed_rank_1_model_5.pdb Chain information for 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb #4 --- Chain | Description A | No description available > select add #4 12225 atoms, 12521 bonds, 1568 residues, 2 models selected > select clear > select #4/A:264 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 60 atoms, 59 bonds, 9 residues, 1 model selected > select up 2943 atoms, 3018 bonds, 377 residues, 1 model selected > select clear Drag select of 132 residues > delete atoms sel > delete bonds sel Drag select of 17 residues > delete atoms sel > delete bonds sel Drag select of 28 residues, 3 pseudobonds > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) Drag select of 4 residues, 2 pseudobonds > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > select clear Drag select of 3 residues, 1 pseudobonds > delete atoms (#!4 & sel) > delete bonds (#!4 & sel) > select clear Drag select of 192 residues, 1 pseudobonds > select clear Alignment identifier is 2/A Alignment identifier is 4/A > select #4/A:293 7 atoms, 7 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select #4/A:227 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 84 atoms, 86 bonds, 10 residues, 1 model selected > select up 1526 atoms, 1573 bonds, 192 residues, 1 model selected > view matrix models #4,1,0,0,72.441,0,1,0,94.915,0,0,1,-80.71 > view matrix models #4,1,0,0,64.732,0,1,0,82.769,0,0,1,189.15 > view matrix models #4,1,0,0,116,0,1,0,91.709,0,0,1,241.17 > view matrix models #4,1,0,0,189.43,0,1,0,188.52,0,0,1,177.36 > volume #3 level 0.1768 > volume #3 level 0.1381 > volume #3 level 0.08296 > volume #3 level 0.1106 > open /Users/kelvinlau/Downloads/cryosparc_P6_J105_000_volume_map_sharp.mrc Opened cryosparc_P6_J105_000_volume_map_sharp.mrc as #5, grid size 300,300,300, pixel 1.38, shown at level 0.0411, step 2, values float32 > volume #5 step 1 > volume #5 level 0.07638 > volume #5 level 0.05993 > volume #3 color #ffffb280 > lighting soft > lighting simple > lighting soft > lighting simple > lighting full > volume #3 color #9fe3ff80 > color #4 #ee4a4fff > view matrix models #4,1,0,0,153.28,0,1,0,146.66,0,0,1,197.88 > volume #3 color #9fe3ff > volume #3 level 0.2128 > view matrix models #4,1,0,0,154.28,0,1,0,146.99,0,0,1,194.61 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.55931,0.59264,-0.57961,172.22,0.3337,0.80101,0.49701,147.24,0.75882,0.084566,-0.64578,164.71 > view matrix models > #4,-0.80216,-0.17769,-0.57006,176.13,-0.47414,0.76984,0.42723,159.07,0.36294,0.613,-0.70179,170.26 > view matrix models > #4,-0.56047,-0.65909,-0.50147,173.12,0.39694,-0.74522,0.5358,146.7,-0.72685,0.10125,0.6793,202.42 > view matrix models > #4,-0.087518,-0.99615,0.0057904,171.32,0.81394,-0.068156,0.57694,140.64,-0.57432,0.055206,0.81677,201.55 > view matrix models > #4,0.24137,-0.93356,-0.26496,163.22,0.72605,-0.0074357,0.6876,143.22,-0.64389,-0.35834,0.67602,201.1 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.24137,-0.93356,-0.26496,204.57,0.72605,-0.0074357,0.6876,157.76,-0.64389,-0.35834,0.67602,176.12 > view matrix models > #4,0.24137,-0.93356,-0.26496,209.09,0.72605,-0.0074357,0.6876,182.17,-0.64389,-0.35834,0.67602,193.12 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.23746,-0.97127,0.015804,212.23,0.65669,0.1725,0.73416,183.76,-0.7158,-0.16396,0.67879,194.26 > select clear > hide #!4 models > show #!4 models > select add #4 1526 atoms, 1573 bonds, 192 residues, 1 model selected > fitmap #4 inMap #3 Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map cryosparc_P6_J103_003_volume_map_sharp.mrc (#3) using 1526 atoms average map value = 0.08419, steps = 100 shifted from previous position = 2.68 rotated from previous position = 7.78 degrees atoms outside contour = 1170, contour level = 0.21283 Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to cryosparc_P6_J103_003_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.36206110 -0.93104562 0.04545116 211.40525616 0.63727304 0.28281559 0.71686708 181.56403030 -0.68029025 -0.23058489 0.69572680 192.78660277 Axis -0.48074878 0.36825012 0.79578418 Axis point 61.05282466 246.49229503 0.00000000 Rotation angle (degrees) 80.19463617 Shift along axis 118.64468512 > view matrix models > #4,0.34203,-0.9275,-0.15084,209.56,0.86024,0.24446,0.44747,175.13,-0.37815,-0.28281,0.88149,190.11 > view matrix models > #4,0.42032,-0.84767,-0.32371,206.44,0.86893,0.27328,0.41264,174.61,-0.26131,-0.45472,0.85144,187.96 > view matrix models > #4,0.56188,-0.74319,-0.36326,203.8,0.75057,0.27342,0.60158,178.53,-0.34776,-0.61066,0.71144,187.78 > view matrix models > #4,0.44402,-0.76285,-0.47002,204.47,0.79699,0.096531,0.59623,177.75,-0.40946,-0.63933,0.65084,188.08 > select clear > volume flip #3 Opened cryosparc_P6_J103_003_volume_map_sharp.mrc z flip as #6, grid size 300,300,300, pixel 1.38, shown at step 1, values float32 > fitmap #4 inMap #6 Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms average map value = 0.06091, steps = 100 shifted from previous position = 6.54 rotated from previous position = 6.37 degrees atoms outside contour = 1263, contour level = 0.21283 Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates: Matrix rotation and translation 0.49114731 -0.70417853 -0.51274449 206.07445746 0.76098264 0.06041915 0.64595274 184.69476976 -0.42388646 -0.70744761 0.56554235 186.38457813 Axis -0.67786324 -0.04450538 0.73383970 Axis point 56.04003946 241.43186192 0.00000000 Rotation angle (degrees) 86.64315955 Shift along axis -11.13380684 > fitmap #4 inMap #6 Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms average map value = 0.0609, steps = 60 shifted from previous position = 0.0193 rotated from previous position = 0.0396 degrees atoms outside contour = 1267, contour level = 0.21283 Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates: Matrix rotation and translation 0.49138650 -0.70443574 -0.51216169 206.06131280 0.76076653 0.06088596 0.64616344 184.70546684 -0.42399716 -0.70715146 0.56582967 186.37997272 Axis -0.67784031 -0.04415932 0.73388178 Axis point 55.95166640 241.48671085 0.00000000 Rotation angle (degrees) 86.61465388 Shift along axis -11.05226510 > fitmap #4 inMap #6 Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms average map value = 0.06087, steps = 44 shifted from previous position = 0.025 rotated from previous position = 0.0733 degrees atoms outside contour = 1266, contour level = 0.21283 Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates: Matrix rotation and translation 0.49101548 -0.70389658 -0.51325764 206.06476567 0.76119997 0.06014995 0.64572176 184.70941009 -0.42364892 -0.70775108 0.56534061 186.38554941 Axis -0.67788758 -0.04488057 0.73379436 Axis point 56.07098321 241.40822333 0.00000000 Rotation angle (degrees) 86.66045746 Shift along axis -11.20994306 > surface dust #6 size 13.8 > hide #!4 models > show #!4 models > select add #4 1526 atoms, 1573 bonds, 192 residues, 1 model selected > view matrix models > #4,-0.89146,0.45095,0.043991,233.72,-0.01105,0.075423,-0.99709,178.73,-0.45296,-0.88936,-0.062254,179.96 > view matrix models > #4,-0.91028,0.38768,-0.14523,231.94,0.16457,0.016954,-0.98622,176.11,-0.37988,-0.92164,-0.079232,178.63 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.91028,0.38768,-0.14523,248.08,0.16457,0.016954,-0.98622,102.95,-0.37988,-0.92164,-0.079232,207.95 > view matrix models > #4,-0.91028,0.38768,-0.14523,262.5,0.16457,0.016954,-0.98622,107.93,-0.37988,-0.92164,-0.079232,219.32 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.14928,0.85422,0.49802,253.03,-0.48951,0.50146,-0.71339,121.12,-0.85913,-0.13729,0.49301,233.06 > view matrix models > #4,0.52024,0.71757,0.46307,246.86,-0.47325,0.69359,-0.54311,122.73,-0.71091,0.063398,0.70042,233.02 > view matrix models > #4,0.010456,-0.0014918,0.99994,260.72,0.45443,0.89078,-0.0034227,114.18,-0.89072,0.45444,0.0099916,228.24 > view matrix models > #4,-0.60486,-0.13448,0.7849,267.96,0.29107,0.8801,0.3751,120.88,-0.74123,0.45534,-0.49319,220.39 > view matrix models > #4,0.046977,-0.75109,-0.65853,241.96,-0.83002,0.33744,-0.44408,129.38,0.55576,0.56745,-0.60756,198.9 > view matrix models > #4,0.47398,-0.65094,-0.59298,236.02,-0.78076,0.00068232,-0.62483,126.64,0.40713,0.75913,-0.5079,202.31 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.47398,-0.65094,-0.59298,183.09,-0.78076,0.00068232,-0.62483,173.32,0.40713,0.75913,-0.5079,244.3 > view matrix models > #4,0.47398,-0.65094,-0.59298,178.72,-0.78076,0.00068232,-0.62483,184.82,0.40713,0.75913,-0.5079,234.87 > view matrix models > #4,0.47398,-0.65094,-0.59298,197.08,-0.78076,0.00068232,-0.62483,185.77,0.40713,0.75913,-0.5079,233.28 > view matrix models > #4,0.47398,-0.65094,-0.59298,195.81,-0.78076,0.00068232,-0.62483,181.62,0.40713,0.75913,-0.5079,237.62 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.19048,-0.50759,-0.84028,197.51,-0.75338,0.4732,-0.45662,183.03,0.62939,0.72003,-0.29227,236.52 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.19048,-0.50759,-0.84028,198.54,-0.75338,0.4732,-0.45662,190.6,0.62939,0.72003,-0.29227,241.97 > fitmap #4 inMap #6 Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms average map value = 0.1316, steps = 84 shifted from previous position = 4.3 rotated from previous position = 8.9 degrees atoms outside contour = 1061, contour level = 0.21283 Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates: Matrix rotation and translation 0.24636656 -0.38602508 -0.88898153 195.59638625 -0.72305283 0.53758348 -0.43381862 194.12555926 0.64536667 0.74965901 -0.14667393 241.89623326 Axis 0.60171745 -0.78011113 -0.17135556 Axis point 50.47811682 0.00000000 228.12751276 Rotation angle (degrees) 100.44909898 Shift along axis -75.19601607 > view matrix models > #4,0.24637,-0.38603,-0.88898,195,-0.72305,0.53758,-0.43382,195,0.64537,0.74966,-0.14667,242.93 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.11804,-0.51068,-0.85163,197.42,-0.64468,0.6129,-0.45688,193.52,0.75528,0.60296,-0.25687,240.01 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #4,0.11804,-0.51068,-0.85163,197.16,-0.64468,0.6129,-0.45688,193.66,0.75528,0.60296,-0.25687,235.12 > fitmap #4 inMap #6 Fit molecule 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) to map cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) using 1526 atoms average map value = 0.3923, steps = 84 shifted from previous position = 1.86 rotated from previous position = 16.9 degrees atoms outside contour = 483, contour level = 0.21283 Position of 30BRBD_819d3_unrelaxed_rank_1_model_5.pdb (#4) relative to cryosparc_P6_J103_003_volume_map_sharp.mrc z flip (#6) coordinates: Matrix rotation and translation 0.14031735 -0.38665532 -0.91148709 196.13561642 -0.44327644 0.79864567 -0.40702712 190.95763357 0.88533443 0.46115373 -0.05933135 233.46609381 Axis 0.43487873 -0.90004227 -0.02836198 Axis point 23.47046957 0.00000000 237.51027308 Rotation angle (degrees) 93.45038349 Shift along axis -93.19629312 > select subtract #4 Nothing selected > color #6 #9fe3ffa1 models > save /Users/kelvinlau/Desktop/image1.png supersample 3 > save /Users/kelvinlau/Downloads/103_sharp_zflipped.ccp4 models #6 > save /Users/kelvinlau/Downloads/RBD-docked-103.pdb models #4 relModel #6 > open /Users/kelvinlau/Downloads/RBD-docked-103-coot-0.pdb Chain information for RBD-docked-103-coot-0.pdb #7 --- Chain | Description A | No description available > hide #!6 models > color #7 #2166acff > close #7 > open /Users/kelvinlau/Downloads/RBD-docked-103-coot-0.pdb Chain information for RBD-docked-103-coot-0.pdb #7 --- Chain | Description A | No description available > color #7 #6bffd5ff > color #4,7 byhetero > open 7m0j Summary of feedback from opening 7m0j fetched from pdb --- note | Fetching compressed mmCIF 7m0j from http://files.rcsb.org/download/7m0j.cif 7m0j title: SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer - asymmetric refinement [more info...] Chain information for 7m0j #8 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_SARS2 > mmaker £7 to £8 > matchmaker £7 to £8 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > mmaker #8 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7m0j, chain B (#8), sequence alignment score = 1146.2 RMSD between 138 pruned atom pairs is 0.941 angstroms; (across all 161 pairs: 1.831) > mmaker #8 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7m0j, chain B (#8), sequence alignment score = 1146.2 RMSD between 138 pruned atom pairs is 0.941 angstroms; (across all 161 pairs: 1.831) > close #8 > open 7pki format mmcif fromDatabase pdb 7pki title: Crystal structure of human ACE2 bound to the spike receptor-binding domain from a cave bat sarbecovirus closely related to SARS-CoV-2. [more info...] Chain information for 7pki #8 --- Chain | Description | UniProt A | Processed angiotensin-converting enzyme 2 | ACE2_HUMAN E | BANAL 236 coronavirus spike receptor-binding domain | Non-standard residues in 7pki #8 --- CL — chloride ion GOL — glycerol (glycerin; propane-1,2,3-triol) 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) PEG — di(hydroxyethyl)ether SO4 — sulfate ion TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) ZN — zinc ion > mmaker #8 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7pki, chain E (#8), sequence alignment score = 703.4 RMSD between 158 pruned atom pairs is 0.966 angstroms; (across all 190 pairs: 2.336) > open 6m0j 6m0j title: Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2 [more info...] Chain information for 6m0j #9 --- Chain | Description | UniProt A | Angiotensin-converting enzyme 2 | ACE2_HUMAN E | Spike protein S1 | SPIKE_SARS2 Non-standard residues in 6m0j #9 --- CL — chloride ion 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) ZN — zinc ion > mmaker #9 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with 6m0j, chain E (#9), sequence alignment score = 786.1 RMSD between 160 pruned atom pairs is 0.959 angstroms; (across all 189 pairs: 2.241) > hide #8 models > hide #!4 models Drag select of 309 residues, 103 atoms, 98 bonds > show sel atoms > select clear > select #7/A:121 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > view matrix models #7,1,0,0,3.1773,0,1,0,0.72743,0,0,1,0.90934 > select add #7 1554 atoms, 1601 bonds, 194 residues, 1 model selected > select subtract #7 Nothing selected > mmaker #7 to #9 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 6m0j, chain E (#9) with RBD-docked-103-coot-0.pdb, chain A (#7), sequence alignment score = 786.1 RMSD between 160 pruned atom pairs is 0.959 angstroms; (across all 189 pairs: 2.241) > select clear > hide #!9 models > show #!9 models > select add #9/A:35 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 279 atoms, 286 bonds, 33 residues, 1 model selected > select up 4926 atoms, 5070 bonds, 601 residues, 1 model selected > hide sel cartoons > hide sel atoms > select clear Drag select of 1 atoms > hide sel atoms > select clear > movie record > turn y 2 180 > wait 180 > movie encode /Users/kelvinlau/Desktop/movie1.mp4 Movie saved to /Users/kelvinlau/Desktop/movie1.mp4 > hide #7#!9 atoms > select > ::name=""CL""::name=""GOL""::name=""HOH""::name=""NAG""::name=""PEG""::name=""SO4""::name=""TRS""::name=""ZN"" 372 atoms, 269 bonds, 119 residues, 3 models selected > show (#7#!9 & sel) target ab > select > ::name=""CL""::name=""GOL""::name=""HOH""::name=""NAG""::name=""PEG""::name=""SO4""::name=""TRS""::name=""ZN"" 372 atoms, 269 bonds, 119 residues, 3 models selected > hide sel & #7#!9 atoms > select ::name=""NAG"" 210 atoms, 211 bonds, 15 residues, 3 models selected > show (#7#!9 & sel) target ab > select clear Drag select of 14 atoms, 14 bonds > hide sel atoms Drag select of 42 atoms, 42 bonds > hide sel atoms > select #7/A:60 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select add #9/E:343 16 atoms, 14 bonds, 2 residues, 2 models selected > show sel atoms > select clear > select add #7/A:87 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > save /Users/kelvinlau/Desktop/image2.png supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode /Users/kelvinlau/Desktop/movie2.mp4 Movie saved to /Users/kelvinlau/Desktop/movie2.mp4 > show #!4 models > hide #!4 models > select #9?A Expected an objects specifier or a keyword > select #9/B Nothing selected > select #9/D Nothing selected > select #9/C Nothing selected > select #9/F Nothing selected > select #9/G Nothing selected > select #9/A 4999 atoms, 5070 bonds, 3 pseudobonds, 674 residues, 2 models selected > show sel atoms > hide sel atoms > show sel cartoons > select clear > save /Users/kelvinlau/Desktop/image3.png supersample 3 > hide #7 models > show #7 models > hide #!9 models > hide #7 models > show #!6 models > color #6 #9fe3ffff models > color #6 #999999ff models > color #6 #f4a582ff models > color #6 #4393c3ff models > color #6 #d1e5f04c models > color #6 #666666ff models > color #6 #a4a4a4ff models > color #6 #c7c7c7ff models > lighting soft > movie record > turn y 2 180 > wait 180 > movie encode /Users/kelvinlau/Desktop/movie3.mp4 Movie saved to /Users/kelvinlau/Desktop/movie3.mp4 > open /Users/kelvinlau/Downloads/cryosparc_P6_J107_map_locres.mrc Opened cryosparc_P6_J107_map_locres.mrc as #10, grid size 300,300,300, pixel 1.38, shown at level 6.75, step 2, values float32 > volume flip #10 Opened cryosparc_P6_J107_map_locres.mrc z flip as #11, grid size 300,300,300, pixel 1.38, shown at step 1, values float32 > hide #!11 models > show #!11 models > volume #11 level 5.713 > ui tool show ""Surface Color"" > color sample #6.1 map #11 palette #ff0000:#ffffff:#0000ff Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette 0,#ff0000:18.07,#ffffff:36.14,#0000ff Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > key red-white-blue :0.0 :18.1 :36.1 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > color sample #6.1 map #11 palette 0,#0000ff:18.07,#00ffff:36.14,#00ff00 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 1,#0000ff:2,#00ffff:3,#00ff00:4,#ffff00:5,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > key rainbow :1 :2 :3 :4 :5 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > color sample #6.1 map #11 palette > 1.5,#0000ff:2,#00ffff:2.5,#00ff00:3,#ffff00:4,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:2.5,#00ffff:3,#00ff00:3.5,#ffff00:4,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:2.5,#00ffff:3,#00ff00:3.5,#ffff00:5,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:2.5,#00ffff:3,#00ff00:3.5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2.5,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 3,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 3,#0000ff:3.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:3.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:2.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:2.5,#00ffff:3,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2,#0000ff:2.5,#00ffff:3,#00ff00:4,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2.5,#0000ff:2.75,#00ffff:3,#00ff00:4,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2.5,#0000ff:3,#00ffff:3,#00ff00:4,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2.5,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color single #6.1 > color sample #6.1 map #11 palette > 2.5,#0000ff:3,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 2.5,#0000ff:3,#00ffff:3.5,#00ff00:4,#ffff00:5,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > color sample #6.1 map #11 palette > 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:5,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.554, maximum 36.14 > volume #6 level 0.139 > surface dust #6 size 13.8 > volume #6 level 0.1446 > color sample #6.1 map #11 palette > 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.239, maximum 49.25 > color sample #6.1 map #11 palette > 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:7,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.239, maximum 49.25 > color sample #6.1 map #11 palette > 3,#0000ff:3.25,#00ffff:3.5,#00ff00:4,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.239, maximum 49.25 > key rainbow :3.00 :3.25 :3.50 :4.00 :6.00 showTool true > ui mousemode right ""color key"" > key delete > ui mousemode right ""translate selected models"" > key rainbow :3.00 :3.25 :3.50 :4.00 :6.00 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > color sample #6.1 map #11 palette > 3,#0000ff:3.5,#00ffff:4,#00ff00:5,#ffff00:6,#ff0000 Map values for surface ""surface"": minimum 0, mean 3.239, maximum 49.25 > key rainbow :3.0 :3.5 :4.0 :5.0 :6.0 showTool true > ui mousemode right ""color key"" > ui mousemode right ""translate selected models"" > save /Users/kelvinlau/Desktop/image4.png supersample 3 > ui tool show ""Side View"" > show #!4 models > show #!4 surfaces > hide #!4 surfaces > show #!4 surfaces > hide #13 models > volume #6 color #45c0d1 > hide #!4 surfaces > volume #6 color #45c0d1e6 > rainbow #!4 > lighting soft > lighting simple > lighting shadows true > lighting shadows false > lighting flat > lighting full > lighting simple > lighting full > volume #6 color #45c0d191 > hide #!4 models > show #7 models > open > /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb Chain information for SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb #14 --- Chain | Description A | No description available > select add #14 9282 atoms, 9503 bonds, 1191 residues, 1 model selected > view matrix models #14,1,0,0,77.646,0,1,0,100.38,0,0,1,258.11 > view matrix models #14,1,0,0,118.78,0,1,0,136,0,0,1,199.53 > ui mousemode right ""rotate selected models"" > view matrix models > #14,0.79311,0.30353,-0.52806,116.21,-0.52524,0.7798,-0.34064,130.01,0.30839,0.54752,0.77789,202.82 > view matrix models > #14,-0.51061,0.61006,-0.60589,100.88,0.74761,0.66308,0.037593,144.88,0.42468,-0.43377,-0.79466,204.71 > view matrix models > #14,-0.037789,-0.99929,0.00062917,107.26,-0.51217,0.018828,-0.85868,130.58,0.85805,-0.032771,-0.51252,209.53 > select subtract #14 Nothing selected > mmaker #14 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 1592.9 RMSD between 152 pruned atom pairs is 0.944 angstroms; (across all 192 pairs: 2.028) > select add #14 9282 atoms, 9503 bonds, 1191 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #14,-0.064575,-0.9537,-0.29374,128.07,-0.70505,0.25192,-0.66291,235.4,0.70622,0.1643,-0.68867,199.47 > view matrix models > #14,-0.064575,-0.9537,-0.29374,79.561,-0.70505,0.25192,-0.66291,258.78,0.70622,0.1643,-0.68867,179.1 > select subtract #14 Nothing selected > select #14:1-283 2264 atoms, 2331 bonds, 283 residues, 1 model selected > save /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb relModel > #14 > open /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb Summary of feedback from opening /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 286 THR A 294 1 9 Start residue of secondary structure not found: HELIX 2 2 PHE A 329 PHE A 333 1 5 Start residue of secondary structure not found: HELIX 3 3 VAL A 341 ALA A 343 1 3 Start residue of secondary structure not found: HELIX 4 4 TYR A 356 LEU A 359 1 4 Start residue of secondary structure not found: HELIX 5 5 PRO A 376 ASP A 381 1 6 207 messages similar to the above omitted End residue of secondary structure not found: SHEET 16 16 1 SER A 254 TYR A 260 0 Start residue of secondary structure not found: SHEET 17 17 1 GLN A 262 PHE A 270 0 Start residue of secondary structure not found: SHEET 18 18 1 ILE A 276 ASP A 281 0 Start residue of secondary structure not found: SHEET 19 19 1 GLY A 302 THR A 306 0 Start residue of secondary structure not found: SHEET 20 20 1 THR A 315 ARG A 319 0 Start residue of secondary structure not found: SHEET 21 21 1 GLU A 345 ILE A 349 0 77 messages similar to the above omitted End residue of secondary structure not found: SHEET 16 16 1 SER A 254 TYR A 260 0 Start residue of secondary structure not found: SHEET 17 17 1 GLN A 262 PHE A 270 0 Start residue of secondary structure not found: SHEET 18 18 1 ILE A 276 ASP A 281 0 Start residue of secondary structure not found: SHEET 19 19 1 GLY A 302 THR A 306 0 Start residue of secondary structure not found: SHEET 20 20 1 THR A 315 ARG A 319 0 Start residue of secondary structure not found: SHEET 21 21 1 GLU A 345 ILE A 349 0 31 messages similar to the above omitted Chain information for NTD.pdb --- Chain | Description 15.1/A 15.6/A | No description available 15.2/A 15.3/A | No description available 15.4/A | No description available 15.5/A | No description available 15.4/E | No description available 15.5/E | No description available > hide #!15 models > hide #14 models > show #14 models > hide #14 models > show #!15 models > hide #!15 models > show #!15 models > select add #15 37076 atoms, 37963 bonds, 3 pseudobonds, 4752 residues, 9 models selected > hide #!15 models > show #!15 models > select add #14 44094 atoms, 45135 bonds, 3 pseudobonds, 5660 residues, 9 models selected > select subtract #14 34812 atoms, 35632 bonds, 3 pseudobonds, 4469 residues, 8 models selected > close #15 > show #14 models > select #14:1-283 2264 atoms, 2331 bonds, 283 residues, 1 model selected > save /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb > selectedOnly true relModel #14 > open /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb Summary of feedback from opening /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/NTD.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 286 THR A 294 1 9 Start residue of secondary structure not found: HELIX 2 2 PHE A 329 PHE A 333 1 5 Start residue of secondary structure not found: HELIX 3 3 VAL A 341 ALA A 343 1 3 Start residue of secondary structure not found: HELIX 4 4 TYR A 356 LEU A 359 1 4 Start residue of secondary structure not found: HELIX 5 5 PRO A 376 ASP A 381 1 6 60 messages similar to the above omitted Chain information for NTD.pdb #12 --- Chain | Description A | No description available > hide #14 models > select add #14 9282 atoms, 9503 bonds, 1191 residues, 1 model selected > select subtract #14 Nothing selected > hide #12 models > show #12 models > show #14 models > mmaker #12 to #14 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 SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14) with NTD.pdb, chain A (#12), sequence alignment score = 1473.7 RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs: 0.000) > select add #12 2264 atoms, 2331 bonds, 283 residues, 1 model selected > view matrix models > #12,-0.064575,-0.9537,-0.29374,79.168,-0.70505,0.25192,-0.66291,259.2,0.70622,0.1643,-0.68867,179.81 > mmaker #14 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 1592.9 RMSD between 152 pruned atom pairs is 0.944 angstroms; (across all 192 pairs: 2.028) > mmaker #12 to #14 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 SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14) with NTD.pdb, chain A (#12), sequence alignment score = 1473.7 RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs: 0.000) > select clear > select add #12 2264 atoms, 2331 bonds, 283 residues, 1 model selected > fitmap #12 inMap #6 Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264 atoms average map value = 0.09224, steps = 116 shifted from previous position = 2.08 rotated from previous position = 14.4 degrees atoms outside contour = 1596, contour level = 0.14464 Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation 0.00130686 -0.97036728 -0.24163119 184.93620442 -0.85371786 0.12474320 -0.50557388 212.99101580 0.52073420 0.20694558 -0.82825686 210.29703969 Axis 0.67859241 -0.72606489 0.11109509 Axis point 150.80219786 0.00000000 158.32988633 Rotation angle (degrees) 148.33188418 Shift along axis -5.78602738 > hide #14 models > view matrix models > #12,0.0013069,-0.97037,-0.24163,175.33,-0.85372,0.12474,-0.50557,214.14,0.52073,0.20695,-0.82826,202.9 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.55681,-0.60717,-0.56684,159.86,-0.52018,0.78692,-0.33192,198.21,0.64759,0.11004,-0.754,206.82 > fitmap #12 inMap #6 Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264 atoms average map value = 0.08266, steps = 92 shifted from previous position = 5.15 rotated from previous position = 5.35 degrees atoms outside contour = 1631, contour level = 0.14464 Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation -0.49363864 -0.59548276 -0.63381478 162.45050676 -0.51432470 0.78758617 -0.33937903 197.48970209 0.70127812 0.15845599 -0.69505446 206.26089766 Axis 0.34881942 -0.93546318 0.05686524 Axis point 70.29966497 0.00000000 154.67157935 Rotation angle (degrees) 134.47142525 Shift along axis -116.34937655 > volume #6 level 0.2412 > view matrix models > #12,-0.034324,-0.92637,-0.37504,175.77,-0.84309,0.22835,-0.48688,211.4,0.53667,0.29948,-0.78886,200.83 > fitmap #12 inMap #6 Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264 atoms average map value = 0.108, steps = 84 shifted from previous position = 3.49 rotated from previous position = 8.83 degrees atoms outside contour = 1787, contour level = 0.24124 Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation -0.17565064 -0.92925889 -0.32499965 180.67796779 -0.81419831 0.32270170 -0.48264347 207.16698866 0.55337868 0.17983753 -0.81328378 201.14249518 Axis 0.59888239 -0.79405342 0.10401468 Axis point 129.54834619 0.00000000 152.49202223 Rotation angle (degrees) 146.42020738 Shift along axis -35.37503108 > ui mousemode right select > select clear > select add #12 2264 atoms, 2331 bonds, 283 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.11871,-0.94131,-0.31597,180.73,-0.77934,0.28551,-0.55778,205.25,0.61526,0.18003,-0.7675,202.07 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.11871,-0.94131,-0.31597,185.09,-0.77934,0.28551,-0.55778,205.17,0.61526,0.18003,-0.7675,200 > ui mousemode right ""rotate selected models"" > view matrix models > #12,-0.071375,-0.95287,-0.29486,185.65,-0.70164,0.25808,-0.66415,201.46,0.70895,0.15948,-0.68699,202.37 > ui mousemode right ""translate selected models"" > view matrix models > #12,-0.071375,-0.95287,-0.29486,185.88,-0.70164,0.25808,-0.66415,201.41,0.70895,0.15948,-0.68699,201.43 > fitmap #12 inMap #6 Fit molecule NTD.pdb (#12) to map 103_sharp_zflipped.ccp4 (#6) using 2264 atoms average map value = 0.1143, steps = 76 shifted from previous position = 4.63 rotated from previous position = 5.18 degrees atoms outside contour = 1724, contour level = 0.24124 Position of NTD.pdb (#12) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation 0.00304568 -0.93921916 -0.34330466 180.66644685 -0.69529462 0.24475271 -0.67576734 204.60385803 0.71871838 0.24075606 -0.65228859 201.64373900 Axis 0.64368451 -0.74587052 0.17131090 Axis point 122.00043841 0.00000000 175.29096637 Rotation angle (degrees) 134.60740732 Shift along axis -1.77202171 > show #14 models > mmaker #14 to #12 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 NTD.pdb, chain A (#12) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 1473.7 RMSD between 283 pruned atom pairs is 0.000 angstroms; (across all 283 pairs: 0.000) > mmaker #14 to #17 No 'to' model specified > mmaker #14 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 1592.9 RMSD between 152 pruned atom pairs is 0.944 angstroms; (across all 192 pairs: 2.028) > select subtract #12 Nothing selected > select add #14 9282 atoms, 9503 bonds, 1191 residues, 1 model selected > view matrix models > #14,-0.064575,-0.9537,-0.29374,123.48,-0.70505,0.25192,-0.66291,241.1,0.70622,0.1643,-0.68867,166.98 > select clear Drag select of 280 residues > delete sel Drag select of 8 residues, 1 pseudobonds > delete sel Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 8/A Alignment identifier is 8/E Alignment identifier is 9/A Alignment identifier is 9/E Alignment identifier is 12/A > select add #14/A:940 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #14.1 models > select add #14 6978 atoms, 7126 bonds, 5 pseudobonds, 903 residues, 2 models selected > view matrix models > #14,-0.064575,-0.9537,-0.29374,111.24,-0.70505,0.25192,-0.66291,261.75,0.70622,0.1643,-0.68867,156.73 > select clear Drag select of 168 residues > delete sel Drag select of 6 103_sharp_zflipped.ccp4 , 89 residues > select clear Drag select of 94 residues > delete sel Drag select of 3 residues > delete sel Drag select of 6 residues > delete sel Drag select of 125 residues > delete sel > select add #14 3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected > view matrix models > #14,-0.064575,-0.9537,-0.29374,193.01,-0.70505,0.25192,-0.66291,213.3,0.70622,0.1643,-0.68867,216.04 > view matrix models > #14,-0.064575,-0.9537,-0.29374,193.57,-0.70505,0.25192,-0.66291,212.78,0.70622,0.1643,-0.68867,214.23 > view matrix models > #14,-0.064575,-0.9537,-0.29374,192,-0.70505,0.25192,-0.66291,212.94,0.70622,0.1643,-0.68867,205.49 > select subtract #14 Nothing selected > select add #14 3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected > fitmap #14 inMap #6 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map 103_sharp_zflipped.ccp4 (#6) using 3902 atoms average map value = 0.08889, steps = 80 shifted from previous position = 3.54 rotated from previous position = 5.3 degrees atoms outside contour = 3133, contour level = 0.24124 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation -0.08749166 -0.97443388 -0.20693918 186.20184862 -0.71402959 0.20619847 -0.66906197 211.51077507 0.69462720 0.08922336 -0.71381527 207.33430825 Axis 0.62850293 -0.74726108 0.21583545 Axis point 135.67300670 0.00000000 175.49880919 Rotation angle (degrees) 142.89717947 Shift along axis 3.72473183 > open 7m0j 7m0j title: SARS-CoV-2 u1S2q All Down RBD State Spike Protein Trimer - asymmetric refinement [more info...] Chain information for 7m0j #15 --- Chain | Description | UniProt A B C | Spike glycoprotein | SPIKE_SARS2 > mmaker #15 to #7 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 RBD-docked-103-coot-0.pdb, chain A (#7) with 7m0j, chain B (#15), sequence alignment score = 1146.2 RMSD between 138 pruned atom pairs is 0.941 angstroms; (across all 161 pairs: 1.831) > select clear > mmaker #14 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7m0j, chain A (#15) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 3555.4 RMSD between 144 pruned atom pairs is 1.026 angstroms; (across all 424 pairs: 22.222) Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 4 atomic models, 1 maps. > select add #14 3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected > fitmap #14 inMap #6 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map 103_sharp_zflipped.ccp4 (#6) using 3902 atoms average map value = 0.07006, steps = 60 shifted from previous position = 1.7 rotated from previous position = 3.57 degrees atoms outside contour = 3260, contour level = 0.24124 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation 0.74110998 -0.00998632 0.67130937 227.62585019 -0.02534229 -0.99959289 0.01310748 185.06534394 0.67090518 -0.02672660 -0.74106134 209.81841633 Axis -0.93302746 0.00946719 -0.35968059 Axis point 0.00000000 94.29909756 59.96036905 Rotation angle (degrees) 178.77683225 Shift along axis -286.09673216 > hide #!14 models > hide #!15 models > show #!14 models > view matrix models > #14,0.74111,-0.0099863,0.67131,222.62,-0.025342,-0.99959,0.013107,192.08,0.67091,-0.026727,-0.74106,208.83 > view matrix models > #14,0.74111,-0.0099863,0.67131,221.54,-0.025342,-0.99959,0.013107,188.78,0.67091,-0.026727,-0.74106,208.92 > view matrix models > #14,0.74111,-0.0099863,0.67131,220.48,-0.025342,-0.99959,0.013107,189.93,0.67091,-0.026727,-0.74106,208.73 > view matrix models > #14,0.74111,-0.0099863,0.67131,219.14,-0.025342,-0.99959,0.013107,188.6,0.67091,-0.026727,-0.74106,208.5 > fitmap #14 inMap #6 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map 103_sharp_zflipped.ccp4 (#6) using 3902 atoms average map value = 0.1319, steps = 172 shifted from previous position = 7.13 rotated from previous position = 11.3 degrees atoms outside contour = 2925, contour level = 0.24124 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation 0.70249513 0.15150720 0.69537483 225.20282243 0.01747413 -0.98045480 0.19596694 188.67170643 0.71147399 -0.12551475 -0.69141218 205.56812359 Axis -0.92200855 -0.04617235 -0.38440648 Axis point 0.00000000 93.08070335 47.50006476 Rotation angle (degrees) 169.95988165 Shift along axis -295.37206341 > show #!15 models > view matrix models > #14,0.7025,0.15151,0.69537,289.13,0.017474,-0.98045,0.19597,224.01,0.71147,-0.12551,-0.69141,170.98 > select #15/B:340 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 49 atoms, 51 bonds, 6 residues, 1 model selected > select up 2610 atoms, 2673 bonds, 336 residues, 1 model selected > select up 2750 atoms, 2815 bonds, 353 residues, 1 model selected > select up 4361 atoms, 4465 bonds, 556 residues, 1 model selected > select up 4463 atoms, 4567 bonds, 568 residues, 1 model selected > select up 7245 atoms, 7410 bonds, 929 residues, 1 model selected > select up 7268 atoms, 7433 bonds, 932 residues, 1 model selected > select up 7609 atoms, 7789 bonds, 972 residues, 1 model selected > select up 22827 atoms, 23367 bonds, 2916 residues, 1 model selected > select down 7609 atoms, 7789 bonds, 972 residues, 1 model selected > select up 22827 atoms, 23367 bonds, 2916 residues, 1 model selected > select down 7609 atoms, 7789 bonds, 972 residues, 1 model selected > select ~sel 46914 atoms, 48010 bonds, 28 pseudobonds, 6012 residues, 24 models selected > select ~sel 7609 atoms, 7789 bonds, 11 pseudobonds, 972 residues, 2 models selected > select #15/A,C 15218 atoms, 15578 bonds, 22 pseudobonds, 1944 residues, 2 models selected > delete atoms (#!15 & sel) > delete bonds (#!15 & sel) Drag select of 6 103_sharp_zflipped.ccp4 , 19 residues > select clear > mmaker #14 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7m0j, chain B (#15) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 3587.5 RMSD between 147 pruned atom pairs is 1.000 angstroms; (across all 424 pairs: 22.421) > hide #!15 models > select add #14 3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected > view matrix models > #14,-0.272,0.8417,-0.46643,217.94,0.70201,0.50508,0.50207,231.22,0.65818,-0.19088,-0.72826,207.77 > ui tool show ""Side View"" > view matrix models > #14,-0.272,0.8417,-0.46643,215.34,0.70201,0.50508,0.50207,231.83,0.65818,-0.19088,-0.72826,208.77 > view matrix models > #14,-0.272,0.8417,-0.46643,217.03,0.70201,0.50508,0.50207,230.24,0.65818,-0.19088,-0.72826,208.4 > select subtract #14 Nothing selected > select add #14 3902 atoms, 3972 bonds, 3 pseudobonds, 507 residues, 2 models selected > view matrix models > #14,-0.272,0.8417,-0.46643,148.43,0.70201,0.50508,0.50207,261.82,0.65818,-0.19088,-0.72826,195.75 > select clear Drag select of 63 residues > select clear Drag select of 72 residues > delete sel Drag select of 8 residues > delete sel Drag select of 9 residues > delete sel > hide #!6 models > hide #7 models > hide #12 models Drag select of 24 residues Drag select of 20 residues Drag select of 7 residues > delete sel Drag select of 30 residues > delete sel Drag select of 9 residues > delete sel Drag select of 130 residues > delete sel > show #12 models > show #7 models > show #!6 models > show #!15 models > mmaker #14 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7m0j, chain B (#15) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 3403.3 RMSD between 147 pruned atom pairs is 1.000 angstroms; (across all 223 pairs: 5.995) Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 4 atomic models, 1 maps. > select add #14 1857 atoms, 1874 bonds, 5 pseudobonds, 242 residues, 2 models selected > fitmap #14 inMap #6 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map 103_sharp_zflipped.ccp4 (#6) using 1857 atoms average map value = 0.2211, steps = 104 shifted from previous position = 6.64 rotated from previous position = 8.26 degrees atoms outside contour = 1102, contour level = 0.24124 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation -0.35566557 0.78596340 -0.50573069 215.16698249 0.60314833 0.60637167 0.51819445 231.94554747 0.71394263 -0.12072670 -0.68971804 205.55029546 Axis -0.45999554 -0.87811193 -0.13161892 Axis point 9.54006040 -0.00000000 99.99657948 Rotation angle (degrees) 136.01370802 Shift along axis -329.70431277 > select subtract #14 Nothing selected > hide #7 models > hide #!6 models > delete #14:902-906 > delete #14:902-967 > mmaker #14 to #15 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7m0j, chain B (#15) with SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb, chain A (#14), sequence alignment score = 3331.9 RMSD between 135 pruned atom pairs is 0.954 angstroms; (across all 157 pairs: 4.833) > show #!6 models > select add #14 1358 atoms, 1373 bonds, 5 pseudobonds, 176 residues, 2 models selected > fitmap #14 inMap #6 Fit molecule SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) to map 103_sharp_zflipped.ccp4 (#6) using 1358 atoms average map value = 0.1302, steps = 88 shifted from previous position = 5.52 rotated from previous position = 5.53 degrees atoms outside contour = 971, contour level = 0.24124 Position of SPIKE30BFULL_b90e6_unrelaxed_rank_1_model_4.pdb (#14) relative to 103_sharp_zflipped.ccp4 (#6) coordinates: Matrix rotation and translation -0.29473057 0.79460140 -0.53079422 217.14718767 0.64777107 0.57449873 0.50034372 231.94420529 0.70251443 -0.19636655 -0.68404214 210.08107646 Axis -0.48923405 -0.86603659 -0.10310512 Axis point 0.50862202 0.00000000 104.83151306 Rotation angle (degrees) 134.59870751 Shift along axis -328.76840174 > hide #!15 models > select clear > select #14 1358 atoms, 1373 bonds, 5 pseudobonds, 176 residues, 2 models selected > save > /Users/kelvinlau/Downloads/SPIKE30BFULL_b90e6.result/round1-twohelices.pdb > selectedOnly true relModel #7 > show #2 models > hide #2 models > close #4 > close #8 > close #9 > hide #!6 models Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: > graphics silhouettes true > lighting soft > windowsize 800 800 UCSF ChimeraX version: 1.6.dev202212061854 (2022-12-06) © 2016-2022 Regents of the University of California. 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How to cite UCSF ChimeraX 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 6.4.0, Qt 6.4.0 Qt runtime version: 6.4.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,4 Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 8419.41.10 OS Loader Version: 7459.141.1 Software: System Software Overview: System Version: macOS 12.6.1 (21G217) Kernel Version: Darwin 21.6.0 Time since boot: 46 days 17:26 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: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.5.7 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.8 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.43.4 ChimeraX-AtomicLibrary: 8.0.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.7.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.dev202212061854 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 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-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.9 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.7 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.3 ChimeraX-PDB: 2.6.9 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.4 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.25.2 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.6 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 contourpy: 1.0.6 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.6.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.8 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.6.0 prompt-toolkit: 3.0.36 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.4.0 PyQt6-Qt6: 6.4.1 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.1 python-dateutil: 2.8.2 pytz: 2022.6 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.3 setuptools: 65.1.1 setuptools-scm: 7.0.5 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 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 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 typing-extensions: 4.4.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 zipp: 3.11.0 }}} " defect closed normal Window Toolkit limitation Tom Goddard all ChimeraX