id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9655 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-13.5-arm64-arm-64bit ChimeraX Version: 1.6 (2023-03-23 07:59:11 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 0x0000000204392080 (most recent call first): File ""/Applications/ChimeraX-1.6.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-1.6.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-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.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"":""2023-08-28 20:15:07.00 -0400"",""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 13.5 (22G74)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""F2A8E741-DD3E-49F4-A6BA-4037B62BDD41""} { ""uptime"" : 430000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 1195785599, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,5"", ""coalitionID"" : 19447, ""osVersion"" : { ""train"" : ""macOS 13.5"", ""build"" : ""22G74"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-08-28 20:14:56.2343 -0400"", ""incident"" : ""F2A8E741-DD3E-49F4-A6BA-4037B62BDD41"", ""pid"" : 80347, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-08-17 10:47:57.1630 -0400"", ""procStartAbsTime"" : 2412236487466, ""procExitAbsTime"" : 10432316187361, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""5D7F61D5-4358-59F6-8958-D2D0504A73D5"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""AAE09EAA-E991-08DE-E25C-56BCD904E286"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""wakeTime"" : 5, ""sleepWakeUUID"" : ""7722D4FF-282D-40FF-ABD1-7266A09A3A27"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 105554055790568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":80347}, ""vmregioninfo"" : ""0x18 is not in any region. 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(unallocated)\nMach message 64K 3 \nOpenGL GLSL 384K 4 \nSTACK GUARD 56.8M 49 \nStack 168.2M 49 \nVM_ALLOCATE 349.4M 696 \nVM_ALLOCATE (reserved) 256.0M 3 reserved VM address space (unallocated)\n__AUTH 1850K 373 \n__AUTH_CONST 28.8M 607 \n__CTF 824 1 \n__DATA 20.3M 752 \n__DATA_CONST 39.0M 761 \n__DATA_DIRTY 1983K 233 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 831.4M 153 \n__OBJC_RO 66.4M 1 \n__OBJC_RW 2012K 1 \n__TEXT 852.4M 781 \ndyld private memory 272K 2 \nmapped file 246.6M 79 \nshared memory 3248K 31 \n=========== ======= ======= \nTOTAL 10.1G 6229 \nTOTAL, minus reserved VM space 8.6G 6229 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""18057e587622bd37e81a368854adad8ca1a608f2"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""3a3cf641-8471-4e4e-9ad4-81d0ede970fd"", ""experimentId"" : ""64a84dae90d82611a0bd7d3d"", ""deploymentId"" : 400000004 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/dout2/Downloads/InitialModels/h2B1-Apo_200_083_Protein_Mask_10x10.mrc Opened h2B1-Apo_200_083_Protein_Mask_10x10.mrc as #1, grid size 200,200,200, pixel 0.83, shown at level 1, step 1, values float32 > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_200_083_Mask_10x10.mrc Opened h2B1-Apo_200_083_Mask_10x10.mrc as #2, grid size 200,200,200, pixel 0.83, shown at level 1, step 1, values float32 > set bgColor white > volume #1 level 0.9857 > volume #2 level 0.9695 > view > close #1-2 > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_region_536_200_083.mrc Failed opening file /Users/dout2/Downloads/InitialModels/h2B1-Apo_region_536_200_083.mrc: File size 1736704 too small for grid size (200,200,200) > open /Users/dout2/Downloads/InitialModels/h2B1-GDN_200_083.mrc Opened h2B1-GDN_200_083.mrc as #1, grid size 200,200,200, pixel 0.83, shown at level 0.0113, step 1, values float32 > open /Users/dout2/Downloads/InitialModels/h2B1-GDN_All_mask_200_083.mrc Opened h2B1-GDN_All_mask_200_083.mrc as #2, grid size 200,200,200, pixel 0.83, shown at level 1, step 1, values float32 > volume #1 level 0.0169 > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_region_536_200_083.mrc Failed opening file /Users/dout2/Downloads/InitialModels/h2B1-Apo_region_536_200_083.mrc: File size 1736704 too small for grid size (200,200,200) > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_region_536_200_083.mrc Failed opening file /Users/dout2/Downloads/InitialModels/h2B1-Apo_region_536_200_083.mrc: File size 1736704 too small for grid size (200,200,200) > open > /Users/dout2/Downloads/InitialModels/h2B1-LMNG_region_536_lp15_0.00112.mrc Opened h2B1-LMNG_region_536_lp15_0.00112.mrc as #3, grid size 200,200,200, pixel 0.83, shown at level 0.00462, step 1, values float32 > volume #2 level 1 > volume #1 level 0.008052 > hide #!3 models > show #!3 models > volume #1 level 0.01195 > select add #3 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.58085,-0.80991,-0.081622,201.7,-0.17874,0.22472,-0.95789,157.43,0.79414,-0.5418,-0.27529,85.476 > view matrix models > #3,-0.65613,-0.60705,-0.4483,221.86,-0.11831,0.66946,-0.73336,97.611,0.74531,-0.42814,-0.51108,99.839 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.65613,-0.60705,-0.4483,213.76,-0.11831,0.66946,-0.73336,103.14,0.74531,-0.42814,-0.51108,108.38 > view matrix models > #3,-0.65613,-0.60705,-0.4483,218.12,-0.11831,0.66946,-0.73336,103.5,0.74531,-0.42814,-0.51108,109.76 > view matrix models > #3,-0.65613,-0.60705,-0.4483,219.54,-0.11831,0.66946,-0.73336,102.46,0.74531,-0.42814,-0.51108,111.12 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.5289,-0.57414,-0.62501,221.19,0.060212,0.7092,-0.70243,82.086,0.84655,-0.40915,-0.34052,87.114 > view matrix models > #3,-0.63255,-0.59214,-0.49925,220.64,-0.076238,0.68906,-0.72068,96.378,0.77076,-0.4178,-0.48101,105.7 > view matrix models > #3,-0.47597,-0.54409,-0.69095,219.92,0.10382,0.7454,-0.65848,71.923,0.87331,-0.38515,-0.2983,79.462 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.47597,-0.54409,-0.69095,222.95,0.10382,0.7454,-0.65848,73.191,0.87331,-0.38515,-0.2983,79.842 > view matrix models > #3,-0.47597,-0.54409,-0.69095,222.66,0.10382,0.7454,-0.65848,75.09,0.87331,-0.38515,-0.2983,79.639 > view matrix models > #3,-0.47597,-0.54409,-0.69095,223.27,0.10382,0.7454,-0.65848,74.722,0.87331,-0.38515,-0.2983,79.835 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.43094,-0.53747,-0.72486,221.88,-0.083361,0.82355,-0.56108,75.525,0.89852,-0.18137,-0.3997,69.633 > view matrix models > #3,-0.55558,-0.59752,-0.57818,224.73,-0.26734,0.78683,-0.55626,93.124,0.78731,-0.15448,-0.59689,92.935 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.55558,-0.59752,-0.57818,222.44,-0.26734,0.78683,-0.55626,90.268,0.78731,-0.15448,-0.59689,93.174 > vop resample #3 onGrid #1 Opened h2B1-LMNG_region_536_lp15_0.00112.mrc resampled as #4, grid size 200,200,200, pixel 0.83, shown at step 1, values float32 > close #3 > volume #4 level 0.003042 > volume #4 level 0.00112 > volume #1 level 0.008186 > show #!2 models > hide #!2 models > select add #4 2 models selected > view matrix models #4,1,0,0,2.3279,0,1,0,-0.39672,0,0,1,-5.7749 > view matrix models #4,1,0,0,1.4657,0,1,0,-4.2368,0,0,1,-4.4723 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.99915,0.039781,0.011152,-3.0524,-0.041017,0.98748,0.15234,-13.707,-0.0049521,-0.15267,0.98826,10.696 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.99915,0.039781,0.011152,-2.5242,-0.041017,0.98748,0.15234,-14.706,-0.0049521,-0.15267,0.98826,7.7615 > vop resample #4 onGrid #1 Opened h2B1-LMNG_region_536_lp15_0.00112.mrc resampled resampled as #3, grid size 200,200,200, pixel 0.83, shown at step 1, values float32 > close #4 > show #!2 models > hide #!2 models > select add #3 2 models selected > view matrix models #3,1,0,0,0.73077,0,1,0,-0.95869,0,0,1,-5.9547 > show #!2 models > hide #!2 models > view matrix models #3,1,0,0,0.58643,0,1,0,-0.65131,0,0,1,-5.3452 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.51097,0.74697,-0.42537,14.387,-0.85036,0.51161,-0.12308,123.53,0.12568,0.42461,0.89661,-43.454 > ui tool show ""Fit in Map"" > fitmap #3 inMap #1 Fit map h2B1-LMNG_region_536_lp15_0.00112.mrc resampled resampled in map h2B1-GDN_200_083.mrc using 180382 points correlation = 0.6646, correlation about mean = 0.1066, overlap = 5.459 steps = 200, shift = 12.4, angle = 31 degrees Position of h2B1-LMNG_region_536_lp15_0.00112.mrc resampled resampled (#3) relative to h2B1-GDN_200_083.mrc (#1) coordinates: Matrix rotation and translation 0.62938933 0.50771743 -0.58829591 40.10468692 -0.77328723 0.33439890 -0.53870608 154.15519843 -0.07678496 0.79397757 0.60307851 -35.59247163 Axis 0.69483569 -0.26669200 -0.66789126 Axis point 0.00000000 112.28073278 152.64028403 Rotation angle (degrees) 73.53477388 Shift along axis 10.52611098 > undo > view matrix models > #3,0.99591,0.027233,0.086137,-8.7461,-0.030519,0.99885,0.037072,-1.1347,-0.085028,-0.039549,0.99559,5.6039 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.99591,0.027233,0.086137,-9.2248,-0.030519,0.99885,0.037072,-0.7938,-0.085028,-0.039549,0.99559,9.59 > show #!2 models > hide #!2 models > vop resample #5 onGrid #1 > vop resample #3 onGrid #1 Opened h2B1-LMNG_region_536_lp15_0.00112.mrc resampled resampled resampled as #4, grid size 200,200,200, pixel 0.83, shown at step 1, values float32 > close #3 > save /Users/dout2/Downloads/InitialModels/h2B1-GDN_Protein_200_083.mrc > models #4 > show #!1 models > volume #1 level 0.003793 > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_200_083.mrc Opened h2B1-Apo_200_083.mrc as #3, grid size 200,200,200, pixel 0.83, shown at level 0.00411, step 1, values float32 > hide #!4 models > volume #3 level 0.005579 > volume #3 level 0.006088 > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_200_083_Mask.mrc Opened h2B1-Apo_200_083_Mask.mrc as #5, grid size 200,200,200, pixel 0.83, shown at level 1, step 1, values float32 > open /Users/dout2/Downloads/InitialModels/h2B1-Apo_200_083_Protein_Mask.mrc Opened h2B1-Apo_200_083_Protein_Mask.mrc as #6, grid size 200,200,200, pixel 0.83, shown at level 1, step 1, values float32 > volume #5 level 0.9847 > volume #6 level 0.9762 > volume #3 level 0.003031 > show #!4 models > hide #!4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!1 models > hide #!1 models > hide #!6 models > show #!4 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!4 models > show #!4 models > hide #!1 models > show #!1 models > hide #!4 models > show #!4 models > hide #!1 models > open /Users/dout2/Downloads/InitialModels/h2B1-GDN_Protein_mask_200_083.mrc Opened h2B1-GDN_Protein_mask_200_083.mrc as #7, grid size 200,200,200, pixel 0.83, shown at level 1, step 1, values float32 > volume #7 level 1 > show #!1 models > view > ui tool show ""Side View"" > hide #!4 models > show #!2 models > hide #!2 models > hide #!1 models > show #!1 models > view > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!7 models > volume #1 level 0.01603 > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > volume #1 level 0.004316 > hide #!1 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > close #6 > close #5 > close #3 > show #!1 models > volume #1 level 0.01212 > hide #!7 models > show #!7 models > hide #!7 models > open /Users/dout2/Downloads/20230711Krios_mOCT1-HEPES- > LMNG/job160/run_class001.mrc Opened run_class001.mrc as #3, grid size 160,160,160, pixel 0.83, shown at level 0.00436, step 1, values float32 > open /Users/dout2/Downloads/20230711Krios_mOCT1-HEPES- > LMNG/job160/run_class001_angdist.bild Opened BILD data containing 3063 objects > hide #!1 models > close #1-2 > close #4 > close #7 > view > hide #5 models > lighting soft > lighting simple > open ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" Opened cryosparc_P4_J16__localfilter_240.mrc as #2, grid size 240,240,240, pixel 0.553, shown at level 0.238, step 1, values float32 Opened cryosparc_P4_J89__localfilter_160.mrc as #3, grid size 160,160,160, pixel 0.83, shown at level 0.134, step 1, values float32 Opened cryosparc_P4_J55__localfilter_160.mrc as #5, grid size 160,160,160, pixel 0.83, shown at level 0.136, step 1, values float32 Opened rOAT1-AKG_8bw7_emd_16280.map as #7, grid size 288,288,288, pixel 0.832, shown at level 0.514, step 1, values float32 Opened rOAT1-AKG_8omu_emd_16977.map as #9, grid size 288,288,288, pixel 0.832, shown at level 0.397, step 1, values float32 Opened rOAT1-apo_8bvr_emd_16269.map as #11, grid size 288,288,288, pixel 0.832, shown at level 0.628, step 1, values float32 Opened rOAT1-PBD_8bvt_emd_16271.map as #13, grid size 288,288,288, pixel 0.832, shown at level 0.182, step 2, values float32 Opened rOAT1-TFV_8bvs_emd_16270.map as #15, grid size 288,288,288, pixel 0.832, shown at level 0.191, step 2, values float32 opened ChimeraX session > show #!2 models > hide #!2 models > show #1 models > view > hide #1 models > show #!4 models > hide #!4 models > show #6 models > select clear > select #6/B:601@O10 1 atom, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > show #!14 models > view > ui tool show Matchmaker > matchmaker #!14 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PBD_8bvt.pdb, chain A (#14), sequence alignment score = 2439.7 RMSD between 487 pruned atom pairs is 0.832 angstroms; (across all 498 pairs: 0.989) > view matrix models #6,1,0,0,-1.377,0,1,0,0.17197,0,0,1,-0.2168 > select clear > select #6/B:601@C17 1 atom, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > matchmaker #!10 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8omu.pdb, chain A (#10), sequence alignment score = 2456.5 RMSD between 480 pruned atom pairs is 0.876 angstroms; (across all 492 pairs: 0.968) > matchmaker #!12 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo_8bvr.pdb, chain A (#12), sequence alignment score = 2447.5 RMSD between 481 pruned atom pairs is 0.838 angstroms; (across all 495 pairs: 0.921) > matchmaker #!16 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-TFV_8bvs.pdb, chain A (#16), sequence alignment score = 2464.3 RMSD between 483 pruned atom pairs is 0.804 angstroms; (across all 495 pairs: 0.869) > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!16 models > select > #6/A:28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 232 atoms, 216 bonds, 29 residues, 1 model selected > show sel atoms > save ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" includeMaps true > color #16 #8b7338ff > color #16 #897338ff > color #16 #897354ff > color #16 #89735fff > color #16 #89805fff > color #16 #896e5fff > color #16 #926e5fff > color #16 #9b6e5fff > select add #6 3905 atoms, 3985 bonds, 515 residues, 1 model selected > select subtract #6 Nothing selected > select add #16 4799 atoms, 4916 bonds, 2 pseudobonds, 619 residues, 2 models selected > color (#!16 & sel) byhetero > select > #/A:28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 Expected an objects specifier or a keyword > select > :28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 1966 atoms, 1824 bonds, 250 residues, 8 models selected > show sel & #6#!14,16 atoms > hide #!16 models > hide #!14 models > show #!14 models > matchmaker #!14 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PBD_8bvt.pdb, chain A (#14), sequence alignment score = 2439.7 RMSD between 487 pruned atom pairs is 0.832 angstroms; (across all 498 pairs: 0.989) > matchmaker #!16 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-TFV_8bvs.pdb, chain A (#16), sequence alignment score = 2464.3 RMSD between 483 pruned atom pairs is 0.804 angstroms; (across all 495 pairs: 0.869) > matchmaker #!12 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo_8bvr.pdb, chain A (#12), sequence alignment score = 2447.5 RMSD between 481 pruned atom pairs is 0.838 angstroms; (across all 495 pairs: 0.921) > matchmaker #!10 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8omu.pdb, chain A (#10), sequence alignment score = 2456.5 RMSD between 480 pruned atom pairs is 0.876 angstroms; (across all 492 pairs: 0.968) > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > hide #!14 models > show #!16 models > hide #6 models > show #!14 models > hide #!14 models > hide #!16 models > show #6 models > select clear > show #!14 models > lighting soft > show #!10 models > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > view sel > show #6#!10,14 atoms > undo > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > show #6#!10,14 atoms > undo > view > hide #!14 models > hide #6 models > show #!8 models > hide #!10 models > show #!14 models > show #6 models > hide #!8 models > select add #8 4748 atoms, 4863 bonds, 2 pseudobonds, 614 residues, 2 models selected > select subtract #8 Nothing selected > hide #!14 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > show #!8 models > hide #!8 models > show #!8 models > show #!14 models > show #!16 models > show #!12 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > hide #!12 models > select ::name=""CL"" 2 atoms, 2 residues, 2 models selected > show sel atoms > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > hide sel atoms > select add #14 4518 atoms, 4615 bonds, 2 pseudobonds, 625 residues, 3 models selected > select subtract #14 1 atom, 1 residue, 1 model selected > select add #16 4799 atoms, 4916 bonds, 2 pseudobonds, 619 residues, 2 models selected > select add #14 9316 atoms, 9531 bonds, 4 pseudobonds, 1243 residues, 4 models selected > select add #12 14110 atoms, 14439 bonds, 6 pseudobonds, 1863 residues, 6 models selected > select add #8 18858 atoms, 19302 bonds, 8 pseudobonds, 2477 residues, 8 models selected > select add #6 22763 atoms, 23287 bonds, 8 pseudobonds, 2992 residues, 9 models selected > select subtract #12 17969 atoms, 18379 bonds, 6 pseudobonds, 2372 residues, 7 models selected > hide sel atoms > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""CL"" 2 atoms, 2 residues, 2 models selected > show sel atoms > select add #16 4800 atoms, 4916 bonds, 2 pseudobonds, 620 residues, 3 models selected > select subtract #16 1 atom, 1 residue, 1 model selected > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > hide sel atoms > select ::name=""LIG"" 42 atoms, 42 bonds, 2 residues, 2 models selected > show sel & #6 atoms > select ::name=""RTO"" 19 atoms, 19 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""TFO"" 19 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!16 models > show #!16 models > hide #!16 models > hide #!14 models > show #!14 models > show #!16 models > hide #6 models > show #6 models > show #!4 models > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > movie record > turn y 2 180 > wait 180 > movie encode /Users/dout2/Desktop/movie1.mp4 Movie saved to /Users/dout2/Desktop/movie1.mp4 > hide #!16 models > hide #!14 models > hide #!8 models > hide #6 models > show #6 models > select > :28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 1966 atoms, 1824 bonds, 250 residues, 8 models selected > show sel & #6#!4 atoms > hide sel & #6#!4 atoms > show #!16 models > show #!14 models > show #!10 models > hide #!10 models > show #!8 models > show #1 models > view > select clear Drag select of 23 residues > select clear > matchmaker #1 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo-coot-4_real_space_refined_004.pdb, chain A (#1), sequence alignment score = 2582.7 RMSD between 500 pruned atom pairs is 0.389 angstroms; (across all 500 pairs: 0.389) > matchmaker #1 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo-coot-4_real_space_refined_004.pdb, chain A (#1), sequence alignment score = 2582.7 RMSD between 500 pruned atom pairs is 0.389 angstroms; (across all 500 pairs: 0.389) > matchmaker #1 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo-coot-4_real_space_refined_004.pdb, chain A (#1), sequence alignment score = 2582.7 RMSD between 500 pruned atom pairs is 0.389 angstroms; (across all 500 pairs: 0.389) > matchmaker #!4 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PAH-coot-7_real_space_refined_007.pdb, chain A (#4), sequence alignment score = 2547.2 RMSD between 494 pruned atom pairs is 0.541 angstroms; (across all 494 pairs: 0.541) > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > matchmaker #!10 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8omu.pdb, chain A (#10), sequence alignment score = 2456.5 RMSD between 480 pruned atom pairs is 0.876 angstroms; (across all 492 pairs: 0.968) > matchmaker #!12 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo_8bvr.pdb, chain A (#12), sequence alignment score = 2447.5 RMSD between 481 pruned atom pairs is 0.838 angstroms; (across all 495 pairs: 0.921) > matchmaker #!14 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PBD_8bvt.pdb, chain A (#14), sequence alignment score = 2439.7 RMSD between 487 pruned atom pairs is 0.832 angstroms; (across all 498 pairs: 0.989) > matchmaker #!16 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-TFV_8bvs.pdb, chain A (#16), sequence alignment score = 2464.3 RMSD between 483 pruned atom pairs is 0.804 angstroms; (across all 495 pairs: 0.869) > save ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" includeMaps true > select clear > select > :28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 1966 atoms, 1824 bonds, 250 residues, 8 models selected > show sel & #1,6#!4,8,14,16 atoms > select clear > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > hide #!16 models > hide #!14 models > hide #6 models > hide #!4 models > hide #1 models > view sel > select #8/A:227 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!8 models > show #!4 models > hide #!4 models > show #6 models > hide #6 models > show #!8 models > show #!7 models > view > select add #7 2 models selected > view matrix models #7,1,0,0,-36.048,0,1,0,-57.002,0,0,1,-43.227 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.66795,0.62893,-0.39786,126.1,0.6813,0.73189,0.013168,-103.71,0.29947,-0.26226,-0.91735,187.58 > view matrix models > #7,-0.4798,0.59643,0.64348,-18.089,0.82458,0.055961,0.56296,-106.32,0.29976,0.80071,-0.51866,12.357 > view matrix models > #7,-0.52351,-0.34401,0.77948,82.349,0.27498,-0.93413,-0.22758,170.05,0.80643,0.0952,0.58362,-95.083 > view matrix models > #7,-0.31083,-0.81764,0.48461,150.63,-0.057776,-0.49267,-0.8683,233.09,0.94871,-0.29789,0.1059,-6.178 > view matrix models > #7,-0.23651,-0.97114,0.030936,215.74,0.28098,-0.098839,-0.95461,158.36,0.93012,-0.21708,0.29624,-36.877 > view matrix models > #7,-0.35413,-0.91884,0.17413,205.38,0.16914,-0.24605,-0.95438,188.53,0.91977,-0.30852,0.24254,-18.275 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.35413,-0.91884,0.17413,200.43,0.16914,-0.24605,-0.95438,188.63,0.91977,-0.30852,0.24254,-40.45 > view matrix models > #7,-0.35413,-0.91884,0.17413,196.88,0.16914,-0.24605,-0.95438,189.66,0.91977,-0.30852,0.24254,-37.373 > view matrix models > #7,-0.35413,-0.91884,0.17413,193.59,0.16914,-0.24605,-0.95438,189.73,0.91977,-0.30852,0.24254,-33.699 > view matrix models > #7,-0.35413,-0.91884,0.17413,196.46,0.16914,-0.24605,-0.95438,189.46,0.91977,-0.30852,0.24254,-37.728 > view matrix models > #7,-0.35413,-0.91884,0.17413,196.58,0.16914,-0.24605,-0.95438,187.09,0.91977,-0.30852,0.24254,-40.121 > view matrix models > #7,-0.35413,-0.91884,0.17413,198.44,0.16914,-0.24605,-0.95438,188.26,0.91977,-0.30852,0.24254,-37.343 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.26315,-0.91847,0.29525,173.36,0.1482,-0.34089,-0.92835,198.75,0.9533,-0.20054,0.22583,-51.965 > ui tool show ""Fit in Map"" > fitmap #7 inMap #5 Fit map rOAT1-AKG_8bw7_emd_16280.map in map cryosparc_P4_J55__localfilter_160.mrc using 36334 points correlation = 0.6898, correlation about mean = 0.4442, overlap = 6999 steps = 76, shift = 2.49, angle = 6.77 degrees Position of rOAT1-AKG_8bw7_emd_16280.map (#7) relative to cryosparc_P4_J55__localfilter_160.mrc (#5) coordinates: Matrix rotation and translation -0.18514202 -0.94582948 0.26670025 170.30685051 0.08128383 -0.28520123 -0.95501476 202.77297048 0.97934435 -0.15513494 0.12968338 -51.08266521 Axis 0.53895668 -0.48017751 0.69206594 Axis point 46.26900426 145.40872259 0.00000000 Rotation angle (degrees) 132.09253462 Shift along axis -40.93157825 > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > view sel > fitmap #8 inMap #7 Fit molecule rOAT1-AKG_8bw7.pdb (#8) to map rOAT1-AKG_8bw7_emd_16280.map (#7) using 4748 atoms average map value = 0.6152, steps = 52 shifted from previous position = 1.37 rotated from previous position = 0.365 degrees atoms outside contour = 2313, contour level = 0.51433 Position of rOAT1-AKG_8bw7.pdb (#8) relative to rOAT1-AKG_8bw7_emd_16280.map (#7) coordinates: Matrix rotation and translation 0.99999987 -0.00029192 -0.00044187 0.10650603 0.00029139 0.99999925 -0.00119303 0.10176166 0.00044222 0.00119290 0.99999920 -0.19755122 Axis 0.91398689 -0.33867000 0.22345154 Axis point 0.00000000 169.17719005 90.50923993 Rotation angle (degrees) 0.07478432 Shift along axis 0.01873837 > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > show sel atoms > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > show sel atoms > hide sel atoms > hide #!8 models > hide #!7 models > select add #8 4748 atoms, 4863 bonds, 2 pseudobonds, 614 residues, 2 models selected > select subtract #8 Nothing selected > show #6 models > show #!5 models > volume #5 level 0.1927 > fitmap #6 inMap #5 Fit molecule rOAT1-PBD-coot-4_real_space_refined_004.pdb (#6) to map cryosparc_P4_J55__localfilter_160.mrc (#5) using 3905 atoms average map value = 0.3521, steps = 56 shifted from previous position = 1.42 rotated from previous position = 0.0512 degrees atoms outside contour = 1233, contour level = 0.19268 Position of rOAT1-PBD-coot-4_real_space_refined_004.pdb (#6) relative to cryosparc_P4_J55__localfilter_160.mrc (#5) coordinates: Matrix rotation and translation 0.99999961 0.00031734 0.00082049 -0.06413452 -0.00031721 0.99999994 -0.00015651 0.02835017 -0.00082053 0.00015625 0.99999965 0.05609006 Axis 0.17502166 0.91830279 -0.35508787 Axis point 66.11473996 0.00000000 77.10818900 Rotation angle (degrees) 0.05119419 Shift along axis -0.00510779 > color #5 #b2ffff82 models > color #5 #b2ffff81 models > color #5 #b2ffffce models > color #5 #b2ffffcd models > view Drag select of 5 cryosparc_P4_J55__localfilter_160.mrc , 4 atoms, 3 residues, 5 bonds > select clear > hide #!5 models > select #6/A:466@CD 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > view sel > show #!7 models > hide #!7 models > show #!5 models > hide #6 models > show #6 models > hide #!5 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > show #!5 models > volume #5 level 0.3052 > show #!8 models > select ::name=""CL"" 2 atoms, 2 residues, 2 models selected > show sel & #!8 atoms > hide #!8 models > select add #8 4749 atoms, 4863 bonds, 2 pseudobonds, 615 residues, 3 models selected > hide #6 models > hide #!5 models > select subtract #8 1 atom, 1 residue, 1 model selected > show #1 models > show #!2 models > fitmap #1 inMap #2 Fit molecule rOAT1-apo-coot-4_real_space_refined_004.pdb (#1) to map cryosparc_P4_J16__localfilter_240.mrc (#2) using 3942 atoms average map value = 1.007, steps = 64 shifted from previous position = 1.27 rotated from previous position = 0.342 degrees atoms outside contour = 266, contour level = 0.23806 Position of rOAT1-apo-coot-4_real_space_refined_004.pdb (#1) relative to cryosparc_P4_J16__localfilter_240.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 -0.00003468 -0.00003690 0.00161997 0.00003467 0.99999999 -0.00011321 0.00083435 0.00003691 0.00011321 0.99999999 -0.00970127 Axis 0.91284205 -0.29757638 0.27958485 Axis point 0.00000000 82.03089401 3.46963304 Rotation angle (degrees) 0.00710604 Shift along axis -0.00148184 > color #2 #b2b2b2cc models > volume #2 level 0.4884 > show #!8 models > hide #!8 models > show #!8 models > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > hide #!8 models > volume #2 level 0.5809 > hide #!2 models > hide #1 models > show #!8 models > show #!7 models > show #6 models > hide #!7 models > hide #6 models > select #8/A:463 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:466@NH1 1 atom, 1 residue, 1 model selected > ui tool show Distances No distances to delete! Exactly two atoms must be selected! > select clear > select #8/A:466@NH1 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select subtract #8/A:602@CL Nothing selected > select add #8/A:466@NH1 1 atom, 1 residue, 1 model selected Exactly two atoms must be selected! > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select add #8/A:466@NH1 2 atoms, 2 residues, 1 model selected > distance #8/A:602@CL #8/A:466@NH1 Distance between rOAT1-AKG_8bw7.pdb #8/A CL 602 CL and ARG 466 NH1: 3.468Å > select #8/A:462@OG 1 atom, 1 residue, 1 model selected > select add #8/A:602@CL 2 atoms, 2 residues, 1 model selected > distance #8/A:462@OG #8/A:602@CL Distance between rOAT1-AKG_8bw7.pdb #8/A SER 462 OG and CL 602 CL: 4.399Å > select clear > select add #8/A:602@CL 1 atom, 1 residue, 1 model selected > select add #8/A:463@OG1 2 atoms, 2 residues, 1 model selected > distance #8/A:602@CL #8/A:463@OG1 Distance between rOAT1-AKG_8bw7.pdb #8/A CL 602 CL and THR 463 OG1: 8.777Å > select clear Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" Opened cryosparc_P4_J16__localfilter_240.mrc as #2, grid size 240,240,240, pixel 0.553, shown at level 0.238, step 1, values float32 Opened cryosparc_P4_J89__localfilter_160.mrc as #3, grid size 160,160,160, pixel 0.83, shown at level 0.134, step 1, values float32 Opened cryosparc_P4_J55__localfilter_160.mrc as #5, grid size 160,160,160, pixel 0.83, shown at level 0.136, step 1, values float32 Opened rOAT1-AKG_8bw7_emd_16280.map as #7, grid size 288,288,288, pixel 0.832, shown at level 0.514, step 1, values float32 Opened rOAT1-AKG_8omu_emd_16977.map as #9, grid size 288,288,288, pixel 0.832, shown at level 0.397, step 1, values float32 Opened rOAT1-apo_8bvr_emd_16269.map as #11, grid size 288,288,288, pixel 0.832, shown at level 0.628, step 1, values float32 Opened rOAT1-PBD_8bvt_emd_16271.map as #13, grid size 288,288,288, pixel 0.832, shown at level 0.182, step 2, values float32 Opened rOAT1-TFV_8bvs_emd_16270.map as #15, grid size 288,288,288, pixel 0.832, shown at level 0.191, step 2, values float32 Log from Sun Aug 27 22:20:39 2023UCSF ChimeraX version: 1.6 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" Opened cryosparc_P4_J16__localfilter_240.mrc as #2, grid size 240,240,240, pixel 0.553, shown at level 0.238, step 1, values float32 Opened cryosparc_P4_J89__localfilter_160.mrc as #3, grid size 160,160,160, pixel 0.83, shown at level 0.134, step 1, values float32 Opened cryosparc_P4_J55__localfilter_160.mrc as #5, grid size 160,160,160, pixel 0.83, shown at level 0.136, step 1, values float32 Opened rOAT1-AKG_8bw7_emd_16280.map as #7, grid size 288,288,288, pixel 0.832, shown at level 0.514, step 1, values float32 Opened rOAT1-AKG_8omu_emd_16977.map as #9, grid size 288,288,288, pixel 0.832, shown at level 0.397, step 1, values float32 Opened rOAT1-apo_8bvr_emd_16269.map as #11, grid size 288,288,288, pixel 0.832, shown at level 0.628, step 1, values float32 Opened rOAT1-PBD_8bvt_emd_16271.map as #13, grid size 288,288,288, pixel 0.832, shown at level 0.182, step 2, values float32 Opened rOAT1-TFV_8bvs_emd_16270.map as #15, grid size 288,288,288, pixel 0.832, shown at level 0.191, step 2, values float32 Log from Fri Jul 21 12:35:41 2023UCSF ChimeraX version: 1.6 (2023-03-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/dout2/Downloads/cryosparc_P19_J22__localfilter.mrc format mrc Opened cryosparc_P19_J22__localfilter.mrc as #1, grid size 256,256,256, pixel 0.83, shown at level 0.0383, step 1, values float32 > close session > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-apo_8bvr_emd_16269.map Opened rOAT1-apo_8bvr_emd_16269.map as #1, grid size 288,288,288, pixel 0.832, shown at level 0.196, step 2, values float32 > volume #1 step 1 > volume #1 level 0.5376 > close #1 > open EMD-16271 'EMD-16271' has no suffix > open 8bvt Summary of feedback from opening 8bvt fetched from pdb --- notes | Fetching compressed mmCIF 8bvt from http://files.rcsb.org/download/8bvt.cif Fetching CCD RTO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/RTO/RTO.cif 8bvt title: Cryo-EM structure of rat SLC22A6 bound to probenecid [more info...] Chain information for 8bvt #1 --- Chain | Description | UniProt A | Solute carrier family 22 member 6 | S22A6_RAT 1-541 B | Synthetic nanobody (Sybody) | Non-standard residues in 8bvt #1 --- RTO — 4-(dipropylsulfamoyl)benzoic acid > open 16721 '16721' has no suffix > open emdb:16721 Summary of feedback from opening 16721 fetched from emdb --- note | Fetching compressed map 16721 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-16721/map/emd_16721.map.gz Opened emdb 16721 as #2, grid size 320,320,320, pixel 1.19, shown at level 0.00406, step 2, values float32 > volume #2 step 1 > volume #2 level 0.004057 > volume #2 level 0.006513 > volume #2 level 0.00849 > set bgColor white > close #2 > open emd:16721 No such database 'emd' > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-PBD_8bvt_emd_16271.map Opened rOAT1-PBD_8bvt_emd_16271.map as #2, grid size 288,288,288, pixel 0.832, shown at level 0.182, step 2, values float32 > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-PBD_8bvt.pdb rOAT1-PBD_8bvt.pdb title: Cryo-em structure of rat SLC22A6 bound to probenecid [more info...] Chain information for rOAT1-PBD_8bvt.pdb #3 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_RAT 1-541 B | synthetic nanobody (sybody) | Non-standard residues in rOAT1-PBD_8bvt.pdb #3 --- RTO — 4-(dipropylsulfamoyl)benzoic acid > close #1 > volume #2 step 1 > volume #2 level 0.3522 > close #2-3 > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/OAT1/cryoEM/rOAT1-apo_20220519_cryoSPARC/model/rOAT1-apo- > coot-4_real_space_refined_004.pdb Chain information for rOAT1-apo-coot-4_real_space_refined_004.pdb #1 --- Chain | Description A | No description available > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/OAT1/cryoEM/rOAT1-apo_20220519_cryoSPARC/J12_2.05A_clip-240/cryosparc_P4_J16__localfilter_240.mrc Opened cryosparc_P4_J16__localfilter_240.mrc as #2, grid size 240,240,240, pixel 0.553, shown at level 0.238, step 1, values float32 > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/cryosparc_P4_J89__localfilter_160.mrc > /Users/dout2/Documents/Manuscripts/rOAT1_2023/OAT1/cryoEM/rOAT1-PAH_20220730_20230218/rOAT1-PAH- > coot-7_real_space_refined_007.pdb Opened cryosparc_P4_J89__localfilter_160.mrc as #3, grid size 160,160,160, pixel 0.83, shown at level 0.134, step 1, values float32 Chain information for rOAT1-PAH-coot-7_real_space_refined_007.pdb #4 --- Chain | Description A | No description available > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/OAT1/cryoEM/rOAT1-PBD_20230217/cryosparc_P4_J55__localfilter_160.mrc > /Users/dout2/Documents/Manuscripts/rOAT1_2023/OAT1/cryoEM/rOAT1-PBD_20230217/rOAT1-PBD- > coot-4_real_space_refined_004.pdb Opened cryosparc_P4_J55__localfilter_160.mrc as #5, grid size 160,160,160, pixel 0.83, shown at level 0.131, step 1, values float32 Chain information for rOAT1-PBD-coot-4_real_space_refined_004.pdb #6 --- Chain | Description A | No description available > open > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-AKG_8bw7_emd_16280.map > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-AKG_8bw7.pdb > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-AKG_8omu_emd_16977.map > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-AKG_8omu.pdb > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-apo_8bvr_emd_16269.map > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-apo_8bvr.pdb > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-PBD_8bvt_emd_16271.map > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-PBD_8bvt.pdb > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-TFV_8bvs_emd_16270.map > /Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/rOAT1-TFV_8bvs.pdb Opened rOAT1-AKG_8bw7_emd_16280.map as #7, grid size 288,288,288, pixel 0.832, shown at level 0.199, step 2, values float32 rOAT1-AKG_8bw7.pdb title: Cryo-em structure of rat SLC22A6 bound to α-ketoglutaric acid [more info...] Chain information for rOAT1-AKG_8bw7.pdb #8 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_RAT 1-542 B | synthetic nanobody (sybody) | Non-standard residues in rOAT1-AKG_8bw7.pdb #8 --- AKG — 2-oxoglutaric acid CL — chloride ion Opened rOAT1-AKG_8omu_emd_16977.map as #9, grid size 288,288,288, pixel 0.832, shown at level 0.196, step 2, values float32 rOAT1-AKG_8omu.pdb title: Cryo-em structure of rat SLC22A6 bound to α-ketoglutaric acid In A low occupancy state [more info...] Chain information for rOAT1-AKG_8omu.pdb #10 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_RAT 1-541 B | synthetic nanobody (sybody) | Opened rOAT1-apo_8bvr_emd_16269.map as #11, grid size 288,288,288, pixel 0.832, shown at level 0.196, step 2, values float32 rOAT1-apo_8bvr.pdb title: Cryo-em structure of rat SLC22A6 In the apo state [more info...] Chain information for rOAT1-apo_8bvr.pdb #12 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_RAT 1-542 B | synthetic nanobody (sybody) | Non-standard residues in rOAT1-apo_8bvr.pdb #12 --- PO4 — phosphate ion Opened rOAT1-PBD_8bvt_emd_16271.map as #13, grid size 288,288,288, pixel 0.832, shown at level 0.182, step 2, values float32 rOAT1-PBD_8bvt.pdb title: Cryo-em structure of rat SLC22A6 bound to probenecid [more info...] Chain information for rOAT1-PBD_8bvt.pdb #14 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_RAT 1-541 B | synthetic nanobody (sybody) | Non-standard residues in rOAT1-PBD_8bvt.pdb #14 --- RTO — 4-(dipropylsulfamoyl)benzoic acid Opened rOAT1-TFV_8bvs_emd_16270.map as #15, grid size 288,288,288, pixel 0.832, shown at level 0.191, step 2, values float32 rOAT1-TFV_8bvs.pdb title: Cryo-em structure of rat SLC22A6 bound to tenofovir [more info...] Chain information for rOAT1-TFV_8bvs.pdb #16 --- Chain | Description | UniProt A | solute carrier family 22 member 6 | S22A6_RAT 1-542 B | synthetic nanobody (sybody) | Non-standard residues in rOAT1-TFV_8bvs.pdb #16 --- CL — chloride ion TFO — [2-(6-amino-9H-purin-9-yl)-1-methylethoxy]methylphosphonic acid (tenofovir) > hide #1 models > hide #!2 models > hide #!3 models > hide #!4 models > hide #!5 models > hide #6 models > hide #!7 models > hide #!8 models > hide #!9 models > hide #!10 models > hide #!11 models > hide #!12 models > hide #!13 models > hide #!14 models > hide #!15 models > hide #!16 models > show #!7 models > show #!8 models > volume #5 level 0.1359 > volume #7 step 1 > volume #7 level 0.3473 > volume #7 level 1.729 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 10 atoms, 9 bonds, 1 residue, 1 model selected > volume #7 level 0.6347 > volume #7 level 0.3844 > volume #7 level 0.5698 > view sel > volume #7 color #b2b2ffb3 > select #8:442 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select #8:438 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > select > #8:28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 255 atoms, 237 bonds, 32 residues, 1 model selected > show sel atoms > volume #7 level 0.5698 > select clear > lighting soft [Repeated 1 time(s)] > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > volume #7 style mesh > volume #7 style surface > volume #7 style mesh > volume #1 style mesh level 0.8 No volumes specified > volume #7 style mesh level 0.8 > volume #7 style mesh level 1 > volume #7 level 0.4901 > volume #7 style mesh level 1 color red level 1.2 color 0,50,80 > volume #7 level 1 level 1.2 > volume #7 level 0.9073 level 1.2 > volume #7 style mesh level Missing ""level"" keyword's argument > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > close #7.1-2 > hide #7 models > show #7 models > volume #7 level 0.7554 > select up 10 atoms, 9 bonds, 1 residue, 1 model selected > view sel > select clear > volume #7 level 0.5143 > volume #7 color #b2b2ff85 > select > #8:28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 255 atoms, 237 bonds, 32 residues, 1 model selected > show sel atoms > select clear > hide #!8 models > hide #!7 models > show #!10 models > show #!9 models > select add #10 4737 atoms, 4854 bonds, 2 pseudobonds, 612 residues, 2 models selected > view sel > volume #9 step 1 > volume #9 level 0.3973 > hide #!10 models > select subtract #10 Nothing selected > show #!10 models > hide #!9 models > show #!11 models > volume #11 step 1 > volume #11 level 0.6276 > show #!8 models > hide #!8 models > hide #!11 models > hide #!10 models > save ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" includeMaps true ——— End of log from Fri Jul 21 12:35:41 2023 ——— opened ChimeraX session > show #!2 models > hide #!2 models > show #1 models > view > hide #1 models > show #!4 models > hide #!4 models > show #6 models > select clear > select #6/B:601@O10 1 atom, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > show #!14 models > view > ui tool show Matchmaker > matchmaker #!14 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PBD_8bvt.pdb, chain A (#14), sequence alignment score = 2439.7 RMSD between 487 pruned atom pairs is 0.832 angstroms; (across all 498 pairs: 0.989) > view matrix models #6,1,0,0,-1.377,0,1,0,0.17197,0,0,1,-0.2168 > select clear [Repeated 1 time(s)] > select #6/B:601@C17 1 atom, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > matchmaker #!10 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8omu.pdb, chain A (#10), sequence alignment score = 2456.5 RMSD between 480 pruned atom pairs is 0.876 angstroms; (across all 492 pairs: 0.968) > matchmaker #!12 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo_8bvr.pdb, chain A (#12), sequence alignment score = 2447.5 RMSD between 481 pruned atom pairs is 0.838 angstroms; (across all 495 pairs: 0.921) > matchmaker #!16 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-TFV_8bvs.pdb, chain A (#16), sequence alignment score = 2464.3 RMSD between 483 pruned atom pairs is 0.804 angstroms; (across all 495 pairs: 0.869) > show #!16 models > hide #!16 models > show #!16 models > hide #!16 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!16 models > select > #6/A:28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 232 atoms, 216 bonds, 29 residues, 1 model selected > show sel atoms > save ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" includeMaps true > color #16 #8b7338ff > color #16 #897338ff > color #16 #897354ff > color #16 #89735fff > color #16 #89805fff > color #16 #896e5fff > color #16 #926e5fff > color #16 #9b6e5fff > select add #6 3905 atoms, 3985 bonds, 515 residues, 1 model selected > select subtract #6 Nothing selected > select add #16 4799 atoms, 4916 bonds, 2 pseudobonds, 619 residues, 2 models selected > color (#!16 & sel) byhetero > select > #/A:28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 Expected an objects specifier or a keyword > select > :28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 1966 atoms, 1824 bonds, 250 residues, 8 models selected > show sel & #6#!14,16 atoms > hide #!16 models > hide #!14 models > show #!14 models > matchmaker #!14 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PBD_8bvt.pdb, chain A (#14), sequence alignment score = 2439.7 RMSD between 487 pruned atom pairs is 0.832 angstroms; (across all 498 pairs: 0.989) > matchmaker #!16 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-TFV_8bvs.pdb, chain A (#16), sequence alignment score = 2464.3 RMSD between 483 pruned atom pairs is 0.804 angstroms; (across all 495 pairs: 0.869) > matchmaker #!12 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo_8bvr.pdb, chain A (#12), sequence alignment score = 2447.5 RMSD between 481 pruned atom pairs is 0.838 angstroms; (across all 495 pairs: 0.921) > matchmaker #!10 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8omu.pdb, chain A (#10), sequence alignment score = 2456.5 RMSD between 480 pruned atom pairs is 0.876 angstroms; (across all 492 pairs: 0.968) > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > hide #!14 models > show #!16 models > hide #6 models > show #!14 models > hide #!14 models > hide #!16 models > show #6 models > select clear > show #!14 models > lighting soft > show #!10 models > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > view sel > show #6#!10,14 atoms > undo > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > show #6#!10,14 atoms > undo > view > hide #!14 models > hide #6 models > show #!8 models > hide #!10 models > show #!14 models > show #6 models > hide #!8 models > select add #8 4748 atoms, 4863 bonds, 2 pseudobonds, 614 residues, 2 models selected > select subtract #8 Nothing selected > hide #!14 models > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 19 atoms, 19 bonds, 1 residue, 1 model selected > view sel > show #!8 models > hide #!8 models > show #!8 models > show #!14 models > show #!16 models > show #!12 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > hide #!12 models > select ::name=""CL"" 2 atoms, 2 residues, 2 models selected > show sel atoms > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select #8/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > hide sel atoms > select add #14 4518 atoms, 4615 bonds, 2 pseudobonds, 625 residues, 3 models selected > select subtract #14 1 atom, 1 residue, 1 model selected > select add #16 4799 atoms, 4916 bonds, 2 pseudobonds, 619 residues, 2 models selected > select add #14 9316 atoms, 9531 bonds, 4 pseudobonds, 1243 residues, 4 models selected > select add #12 14110 atoms, 14439 bonds, 6 pseudobonds, 1863 residues, 6 models selected > select add #8 18858 atoms, 19302 bonds, 8 pseudobonds, 2477 residues, 8 models selected > select add #6 22763 atoms, 23287 bonds, 8 pseudobonds, 2992 residues, 9 models selected > select subtract #12 17969 atoms, 18379 bonds, 6 pseudobonds, 2372 residues, 7 models selected > hide sel atoms > select ::name=""AKG"" 10 atoms, 9 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""CL"" 2 atoms, 2 residues, 2 models selected > show sel atoms > select add #16 4800 atoms, 4916 bonds, 2 pseudobonds, 620 residues, 3 models selected > select subtract #16 1 atom, 1 residue, 1 model selected > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > select clear > select #16/A:602@CL 1 atom, 1 residue, 1 model selected > hide sel atoms > select ::name=""LIG"" 42 atoms, 42 bonds, 2 residues, 2 models selected > show sel & #6 atoms > select ::name=""RTO"" 19 atoms, 19 bonds, 1 residue, 1 model selected > show sel atoms > select ::name=""TFO"" 19 atoms, 20 bonds, 1 residue, 1 model selected > show sel atoms > select clear > hide #!16 models > show #!16 models > hide #!16 models > hide #!14 models > show #!14 models > show #!16 models > hide #6 models > show #6 models > show #!4 models > select clear [Repeated 3 time(s)] > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel atoms [Repeated 1 time(s)] > show sel atoms > hide sel atoms > movie record > turn y 2 180 > wait 180 > movie encode /Users/dout2/Desktop/movie1.mp4 Movie saved to /Users/dout2/Desktop/movie1.mp4 > hide #!16 models > hide #!14 models > hide #!8 models > hide #6 models > show #6 models > select > :28,31,35,142,145,200,203,204,207,223,226,227,230,231,234,346,350,353,354,378,382,435,438,439,442,462,465,466,469 1966 atoms, 1824 bonds, 250 residues, 8 models selected > show sel & #6#!4 atoms > hide sel & #6#!4 atoms > show #!16 models > show #!14 models > show #!10 models > hide #!10 models > show #!8 models > show #1 models > view > select clear Drag select of 23 residues > select clear [Repeated 1 time(s)] > matchmaker #1 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo-coot-4_real_space_refined_004.pdb, chain A (#1), sequence alignment score = 2582.7 RMSD between 500 pruned atom pairs is 0.389 angstroms; (across all 500 pairs: 0.389) > matchmaker #1 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo-coot-4_real_space_refined_004.pdb, chain A (#1), sequence alignment score = 2582.7 RMSD between 500 pruned atom pairs is 0.389 angstroms; (across all 500 pairs: 0.389) > matchmaker #1 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo-coot-4_real_space_refined_004.pdb, chain A (#1), sequence alignment score = 2582.7 RMSD between 500 pruned atom pairs is 0.389 angstroms; (across all 500 pairs: 0.389) > matchmaker #!4 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PAH-coot-7_real_space_refined_007.pdb, chain A (#4), sequence alignment score = 2547.2 RMSD between 494 pruned atom pairs is 0.541 angstroms; (across all 494 pairs: 0.541) > matchmaker #!8 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8bw7.pdb, chain A (#8), sequence alignment score = 2492.5 RMSD between 483 pruned atom pairs is 0.880 angstroms; (across all 492 pairs: 0.934) > matchmaker #!10 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-AKG_8omu.pdb, chain A (#10), sequence alignment score = 2456.5 RMSD between 480 pruned atom pairs is 0.876 angstroms; (across all 492 pairs: 0.968) > matchmaker #!12 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-apo_8bvr.pdb, chain A (#12), sequence alignment score = 2447.5 RMSD between 481 pruned atom pairs is 0.838 angstroms; (across all 495 pairs: 0.921) > matchmaker #!14 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-PBD_8bvt.pdb, chain A (#14), sequence alignment score = 2439.7 RMSD between 487 pruned atom pairs is 0.832 angstroms; (across all 498 pairs: 0.989) > matchmaker #!16 to #6 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 rOAT1-PBD-coot-4_real_space_refined_004.pdb, chain A (#6) with rOAT1-TFV_8bvs.pdb, chain A (#16), sequence alignment score = 2464.3 RMSD between 483 pruned atom pairs is 0.804 angstroms; (across all 495 pairs: 0.869) > save ""/Users/dout2/Documents/Manuscripts/rOAT1_2023/rOAT1_SimonLab/Compare > with our structure.cxs"" includeMaps true ——— End of log from Sun Aug 27 22:20:39 2023 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,5 Model Number: MPHG3LL/A Chip: Apple M2 Max Total Number of Cores: 12 (8 performance and 4 efficiency) Memory: 32 GB System Firmware Version: 8422.141.2 OS Loader Version: 8422.141.2 Software: System Software Overview: System Version: macOS 13.5 (22G74) Kernel Version: Darwin 22.6.0 Time since boot: 14 days, 43 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 3 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 R240HY: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 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: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6 ChimeraX-CoreFormats: 1.1 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: 1.3.3 ChimeraX-DockPrep: 1.1.1 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: 1.2.1 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: 1.1.4 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: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7 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: 1.1 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: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 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: 1.10.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 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: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Tom Goddard all ChimeraX