id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17490 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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\npage table in kernel 1875K 1 \nshared memory 3168K 24 \n=========== ======= ======= \nTOTAL 4.8G 6507 \nTOTAL, minus reserved VM space 4.6G 6507 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""4949db760d1d7071cc703d6041af1ba9b743d4c8"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""639124e81d92412bfb4880b3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000012 } ], ""experiments"" : [ { ""treatmentId"" : ""ccf01f2d-382e-4ccc-a332-b3f688bc9bbf"", ""experimentId"" : ""67f46b1a73932228c9baf274"", ""deploymentId"" : 400000001 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/haoranfu/Downloads/cryosparc_P40_J444_015_volume_map.mrc Opened cryosparc_P40_J444_015_volume_map.mrc as #1, grid size 440,440,440, pixel 0.573, shown at level 0.0223, step 2, values float32 > open /Users/haoranfu/Downloads/cryosparc_P40_J443_014_volume_map.mrc Opened cryosparc_P40_J443_014_volume_map.mrc as #2, grid size 440,440,440, pixel 0.573, shown at level 0.0224, step 2, values float32 > volume #1 level 0.02949 > volume #2 level 0.03112 > volume #2 level 0.01776 > volume #2 level 0.05186 > volume #1 level 0.03883 > volume #2 level 0.03251 > surface dust #2 size 5.73 > close #1 > close #2 > open /Users/haoranfu/Downloads/cryosparc_P40_J439_011_volume_map.mrc Opened cryosparc_P40_J439_011_volume_map.mrc as #1, grid size 440,440,440, pixel 0.573, shown at level 0.0225, step 2, values float32 > open /Users/haoranfu/Downloads/cryosparc_P40_J438_014_volume_map.mrc Opened cryosparc_P40_J438_014_volume_map.mrc as #2, grid size 440,440,440, pixel 0.573, shown at level 0.0225, step 2, values float32 > volume #1 level 0.03612 > close #1 > close #2 > open /Users/haoranfu/Downloads/cryosparc_P40_J442_cluster_000.mrc Opened cryosparc_P40_J442_cluster_000.mrc as #1, grid size 440,440,440, pixel 0.573, shown at level 0.0218, step 2, values float32 > open /Users/haoranfu/Downloads/cryosparc_P40_J442_cluster_001.mrc Opened cryosparc_P40_J442_cluster_001.mrc as #2, grid size 440,440,440, pixel 0.573, shown at level 0.0221, step 2, values float32 > open /Users/haoranfu/Downloads/cryosparc_P40_J442_cluster_002.mrc Opened cryosparc_P40_J442_cluster_002.mrc as #3, grid size 440,440,440, pixel 0.573, shown at level 0.0219, step 2, values float32 > volume #3 level 0.02977 > volume #2 level 0.02957 > volume #1 level 0.03002 > close #1 > close #2 > close #3 > open /Users/haoranfu/Downloads/run_it050_class003.mrc Opened run_it050_class003.mrc as #1, grid size 104,104,104, pixel 2.29, shown at level 0.0336, step 1, values float32 > open /Users/haoranfu/Downloads/run_it050_class002.mrc Opened run_it050_class002.mrc as #2, grid size 104,104,104, pixel 2.29, shown at level 0.0403, step 1, values float32 > open /Users/haoranfu/Downloads/run_it050_class001.mrc Opened run_it050_class001.mrc as #3, grid size 104,104,104, pixel 2.29, shown at level 0.0374, step 1, values float32 > volume #2 level 0.001904 > close #1 > close #3 > close #2 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/2024_04_08_cyddc_CRYO_SPARC/NU_refine__cydDC_box416.mrc Opened NU_refine__cydDC_box416.mrc as #1, grid size 416,416,416, pixel 0.573, shown at level 0.0239, step 2, values float32 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/2024_04_08_cyddc_CRYO_SPARC/NU_refine_nomask_cydDC_box440.mrc Opened NU_refine_nomask_cydDC_box440.mrc as #2, grid size 440,440,440, pixel 0.573, shown at level 0.0221, step 2, values float32 > fitmap #1 inMap #2 Fit map NU_refine__cydDC_box416.mrc in map NU_refine_nomask_cydDC_box440.mrc using 89978 points correlation = 0.5212, correlation about mean = 0.07628, overlap = 67.48 steps = 72, shift = 1.57, angle = 0.924 degrees Position of NU_refine__cydDC_box416.mrc (#1) relative to NU_refine_nomask_cydDC_box440.mrc (#2) coordinates: Matrix rotation and translation 0.99994842 0.00745207 -0.00690046 1.03401953 -0.00736507 0.99989414 0.01254817 0.14514317 0.00699324 -0.01249670 0.99989746 1.51003904 Axis -0.77667264 -0.43086121 -0.45949780 Axis point 0.00000000 63.14443179 42.51338384 Rotation angle (degrees) 0.92383036 Shift along axis -1.55949085 > select add #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99995,0.0074521,-0.0069005,2.1576,-0.0073651,0.99989,0.012548,8.1541,0.0069932,-0.012497,0.9999,4.9941 > fitmap #1 inMap #2 Fit map NU_refine__cydDC_box416.mrc in map NU_refine_nomask_cydDC_box440.mrc using 89978 points correlation = 0.9937, correlation about mean = 0.9728, overlap = 211.1 steps = 84, shift = 5.6, angle = 0.931 degrees Position of NU_refine__cydDC_box416.mrc (#1) relative to NU_refine_nomask_cydDC_box440.mrc (#2) coordinates: Matrix rotation and translation 0.99999999 0.00011760 -0.00005705 6.86747790 -0.00011761 0.99999996 -0.00025875 6.92014706 0.00005702 0.00025876 0.99999996 6.84229871 Axis 0.89258965 -0.19673289 -0.40568447 Axis point 0.00000000 -29562.65435451 28263.64445210 Rotation angle (degrees) 0.01660981 Shift along axis 1.99260480 > volume #2 level 0.0302 > volume #1 level 0.02344 > surface dust #2 size 5.73 > view matrix models > #1,1,0.0001176,-5.7047e-05,5.8148,-0.00011761,1,-0.00025875,7.1545,5.7017e-05,0.00025876,1,14.509 > volume #1 level 0.01872 > volume #1 level 0.00738 > volume #1 level 0.03194 > surface dust #1 size 5.73 > volume #2 level 0.03259 > surface dust #2 size 5.73 > volume #2 level 0.07126 > volume #2 level 0.02924 > volume #1 level 0.0173 > fitmap #1 inMap #2 Fit map NU_refine__cydDC_box416.mrc in map NU_refine_nomask_cydDC_box440.mrc using 138729 points correlation = 0.6746, correlation about mean = 0.2569, overlap = 124.3 steps = 92, shift = 3.56, angle = 2.24 degrees Position of NU_refine__cydDC_box416.mrc (#1) relative to NU_refine_nomask_cydDC_box440.mrc (#2) coordinates: Matrix rotation and translation 0.99924259 -0.03717572 0.01149869 10.20711285 0.03719033 0.99930764 -0.00105897 4.50098852 -0.01145136 0.00148581 0.99993333 12.84193160 Axis 0.03268045 0.29472855 0.95502202 Axis point -5.79036417 262.44118568 0.00000000 Rotation angle (degrees) 2.23132971 Shift along axis 13.92447041 > open /Users/haoranfu/Downloads/emd_22457.map Opened emd_22457.map as #3, grid size 256,256,256, pixel 1.05, shown at level 2.36, step 1, values float32 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/cryosparc_P42_J212_011_volume_map.mrc Opened cryosparc_P42_J212_011_volume_map.mrc as #4, grid size 160,160,160, pixel 1.15, shown at level 0.0861, step 1, values float32 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_apo_NU_refine.mrc Opened NaCT_apo_NU_refine.mrc as #5, grid size 320,320,320, pixel 0.573, shown at level 0.0286, step 2, values float32 > view matrix models > #1,0.99924,-0.037176,0.011499,-23.02,0.03719,0.99931,-0.001059,0.46276,-0.011451,0.0014858,0.99993,-30.304 > view matrix models > #1,0.99924,-0.037176,0.011499,-50.176,0.03719,0.99931,-0.001059,-4.0396,-0.011451,0.0014858,0.99993,-66.597 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.99924,-0.037176,0.011499,-79.471,0.03719,0.99931,-0.001059,-7.9812,-0.011451,0.0014858,0.99993,-104.96 > view matrix models > #1,0.99924,-0.037176,0.011499,-95.589,0.03719,0.99931,-0.001059,-9.1788,-0.011451,0.0014858,0.99993,-125.24 > select subtract #1 Nothing selected > ui mousemode right ""rotate selected models"" > select add #4 2 models selected > view matrix models > #4,-0.94342,-0.32747,0.05215,203.24,-0.33159,0.93035,-0.15651,50.989,0.0027364,-0.16495,-0.9863,195.58 > fitmap #4 inMap #5 Fit map cryosparc_P42_J212_011_volume_map.mrc in map NaCT_apo_NU_refine.mrc using 40890 points correlation = 0.5083, correlation about mean = 0.01695, overlap = 122 steps = 136, shift = 4.15, angle = 10.9 degrees Position of cryosparc_P42_J212_011_volume_map.mrc (#4) relative to NaCT_apo_NU_refine.mrc (#5) coordinates: Matrix rotation and translation -0.98693200 -0.16081353 -0.01020943 197.71272290 -0.15514236 0.96542651 -0.20948148 40.51770033 0.04354390 -0.20516006 -0.97775931 195.68536920 Axis 0.07969542 -0.99131735 0.10458752 Axis point 99.14399812 0.00000000 101.33430080 Rotation angle (degrees) 178.44640240 Shift along axis -3.94285474 > volume filp #4 Expected a density maps specifier or a keyword > volume flip #4 Opened cryosparc_P42_J212_011_volume_map.mrc z flip as #6, grid size 160,160,160, pixel 1.15, shown at step 1, values float32 > fitmap #5 inMap #6 Fit map NaCT_apo_NU_refine.mrc in map cryosparc_P42_J212_011_volume_map.mrc z flip using 40901 points correlation = 0.9561, correlation about mean = 0.7806, overlap = 350.6 steps = 112, shift = 8.23, angle = 10.6 degrees Position of NaCT_apo_NU_refine.mrc (#5) relative to cryosparc_P42_J212_011_volume_map.mrc z flip (#6) coordinates: Matrix rotation and translation -0.99904745 -0.01621160 0.04051403 180.80508238 -0.01987401 0.99558866 -0.09169650 14.86628881 -0.03884875 -0.09241433 -0.99496250 195.11226813 Axis -0.00903497 0.99889612 -0.04609678 Axis point 92.41233737 0.00000000 96.10045174 Rotation angle (degrees) 177.72331218 Shift along axis 4.22226231 > volume #5 level 0.0323 > volume #6 level 0.07129 > volume #6 level 0.03084 > volume #4 level 0.1697 > volume #6 level 0.1495 > volume #5 level 0.03719 > volume #6 level 0.1023 > close #4 > volume #3 level 11.24 > surface dust #3 size 10.5 > surface dust #6 size 11.5 > volume #3 level 9.487 > surface dust #3 size 10.5 > surface dust #6 size 11.5 > surface dust #3 size 10.5 > surface dust #6 size 11.5 > surface dust #3 size 10.5 > surface dust #6 size 11.5 > select add #3 2 models selected > view matrix models > #3,-0.37518,0.45482,-0.8077,227.11,-0.9239,-0.25419,0.28602,253.23,-0.075223,0.85354,0.51557,-41.051 > view matrix models > #3,-0.097274,0.67529,-0.73111,150.77,-0.23959,0.6971,0.67576,-15.279,0.96599,0.2409,0.093983,-43.322 > ui mousemode right ""move picked models"" > view matrix models > #3,-0.097274,0.67529,-0.73111,120.33,-0.23959,0.6971,0.67576,-51.339,0.96599,0.2409,0.093983,-82.623 > view matrix models > #3,-0.097274,0.67529,-0.73111,120.21,-0.23959,0.6971,0.67576,-49.765,0.96599,0.2409,0.093983,-81.33 > view matrix models > #3,-0.097274,0.67529,-0.73111,116.74,-0.23959,0.6971,0.67576,-58.349,0.96599,0.2409,0.093983,-78.953 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.39972,-0.40734,-0.82115,206.65,0.16149,0.91312,-0.37435,-4.4632,0.9023,0.017033,0.43077,-84.262 > fitmap #3 inMap #6 Fit map emd_22457.map in map cryosparc_P42_J212_011_volume_map.mrc z flip using 39548 points correlation = 0.5409, correlation about mean = 0.04596, overlap = 3.031e+04 steps = 328, shift = 3.26, angle = 17.4 degrees Position of emd_22457.map (#3) relative to cryosparc_P42_J212_011_volume_map.mrc z flip (#6) coordinates: Matrix rotation and translation -0.13230601 0.14690715 0.98026191 -44.61575484 -0.04161212 0.98726083 -0.15357243 -22.08476534 -0.99033507 -0.06110933 -0.12450743 241.68696977 Axis 0.04665725 0.99437108 -0.09512757 Axis point 82.36251663 0.00000000 138.41289445 Rotation angle (degrees) 97.74568488 Shift along axis -47.03319477 > close #3 > open /Users/haoranfu/Downloads/7jsk.cif Summary of feedback from opening /Users/haoranfu/Downloads/7jsk.cif --- note | Fetching CCD CIT from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/T/CIT/CIT.cif 7jsk.cif title: Structure of the NaCT-Citrate complex [more info...] Chain information for 7jsk.cif #3 --- Chain | Description | UniProt A B | Solute carrier family 13 member 5 | S13A5_HUMAN 1-568 Non-standard residues in 7jsk.cif #3 --- CIT — citric acid NA — sodium 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) > select add #3 15060 atoms, 15248 bonds, 22 pseudobonds, 944 residues, 4 models selected > view matrix models > #3,0.19594,0.66973,-0.71629,116.29,-0.5424,0.68256,0.48982,47.915,0.81695,0.29254,0.497,-79.375 > view matrix models > #3,-0.96815,0.082762,0.23631,220.15,0.24226,0.54812,0.80055,-81.981,-0.063271,0.83229,-0.55071,109.89 > view matrix models > #3,0.34338,-0.22732,-0.91127,244.01,-0.53898,0.7469,-0.38941,159.84,0.76915,0.62488,0.13395,-68.064 > hide #!6 models > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/cryosparc_P42_J212_011_volume_map.mrc Opened cryosparc_P42_J212_011_volume_map.mrc as #4, grid size 160,160,160, pixel 1.15, shown at level 0.0861, step 1, values float32 > volume #4 level 0.1239 > view matrix models > #3,0.94147,-0.21554,0.25918,1.7328,0.24755,-0.079769,-0.96559,244.58,0.2288,0.97323,-0.021742,-21.052 > view matrix models > #3,0.23536,0.0029093,0.9719,-31.075,0.90617,-0.36218,-0.21836,91.347,0.35137,0.9321,-0.08788,-22.852 > view matrix models > #3,0.025251,0.04888,0.99849,-12.755,0.93287,-0.36016,-0.0059607,58.501,0.35933,0.93161,-0.054693,-28.382 > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > view matrix models > #3,0.025251,0.04888,0.99849,-12.668,0.93287,-0.36016,-0.0059607,58.637,0.35933,0.93161,-0.054693,-27.879 > view matrix models > #3,0.025251,0.04888,0.99849,-21.073,0.93287,-0.36016,-0.0059607,19.813,0.35933,0.93161,-0.054693,-76.037 > fitmap #3 inMap #4 Fit molecule 7jsk.cif (#3) to map cryosparc_P42_J212_011_volume_map.mrc (#4) using 15060 atoms average map value = 0.03659, steps = 116 shifted from previous position = 15.1 rotated from previous position = 13.7 degrees atoms outside contour = 13232, contour level = 0.12388 Position of 7jsk.cif (#3) relative to cryosparc_P42_J212_011_volume_map.mrc (#4) coordinates: Matrix rotation and translation 0.17647878 0.20902842 0.96185361 -72.84907273 0.94945420 -0.29387394 -0.11033957 22.39314594 0.25959961 0.93270854 -0.25032542 -34.97682920 Axis 0.71479548 0.48125103 0.50740996 Axis point 0.00000000 37.24100967 23.76758260 Rotation angle (degrees) 133.14604140 Shift along axis -59.04305467 > view matrix models > #3,0.17648,0.20903,0.96185,-92.639,0.94945,-0.29387,-0.11034,24.648,0.2596,0.93271,-0.25033,-34.611 > fitmap #3 inMap #4 Fit molecule 7jsk.cif (#3) to map cryosparc_P42_J212_011_volume_map.mrc (#4) using 15060 atoms average map value = 0.06183, steps = 100 shifted from previous position = 2.97 rotated from previous position = 14.5 degrees atoms outside contour = 11698, contour level = 0.12388 Position of 7jsk.cif (#3) relative to cryosparc_P42_J212_011_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.00988354 0.04310257 0.99902176 -52.82350624 0.95559011 -0.29386677 0.02213268 3.85740032 0.29453327 0.95487407 -0.03828395 -71.39147063 Axis 0.62900509 0.47508007 0.61534667 Axis point 0.00000000 30.70927245 4.12459718 Rotation angle (degrees) 132.14561586 Shift along axis -75.32418401 > view matrix models > #3,-0.0098835,0.043103,0.99902,-51.031,0.95559,-0.29387,0.022133,18.466,0.29453,0.95487,-0.038284,-79.597 > undo > ui mousemode right ""move picked models"" > hide #!3 models > show #!3 models > volume #4 level 0.1805 > ui mousemode right ""rotate selected models"" > select subtract #3 Nothing selected > select add #3 15060 atoms, 15248 bonds, 22 pseudobonds, 944 residues, 4 models selected > view matrix models > #3,-0.0024823,0.078953,0.99688,-58.323,0.88974,-0.45486,0.038241,32.048,0.45645,0.88706,-0.069119,-79.823 > fitmap #3 inMap #4 Fit molecule 7jsk.cif (#3) to map cryosparc_P42_J212_011_volume_map.mrc (#4) using 15060 atoms average map value = 0.1183, steps = 60 shifted from previous position = 4.43 rotated from previous position = 5.93 degrees atoms outside contour = 11190, contour level = 0.18051 Position of 7jsk.cif (#3) relative to cryosparc_P42_J212_011_volume_map.mrc (#4) coordinates: Matrix rotation and translation -0.01560019 0.00574183 0.99986182 -43.06256486 0.92043462 -0.39054375 0.01660369 20.59816672 0.39058512 0.92056646 0.00080758 -84.80031387 Axis 0.63523563 0.42815288 0.64277586 Axis point 3.50991918 39.62659907 -0.00000000 Rotation angle (degrees) 134.64146656 Shift along axis -73.04330565 > select subtract #3 Nothing selected > hide #!3 models > close #4 > close #6 > close #5 > close #2 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/Maps_NaCT_Ö/NaCT_inward_high_res.mrc Opened NaCT_inward_high_res.mrc as #2, grid size 360,360,360, pixel 0.833, shown at level 0.247, step 2, values float32 > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-103.86,0,1,0,24.139,0,0,1,48.094 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_apo_NU_refine.mrc Opened NaCT_apo_NU_refine.mrc as #4, grid size 320,320,320, pixel 0.573, shown at level 0.0286, step 2, values float32 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_inhibitor1_BI_NU_refine.mrc Opened NaCT_inhibitor1_BI_NU_refine.mrc as #5, grid size 320,320,320, pixel 0.573, shown at level 0.0292, step 2, values float32 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_inhibitor2_PF4_NU_refine.mrc Opened NaCT_inhibitor2_PF4_NU_refine.mrc as #6, grid size 160,160,160, pixel 1.15, shown at level 0.0829, step 1, values float32 > set bgColor white > view matrix models #4,1,0,0,-1.1871,0,1,0,-10.342,0,0,1,124.43 > volume #2 level 0.6793 > volume #2 level 0.5682 > surface dust #2 size 8.33 > surface dust #4 size 5.73 > surface dust #5 size 5.73 > surface dust #6 size 11.5 > view matrix models #4,1,0,0,-30.791,0,1,0,22.922,0,0,1,100.9 > select add #4 2 models selected > view matrix models #4,1,0,0,-4.9401,0,1,0,33.234,0,0,1,102.95 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.1481,0.36603,-0.91874,123.01,-0.8961,0.4427,0.031921,163.51,0.41841,0.81856,0.39356,44.673 > view matrix models > #4,0.30782,0.27606,0.91052,-53.125,-0.29735,-0.88113,0.36768,202.67,0.90379,-0.38392,-0.18914,168.1 > view matrix models > #4,0.21298,0.27903,0.93637,-47.25,-0.034676,-0.95559,0.29265,192.94,0.97644,-0.094798,-0.19385,134.8 > ui mousemode right ""move picked models"" > select add #3 15060 atoms, 15248 bonds, 22 pseudobonds, 944 residues, 6 models selected > select subtract #3 2 models selected > select add #2 4 models selected > select subtract #4 2 models selected > view matrix models #2,1,0,0,-100.16,0,1,0,69.512,0,0,1,67.264 > view matrix models > #4,0.21298,0.27903,0.93637,-79.483,-0.034676,-0.95559,0.29265,265.94,0.97644,-0.094798,-0.19385,165.43 > view matrix models > #4,0.21298,0.27903,0.93637,-77.543,-0.034676,-0.95559,0.29265,276.94,0.97644,-0.094798,-0.19385,147.66 > volume #4 level 0.0274 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 4 maps. > select add #4 4 models selected > fitmap #2 inMap #4 Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc using 12008 points correlation = 0.4903, correlation about mean = 0.05277, overlap = 265.4 steps = 160, shift = 5.4, angle = 6.62 degrees Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc (#4) coordinates: Matrix rotation and translation 0.17964141 -0.07351372 0.98098149 -71.03340734 0.17451285 -0.97900576 -0.10532318 221.43040313 0.96812924 0.19011428 -0.16304088 -58.75969336 Axis 0.76545998 0.03329938 0.64262133 Axis point 0.00000000 112.53329075 14.70546258 Rotation angle (degrees) 168.87323496 Shift along axis -84.75996698 > volume #4 level 0.03556 > view matrix models > #4,0.21298,0.27903,0.93637,-22.788,-0.034676,-0.95559,0.29265,256.78,0.97644,-0.094798,-0.19385,148.45 > view matrix models > #4,0.21298,0.27903,0.93637,-75.887,-0.034676,-0.95559,0.29265,276.78,0.97644,-0.094798,-0.19385,147.78 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.97212,-0.22937,0.04881,-68.489,0.22936,0.97332,0.0057035,36.986,-0.048816,0.0056509,0.99879,68.772,#4,0.23938,0.38906,0.88957,-83.699,-0.024754,-0.91346,0.40617,261.41,0.97061,-0.11925,-0.20903,151.92 > view matrix models > #2,0.9265,-0.36856,0.075873,-45.045,0.37027,0.92888,-0.0094282,23.717,-0.067002,0.036829,0.99707,67.323,#4,0.26796,0.51451,0.81454,-90.436,-0.011018,-0.84376,0.5366,241.59,0.96337,-0.15276,-0.22043,156.66 > view matrix models > #2,0.81858,-0.5636,0.11087,-5.0992,0.56774,0.82318,-0.0072013,7.9545,-0.08721,0.068842,0.99381,66.353,#4,0.29725,0.68294,0.66726,-94.462,0.03441,-0.70606,0.70732,208.95,0.95418,-0.18729,-0.23337,161.88 > select subtract #2 2 models selected > view matrix models > #4,0.36385,0.75577,0.54444,-95.632,-0.28474,-0.46628,0.83756,203.83,0.88687,-0.45977,0.045539,166.68 > view matrix models > #4,0.10296,0.73181,0.67368,-81.897,-0.1001,-0.66622,0.73901,214.55,0.98964,-0.14352,0.0046553,132.37 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.10296,0.73181,0.67368,-25.397,-0.1001,-0.66622,0.73901,212.99,0.98964,-0.14352,0.0046553,131.2 > select subtract #4 Nothing selected > select add #5 2 models selected > view matrix models #5,1,0,0,-103.74,0,1,0,121.29,0,0,1,85.619 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.3792,-0.92008,0.098335,28.861,0.2971,0.22171,0.92875,81.833,-0.87632,-0.32297,0.35742,253.58 > view matrix models > #5,0.21638,-0.88766,-0.40649,86.599,-0.058048,-0.42732,0.90224,176.58,-0.97458,-0.17163,-0.14399,294.14 > select subtract #5 Nothing selected > select add #6 2 models selected > view matrix models > #6,0.40652,-0.89106,0.20189,120.72,0.91106,0.41195,-0.016353,-26.133,-0.068595,0.19058,0.97927,-9.9396 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.40652,-0.89106,0.20189,-60.672,0.91106,0.41195,-0.016353,36.715,-0.068595,0.19058,0.97927,104.23 > view matrix models > #6,0.40652,-0.89106,0.20189,-62.907,0.91106,0.41195,-0.016353,20.796,-0.068595,0.19058,0.97927,90.701 > view matrix models > #6,0.40652,-0.89106,0.20189,-60.159,0.91106,0.41195,-0.016353,22.186,-0.068595,0.19058,0.97927,91.068 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.67724,-0.14292,0.72175,-203.81,0.38073,0.90748,-0.17754,38.463,-0.6296,0.39503,0.669,151.51 > view matrix models > #6,0.67631,-0.13663,0.72384,-204.52,0.37634,0.90881,-0.18009,38.973,-0.63322,0.3942,0.66606,152.2 > view matrix models > #6,-0.72985,0.30168,0.61344,-107.1,0.61012,-0.11726,0.78358,26.838,0.30832,0.94617,-0.098477,83.365 > view matrix models > #6,0.0064758,0.93772,0.34732,-210.78,-0.44459,-0.30841,0.84097,136.52,0.89571,-0.15986,0.4149,87.662 > select subtract #6 Nothing selected > hide #!4 models > hide #!6 models > volume flip #4 Opened NaCT_apo_NU_refine.mrc z flip as #7, grid size 320,320,320, pixel 0.573, shown at step 1, values float32 > volume flip #6 Opened NaCT_inhibitor2_PF4_NU_refine.mrc z flip as #8, grid size 160,160,160, pixel 1.15, shown at step 1, values float32 > select add #5 2 models selected > view matrix models > #5,0.19995,-0.88133,-0.4281,89.472,-0.070029,-0.44866,0.89095,180.68,-0.9773,-0.14817,-0.15143,292.89 > ui mousemode right ""move picked models"" > view matrix models > #5,0.19995,-0.88133,-0.4281,137.21,-0.070029,-0.44866,0.89095,190.06,-0.9773,-0.14817,-0.15143,285.39 > view matrix models > #5,0.19995,-0.88133,-0.4281,147.1,-0.070029,-0.44866,0.89095,190.88,-0.9773,-0.14817,-0.15143,324.87 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 4 maps. > select add #2 4 models selected > fitmap #2 inMap #5 Fit map NaCT_inward_high_res.mrc in map NaCT_inhibitor1_BI_NU_refine.mrc using 12008 points correlation = 0.4427, correlation about mean = -0.004388, overlap = 254.9 steps = 108, shift = 2.49, angle = 6.52 degrees Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_inhibitor1_BI_NU_refine.mrc (#5) coordinates: Matrix rotation and translation 0.17645051 -0.13283431 -0.97530522 229.61167585 -0.97475664 0.11412985 -0.19189549 248.01435641 0.13680174 0.98454529 -0.10934285 -69.48523532 Axis 0.64472159 -0.60946490 -0.46139637 Axis point 0.00000000 260.71553975 180.78607152 Rotation angle (degrees) 114.16597137 Shift along axis 28.93979300 > ui mousemode right ""rotate selected models"" > select subtract #5 2 models selected > select subtract #2 Nothing selected > select add #7 2 models selected > view matrix models > #7,-0.38725,0.89133,-0.23571,86.311,0.048509,0.275,0.96022,93.909,0.9207,0.36041,-0.14973,105.45 > ui mousemode right ""move picked models"" > view matrix models > #7,-0.38725,0.89133,-0.23571,24.357,0.048509,0.275,0.96022,114.33,0.9207,0.36041,-0.14973,97.53 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 4 maps. > select add #5 4 models selected > fitmap #5 inMap #7 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_apo_NU_refine.mrc z flip using 40947 points correlation = 0.7424, correlation about mean = 0.3079, overlap = 78.33 steps = 184, shift = 7.91, angle = 23.2 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#5) relative to NaCT_apo_NU_refine.mrc z flip (#7) coordinates: Matrix rotation and translation -0.98626494 -0.16456688 0.01411378 195.96537239 0.16443637 -0.98633735 -0.00996488 164.49166856 0.01556083 -0.00750720 0.99985074 -2.65333105 Axis 0.00746981 -0.00439814 0.99996243 Axis point 91.18124786 90.35563259 0.00000000 Rotation angle (degrees) 170.53135694 Shift along axis -1.91286420 > select subtract #7 2 models selected > select subtract #5 Nothing selected > select add #8 2 models selected > view matrix models > #8,0.0064758,0.93772,0.34732,-75.69,-0.44459,-0.30841,0.84097,194.15,0.89571,-0.15986,0.4149,178.98 > ui mousemode right ""rotate selected models"" > view matrix models > #8,-0.3745,0.925,0.064171,-14.262,-0.67465,-0.31931,0.66549,231.95,0.63607,0.20593,0.74364,138.54 > view matrix models > #8,-0.15425,0.95382,0.25776,-54.491,-0.54199,-0.29981,0.78509,207.25,0.82611,-0.018605,0.5632,158.64 > view matrix models > #8,-0.12189,0.84826,-0.51536,21.598,-0.22728,0.48159,0.84642,98.311,0.96617,0.2203,0.13409,161.27 > ui mousemode right ""move picked models"" > view matrix models > #8,-0.12189,0.84826,-0.51536,38.745,-0.22728,0.48159,0.84642,109.42,0.96617,0.2203,0.13409,85.666 > view matrix models > #8,-0.12189,0.84826,-0.51536,39.692,-0.22728,0.48159,0.84642,118.09,0.96617,0.2203,0.13409,83.622 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 4 maps. > select add #7 4 models selected > fitmap #7 inMap #8 Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inhibitor2_PF4_NU_refine.mrc z flip using 230090 points correlation = 0.5338, correlation about mean = 0.04985, overlap = 653.8 steps = 72, shift = 3.86, angle = 6.23 degrees Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_inhibitor2_PF4_NU_refine.mrc z flip (#8) coordinates: Matrix rotation and translation 0.89404027 0.26672644 -0.35992918 14.62442750 -0.15992037 0.94052072 0.29974368 -13.53301131 0.41847041 -0.21042291 0.88351838 5.62180082 Axis -0.49829811 -0.76029095 -0.41672133 Axis point -2.33529441 0.00000000 42.23120260 Rotation angle (degrees) 30.79107172 Shift along axis 0.65897709 > close #6 > close #4 > hide #!5 models > hide #!8 models > select subtract #8 2 models selected > select add #2 4 models selected > fitmap #2 inMap #7 Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using 12008 points correlation = 0.4951, correlation about mean = 0.0409, overlap = 258.1 steps = 120, shift = 2.18, angle = 5.49 degrees Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z flip (#7) coordinates: Matrix rotation and translation -0.44502245 0.29811526 0.84444201 -7.39893197 0.82320705 -0.23503466 0.51680641 -69.93255855 0.35254101 0.92514107 -0.14081488 -93.96021817 Axis 0.49357512 0.59458604 0.63470547 Axis point 34.12697982 16.61103225 0.00000000 Rotation angle (degrees) 155.56567282 Shift along axis -104.86991660 > view matrix models > #2,0.86869,-0.48801,0.085002,-17.425,0.48678,0.87278,0.036035,15.185,-0.091774,0.010074,0.99573,65.213 > fitmap #2 inMap #7 Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using 12008 points correlation = 0.4675, correlation about mean = 0.01479, overlap = 256.7 steps = 188, shift = 3.8, angle = 10.8 degrees Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z flip (#7) coordinates: Matrix rotation and translation -0.36229365 0.14858152 0.92014501 -14.93075464 0.88733739 -0.24716039 0.38928665 -58.60017223 0.28526420 0.95751515 -0.04229730 -89.82926893 Axis 0.50388066 0.56298506 0.65509701 Axis point 27.70885466 17.58059101 0.00000000 Rotation angle (degrees) 145.67737156 Shift along axis -99.36122595 > select subtract #2 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.21802,0.97462,-0.050922,-17.168,-0.0015979,0.051821,0.99866,132.43,0.97594,0.21781,-0.0097406,93.376 > fitmap #7 inMap #2 Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inward_high_res.mrc using 230090 points correlation = 0.4186, correlation about mean = 0.06045, overlap = 5144 steps = 124, shift = 2.84, angle = 10.6 degrees Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation -0.02246715 0.87576604 0.48221268 25.61585958 0.01574908 -0.48196455 0.87604917 115.85248715 0.99962353 0.02727673 -0.00296415 52.78691291 Axis -0.64572832 -0.39363535 -0.65428292 Axis point 9.03943566 52.59056906 0.00000000 Rotation angle (degrees) 138.91172646 Shift along axis -96.68209645 > view matrix models > #7,-0.081456,0.9815,-0.17329,-18.811,0.084578,0.18004,0.98002,115.97,0.99308,0.065171,-0.097679,111.3 > fitmap #7 inMap #2 Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inward_high_res.mrc using 230090 points correlation = 0.8805, correlation about mean = 0.5675, overlap = 1.683e+04 steps = 80, shift = 5.99, angle = 1.29 degrees Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation -0.00217585 0.96004447 0.27983904 38.90453703 -0.03835313 -0.27971392 0.95931703 92.00569805 0.99926188 -0.00864537 0.03742933 54.95624878 Axis -0.61824220 -0.45949880 -0.63768130 Axis point 9.99940642 35.19629234 0.00000000 Rotation angle (degrees) 128.47918081 Shift along axis -101.37350627 > volume #7 level 0.03133 > surface dust #7 size 5.73 > volume #5 level 0.03014 > volume #2 level 0.5435 > surface dust #7 size 5.73 > fitmap #7 inMap #2 Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inward_high_res.mrc using 275715 points correlation = 0.8714, correlation about mean = 0.5951, overlap = 1.759e+04 steps = 28, shift = 0.0175, angle = 0.0128 degrees Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation -0.00236598 0.96005064 0.27981632 38.92968904 -0.03846887 -0.27969737 0.95931722 92.02372475 0.99925700 -0.00849449 0.03759382 54.91449750 Axis -0.61814880 -0.45951230 -0.63776211 Axis point 10.04374223 35.20779535 0.00000000 Rotation angle (degrees) 128.47951280 Shift along axis -101.37275987 > close #5 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_inhibitor1_BI_NU_refine.mrc Opened NaCT_inhibitor1_BI_NU_refine.mrc as #4, grid size 320,320,320, pixel 0.573, shown at level 0.0292, step 2, values float32 > view matrix models > #7,-0.1165,0.99163,-0.055563,-21.902,0.10693,0.068143,0.99193,122.85,0.98742,0.10962,-0.11398,112.14 > undo > select subtract #7 Nothing selected > save /Users/haoranfu/Desktop/1.tif width 1140 height 765 supersample 3 > transparentBackground true > select add #2 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.89722,-0.43487,-0.076749,-18.192,0.44112,0.89065,0.11027,103.99,0.020402,-0.1328,0.99093,66.392 > view matrix models > #2,0.89722,-0.43487,-0.076749,-24.508,0.44112,0.89065,0.11027,108.57,0.020402,-0.1328,0.99093,63.662 > select subtract #2 Nothing selected > volume #2 step 1 > volume #2 level 0.611 > select add #2 2 models selected > view matrix models > #2,0.89722,-0.43487,-0.076749,-4.0299,0.44112,0.89065,0.11027,12.761,0.020402,-0.1328,0.99093,76.182 > fitmap #2 inMap #7 Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using 89648 points correlation = 0.5704, correlation about mean = 0.08965, overlap = 2750 steps = 68, shift = 3.31, angle = 1.35 degrees Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z flip (#7) coordinates: Matrix rotation and translation -0.00137119 -0.06128358 0.99811945 -42.33647981 0.96165872 -0.27381114 -0.01549065 -11.42941657 0.27424555 0.95982904 0.05930934 -103.10400215 Axis 0.61419226 0.45584822 0.64418186 Axis point 15.30699972 37.52157774 0.00000000 Rotation angle (degrees) 127.44044721 Shift along axis -97.63054498 > view matrix models > #2,0.89968,-0.42775,-0.08723,-7.1165,0.436,0.89046,0.1303,10.364,0.02194,-0.15526,0.98763,78.403 > fitmap #2 inMap #7 Fit map NaCT_inward_high_res.mrc in map NaCT_apo_NU_refine.mrc z flip using 89648 points correlation = 0.9135, correlation about mean = 0.6255, overlap = 6177 steps = 84, shift = 3.51, angle = 1.37 degrees Position of NaCT_inward_high_res.mrc (#2) relative to NaCT_apo_NU_refine.mrc z flip (#7) coordinates: Matrix rotation and translation -0.00242723 -0.03813507 0.99926964 -51.29429941 0.96012555 -0.27944497 -0.00833230 -11.24037149 0.27955863 0.95940410 0.03729274 -101.16223106 Axis 0.61813520 0.45971063 0.63763235 Axis point 10.00656396 35.14956439 0.00000000 Rotation angle (degrees) 128.48353636 Shift along axis -101.37844122 > select subtract #2 Nothing selected > surface dust #2 size 8.33 > surface dust #7 size 5.73 > volume #2 level 0.7459 > volume #7 level 0.03048 > surface dust #2 size 8.33 > surface dust #7 size 5.73 > volume #7 level 0.03217 > volume #7 level 0.03683 > save /Users/haoranfu/Desktop/1.tif width 1140 height 765 supersample 3 > hide #!2 models > show #!2 models > show #!4 models > hide #!7 models > volume #4 level 0.03417 > select add #4 2 models selected > view matrix models #4,1,0,0,7.1755,0,1,0,32.071,0,0,1,88.88 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.068747,-0.92809,0.36595,144.01,-0.0001924,0.36681,0.9303,5.0854,-0.99763,-0.064026,0.025039,275.16 > view matrix models > #4,0.18382,-0.98263,0.025599,170,-0.36701,-0.044449,0.92916,76.611,-0.91188,-0.18019,-0.3688,314.46 > ui mousemode right ""move picked models"" > view matrix models > #4,0.18382,-0.98263,0.025599,173.87,-0.36701,-0.044449,0.92916,187.63,-0.91188,-0.18019,-0.3688,335.75 > view matrix models > #4,0.18382,-0.98263,0.025599,131.18,-0.36701,-0.044449,0.92916,192.68,-0.91188,-0.18019,-0.3688,335.86 > fitmap #4 inMap #2 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using 32734 points correlation = 0.3699, correlation about mean = 0.03798, overlap = 543.2 steps = 104, shift = 1.95, angle = 6.54 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation -0.00651287 -0.92834552 0.37166137 214.64282044 -0.19184472 0.36592529 0.91065597 55.87858123 -0.98140368 -0.06537029 -0.18048141 263.02772364 Axis -0.53519303 0.74193802 0.40385194 Axis point 236.29173317 0.00000000 15.14706755 Rotation angle (degrees) 114.23841547 Shift along axis 32.80735822 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.19837,-0.91909,0.34049,95.13,-0.21102,0.29919,0.93057,144.97,-0.95714,-0.25645,-0.1346,326.88 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.19837,-0.91909,0.34049,89.389,-0.21102,0.29919,0.93057,132.33,-0.95714,-0.25645,-0.1346,325.81 > fitmap #4 inMap #2 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using 32734 points correlation = 0.3616, correlation about mean = 0.04613, overlap = 580.9 steps = 124, shift = 3.61, angle = 6.71 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation 0.16207205 -0.71992036 0.67486838 140.44597548 -0.09276325 0.66976630 0.73675511 29.51839288 -0.98240910 -0.18201040 0.04176824 251.81448512 Axis -0.46030286 0.83029843 0.31420662 Axis point 213.82367910 0.00000000 30.78940695 Rotation angle (degrees) 93.62331921 Shift along axis 38.98317074 > volume flip #4 Opened NaCT_inhibitor1_BI_NU_refine.mrc z flip as #5, grid size 320,320,320, pixel 0.573, shown at step 1, values float32 > select subtract #4 Nothing selected > select add #5 2 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.079183,-0.9604,-0.26714,171.51,-0.70227,-0.13645,0.69871,241.09,-0.70749,0.24293,-0.66366,304.82 > hide #!5 models > select subtract #5 Nothing selected > show #!4 models > select add #4 2 models selected > view matrix models > #4,0.12299,-0.97718,-0.17319,146.66,0.026711,-0.17119,0.98488,152.08,-0.99205,-0.12576,0.0050476,303.88 > fitmap #4 inMap #2 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using 32734 points correlation = 0.6266, correlation about mean = 0.2456, overlap = 1381 steps = 68, shift = 3.18, angle = 7.48 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation 0.16117904 -0.95104108 0.26370853 196.75946006 -0.01094773 0.26546279 0.96405895 38.17398261 -0.98686446 -0.15827311 0.03237530 251.15157306 Axis -0.58289496 0.64949824 0.48824737 Axis point 252.69468206 0.00000000 -14.67837111 Rotation angle (degrees) 105.69351205 Shift along axis 32.72793151 > close #5 > view matrix models > #4,-0.14823,-0.98633,-0.071919,160.18,0.085799,-0.085274,0.99266,136.27,-0.98522,0.14097,0.097266,270.29 > undo > ui mousemode right ""move picked models"" > select subtract #4 Nothing selected > volume #2 color #fbd8b4 > undo > volume #2 color #f3d1af4d > select subtract #4 Nothing selected > undo > ui mousemode right ""rotate selected models"" > volume #2 color #f3d1af00 > volume #2 color #f3d1af > view matrix models > #4,-0.018278,-0.88212,-0.47068,178.07,-0.068217,-0.46856,0.8808,197.87,-0.9975,0.048207,-0.051611,293.46 > fitmap #4 inMap #2 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using 32734 points correlation = 0.4075, correlation about mean = 0.04414, overlap = 684.2 steps = 84, shift = 6.07, angle = 4.23 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation 0.00554612 -0.99959269 -0.02799449 249.99940977 0.09183041 -0.02736752 0.99539851 49.93733654 -0.99575921 -0.00809134 0.09164122 230.79333088 Axis -0.56677476 0.54659707 0.61643978 Axis point 214.09141949 52.91431331 0.00000000 Rotation angle (degrees) 117.71605268 Shift along axis 27.87243665 > ui mousemode right ""move picked models"" > view matrix models > #2,0.89734,-0.43465,-0.07654,-0.25786,0.44087,0.8908,0.11001,16.859,0.020366,-0.13246,0.99098,70.827 > fitmap #4 inMap #2 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using 32734 points correlation = 0.4069, correlation about mean = 0.05245, overlap = 721.4 steps = 144, shift = 4.01, angle = 7.14 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation 0.12039552 -0.99262752 0.01398293 223.64944107 0.06587221 0.02204238 0.99758458 46.16343842 -0.99053812 -0.11918363 0.06804037 244.98964968 Axis -0.60774258 0.54665795 0.57603302 Axis point 0.00000000 246.93866058 212.48367192 Rotation angle (degrees) 113.25106078 Shift along axis 30.43644874 > view matrix models > #4,0.15522,-0.89118,-0.42627,163.07,0.0027916,-0.4311,0.9023,185.81,-0.98788,-0.14124,-0.064427,313.26 > fitmap #4 inMap #2 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_inward_high_res.mrc using 32734 points correlation = 0.6266, correlation about mean = 0.2455, overlap = 1381 steps = 120, shift = 3.35, angle = 14.9 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_inward_high_res.mrc (#2) coordinates: Matrix rotation and translation 0.16132111 -0.95098679 0.26381741 196.72640529 -0.01093279 0.26558029 0.96402676 38.15428550 -0.98684141 -0.15840213 0.03244677 251.15258244 Axis -0.58291710 0.64951145 0.48820336 Axis point 252.69501788 0.00000000 -14.66724141 Rotation angle (degrees) 105.68366153 Shift along axis 32.71999395 > save /Users/haoranfu/Desktop/side-view-BI.tif width 1140 height 765 > supersample 3 > save /Users/haoranfu/Desktop/TOP-VIEW-BI.tif width 1140 height 765 > supersample 3 > volume #2 color #e1c1a1 > select subtract #4 Nothing selected > save /Users/haoranfu/Desktop/SIDE-viw.tif width 1140 height 765 supersample > 3 > save /Users/haoranfu/Desktop/side-view.tif width 1140 height 765 supersample > 3 > save /Users/haoranfu/Desktop/bottom.tif width 1140 height 765 supersample 3 > volume #4 level 0.04044 > surface dust #4 size 5.73 > view > undo > ui tool show ""Side View"" > save /Users/haoranfu/Desktop/inhibitor-bi.tif width 1140 height 765 > supersample 3 > show #!3 models > hide #!3 models > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_PF4_daneng.map Opened NaCT_PF4_daneng.map as #5, grid size 256,256,256, pixel 0.825, shown at level 0.131, step 1, values float32 > volume #5 level 0.3265 > select add #5 3 models selected > view matrix models #5,1,0,0,-35.327,0,1,0,20.771,0,0,1,81.446 > view matrix models #5,1,0,0,-83.4,0,1,0,115.01,0,0,1,90.111 > view matrix models #5,1,0,0,-57.914,0,1,0,119.24,0,0,1,87.364 > view matrix models #5,1,0,0,21.36,0,1,0,154.67,0,0,1,113.03 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.85881,-0.48073,0.17705,67.29,0.49969,0.86225,-0.082626,124.47,-0.11294,0.15943,0.98073,110.62 > view matrix models > #5,0.85904,-0.48107,0.17497,67.521,0.49998,0.86185,-0.08511,124.74,-0.10985,0.16059,0.98089,110.16 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models > #5,0.85904,-0.48107,0.17497,10.614,0.49998,0.86185,-0.08511,107.03,-0.10985,0.16059,0.98089,129.44 > view matrix models > #5,0.85904,-0.48107,0.17497,2.2088,0.49998,0.86185,-0.08511,98.616,-0.10985,0.16059,0.98089,91.451 > fitmap #5 inMap #4 Fit map NaCT_PF4_daneng.map in map NaCT_inhibitor1_BI_NU_refine.mrc using 50301 points correlation = 0.4556, correlation about mean = 0.07124, overlap = 735.2 steps = 192, shift = 7.19, angle = 15.3 degrees Position of NaCT_PF4_daneng.map (#5) relative to NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates: Matrix rotation and translation 0.14390330 -0.11731788 -0.98261302 187.95624798 -0.89799614 0.40173540 -0.17947590 161.30384834 0.41580617 0.90820988 -0.04753996 -43.48613100 Axis 0.56182123 -0.72232405 -0.40324295 Axis point 178.57204019 0.00000000 31.91720460 Rotation angle (degrees) 104.53377251 Shift along axis 6.61963813 > open > /Users/haoranfu/Desktop/mine/data/Data_processing/Nact/NaCT_PF4_daneng.cif NaCT_PF4_daneng.cif title: Structure of NaCT-PF4a complex [more info...] Chain information for NaCT_PF4_daneng.cif #6 --- Chain | Description | UniProt A B | Solute carrier family 13 member 5 | S13A5_HUMAN 1-568 Non-standard residues in NaCT_PF4_daneng.cif #6 --- NA — sodium ion XKC — (2R)-2-hydroxy-2-[2-(2-methoxy-5-methylpyridin-3-yl)ethyl]butanedioic acid > select add #6 7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 7 models selected > view matrix models > #5,0.81464,-0.57854,-0.040648,27.637,0.57983,0.81395,0.035747,82.038,0.012405,-0.05269,0.99853,118.34,#6,1,0,0,-8.8477,0,1,0,0.53453,0,0,1,12.796 > ui mousemode right ""move picked models"" > view matrix models #6,1,0,0,-57.517,0,1,0,52.131,0,0,1,62.792 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.51805,-0.62833,-0.58037,103.22,0.80459,0.58823,0.081362,78.802,0.29027,-0.50911,0.81028,147.17,#6,0.80912,-0.23179,-0.53999,71.252,0.31184,0.94822,0.06023,20.543,0.49807,-0.21712,0.83951,64.613 > ui mousemode right ""move picked models"" > view matrix models > #6,0.80912,-0.23179,-0.53999,7.821,0.31184,0.94822,0.06023,80.549,0.49807,-0.21712,0.83951,68.951 > view matrix models > #6,0.80912,-0.23179,-0.53999,34.654,0.31184,0.94822,0.06023,95.981,0.49807,-0.21712,0.83951,92.407 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.50751,-0.62332,-0.5949,105.33,0.80736,0.58519,0.075608,79.433,0.301,-0.51867,0.80024,148.05,#6,0.79824,-0.23435,-0.55489,37.613,0.31608,0.94715,0.054679,96.28,0.51275,-0.21904,0.83013,92.136 > view matrix models > #5,0.52014,-0.62516,-0.58192,102.7,0.805,0.5865,0.089448,78.091,0.28538,-0.51497,0.80831,148.41,#6,0.80906,-0.22806,-0.54167,34.314,0.31283,0.94734,0.068399,95.089,0.49755,-0.22479,0.8378,93.366 > view matrix models > #5,0.8816,-0.36788,0.2957,-55.502,0.25017,0.89546,0.36818,75.695,-0.40024,-0.25062,0.88148,186.24,#6,0.91901,0.22231,0.32559,-119.41,-0.32922,0.88708,0.32357,137.71,-0.21689,-0.40455,0.88843,178.17 > select subtract #5 7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 4 models selected > view matrix models > #6,0.94287,-0.33053,-0.041868,-23.152,0.3101,0.8247,0.47298,60.13,-0.12181,-0.45894,0.88008,174.76 > fitmap #6 inMap #5 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using 7202 atoms average map value = 0.07183, steps = 72 shifted from previous position = 2.35 rotated from previous position = 2.07 degrees atoms outside contour = 6091, contour level = 0.32651 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.96418056 0.06985697 -0.25588251 30.20411527 -0.01073472 0.97418247 0.22550673 -24.61022187 0.26502947 -0.21468237 0.94003769 -1.41537716 Axis -0.64098436 -0.75852953 -0.11735414 Axis point 30.99943641 0.00000000 112.38023244 Rotation angle (degrees) 20.08230240 Shift along axis -0.52668516 > view matrix models > #6,0.75867,-0.62102,-0.19686,44.144,0.62874,0.61881,0.47092,50.736,-0.17063,-0.48105,0.85993,185 > fitmap #6 inMap #5 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using 7202 atoms average map value = 0.07665, steps = 128 shifted from previous position = 3.56 rotated from previous position = 10.5 degrees atoms outside contour = 6093, contour level = 0.32651 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.88841813 -0.02778485 -0.45819344 67.51213013 0.20848766 0.91369683 0.34884238 -53.89617338 0.40895736 -0.40544557 0.81753763 15.10992979 Axis -0.64285569 -0.73904511 0.20136756 Axis point 25.43974788 0.00000000 140.41065908 Rotation angle (degrees) 35.92103683 Shift along axis -0.52620380 > ui mousemode right ""move picked models"" > view matrix models > #6,0.82746,-0.48052,-0.29053,90.323,0.55952,0.66195,0.49875,13.249,-0.047341,-0.57526,0.8166,175.35 > view matrix models > #6,0.82746,-0.48052,-0.29053,66.082,0.55952,0.66195,0.49875,73.589,-0.047341,-0.57526,0.8166,191.37 > view matrix models > #6,0.82746,-0.48052,-0.29053,74.943,0.55952,0.66195,0.49875,51.153,-0.047341,-0.57526,0.8166,198.64 > view matrix models > #6,0.82746,-0.48052,-0.29053,32.734,0.55952,0.66195,0.49875,45.094,-0.047341,-0.57526,0.8166,192.31 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.8163,-0.28529,0.50226,-72.157,0.27,0.95714,0.10485,86.6,-0.51064,0.050019,0.85834,170.15 > ui mousemode right ""move picked models"" > view matrix models > #5,0.8816,-0.36788,0.2957,-54.624,0.25017,0.89546,0.36818,66.911,-0.40024,-0.25062,0.88148,192.07 > view matrix models > #6,0.8163,-0.28529,0.50226,-78.41,0.27,0.95714,0.10485,88.718,-0.51064,0.050019,0.85834,172.53 > fitmap #6 inMap #5 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using 7202 atoms average map value = 0.08076, steps = 252 shifted from previous position = 2.97 rotated from previous position = 12.5 degrees atoms outside contour = 5935, contour level = 0.32651 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.98915417 -0.05099570 0.13774421 -5.14990174 0.06422743 0.99355594 -0.09338865 5.89485707 -0.13209416 0.10122273 0.98605532 6.62171535 Axis 0.55274230 0.76640475 0.32726092 Axis point 34.75767894 -0.00000000 55.52663058 Rotation angle (degrees) 10.13928373 Shift along axis 3.83830658 > view matrix models > #6,0.80935,-0.38054,0.44737,-60.747,0.25634,0.9142,0.31388,70.333,-0.52843,-0.13936,0.83746,202.62 > fitmap #6 inMap #5 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using 7202 atoms average map value = 0.6612, steps = 84 shifted from previous position = 4.17 rotated from previous position = 10.2 degrees atoms outside contour = 1506, contour level = 0.32651 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.99999938 0.00016146 -0.00110330 0.09457846 -0.00016136 0.99999998 0.00008808 -0.00265260 0.00110331 -0.00008791 0.99999939 -0.08745726 Axis -0.07867179 -0.98640109 -0.14430395 Axis point 78.29591777 0.00000000 86.23500145 Rotation angle (degrees) 0.06408640 Shift along axis 0.00779630 > view matrix models > #6,0.88199,-0.36777,0.29469,-43.365,0.25044,0.89547,0.36799,84.559,-0.39922,-0.25076,0.8819,188.95 > view matrix models > #6,0.88199,-0.36777,0.29469,-37.757,0.25044,0.89547,0.36799,70.733,-0.39922,-0.25076,0.8819,185.76 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.69538,-0.65796,0.28902,13.922,0.70718,0.69805,-0.11235,94.752,-0.12783,0.28251,0.95071,92.154 > ui mousemode right ""move picked models"" > view matrix models > #4,0.22504,-0.95667,-0.18477,132.87,-0.047177,-0.20011,0.97864,163.04,-0.97321,-0.21152,-0.090166,322.46 > view matrix models > #6,0.69538,-0.65796,0.28902,14.565,0.70718,0.69805,-0.11235,95.412,-0.12783,0.28251,0.95071,87.274 > fitmap #6 inMap #4 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_inhibitor1_BI_NU_refine.mrc (#4) using 7202 atoms average map value = 0.01791, steps = 172 shifted from previous position = 3.38 rotated from previous position = 14.4 degrees atoms outside contour = 5619, contour level = 0.04044 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates: Matrix rotation and translation 0.28239059 -0.22147292 -0.93338379 183.11002982 -0.81886620 0.45119115 -0.35480232 165.24220382 0.49971361 0.86450927 -0.05394455 -46.02230615 Axis 0.61763090 -0.72592210 -0.30260399 Axis point 187.56736746 0.00000000 47.29514365 Rotation angle (degrees) 99.21742580 Shift along axis 7.06797705 > view matrix models > #6,0.7546,-0.64122,0.13934,22.902,0.63958,0.7662,0.062241,77.52,-0.14667,0.042153,0.98829,112.85 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.74988,-0.65469,0.095189,29.594,0.6451,0.7555,0.11429,72.49,-0.14674,-0.024299,0.98888,119.93 > fitmap #6 inMap #4 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_inhibitor1_BI_NU_refine.mrc (#4) using 7202 atoms average map value = 0.02009, steps = 212 shifted from previous position = 4.47 rotated from previous position = 10.6 degrees atoms outside contour = 5407, contour level = 0.04044 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates: Matrix rotation and translation 0.14294565 -0.09788775 -0.98487793 186.77354041 -0.89437526 0.41338507 -0.17089669 158.79340772 0.42386252 0.90527939 -0.02845678 -46.11747583 Axis 0.55373792 -0.72485630 -0.40982637 Axis point 177.44399129 0.00000000 31.16696950 Rotation angle (degrees) 103.65429324 Shift along axis 7.22134852 > volume #4 level 0.05388 > view matrix models > #6,0.90058,-0.29224,-0.3218,19.252,0.40221,0.841,0.36186,60.306,0.16489,-0.45532,0.87493,149.01 > undo > ui mousemode right ""move picked models"" > ui tool show ""Side View"" > select subtract #6 Nothing selected > save /Users/haoranfu/Desktop/bi-and-pf4a.tif width 1140 height 765 > supersample 3 > save /Users/haoranfu/Desktop/expand.tif width 1140 height 765 supersample 3 > select add #6 7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 4 models selected > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.91653,-0.39954,-0.018614,-3.4849,0.39988,0.91632,0.021201,89.045,0.0085851,-0.026875,0.9996,106.31 > view matrix models > #6,0.80258,-0.59616,0.021582,25.469,0.59642,0.80263,-0.0081523,83.425,-0.012462,0.019414,0.99973,103.57 > fitmap #6 inMap #4 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_inhibitor1_BI_NU_refine.mrc (#4) using 7202 atoms average map value = 0.02, steps = 96 shifted from previous position = 0.498 rotated from previous position = 4.72 degrees atoms outside contour = 5997, contour level = 0.053878 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_inhibitor1_BI_NU_refine.mrc (#4) coordinates: Matrix rotation and translation 0.12957825 -0.13138116 -0.98282678 191.53602301 -0.91053385 0.37668501 -0.17040103 164.94876921 0.39260359 0.91697731 -0.07081681 -39.41459482 Axis 0.56673665 -0.71686805 -0.40609084 Axis point 180.20016292 0.00000000 31.65342933 Rotation angle (degrees) 106.39613688 Shift along axis 6.30988657 > show #!5 models > select subtract #6 Nothing selected > select add #5 3 models selected > ui mousemode right ""move picked models"" > view matrix models > #5,0.8816,-0.36788,0.2957,-48.563,0.25017,0.89546,0.36818,65.502,-0.40024,-0.25062,0.88148,189.58 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.62203,-0.78139,0.050116,47.833,0.78284,0.62192,-0.019621,78.173,-0.015836,0.051437,0.99855,105.03 > ui mousemode right ""move picked models"" > view matrix models > #5,0.62203,-0.78139,0.050116,59.056,0.78284,0.62192,-0.019621,78.532,-0.015836,0.051437,0.99855,103.76 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > select add #4 6 models selected > fitmap #4 inMap #5 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using 16959 points correlation = 0.2194, correlation about mean = 0.05495, overlap = 100.4 steps = 100, shift = 2.89, angle = 7.58 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation -0.00937606 -0.75750504 0.65276198 118.86565169 -0.28782334 0.62720880 0.72371738 11.93407458 -0.95763762 -0.18109451 -0.22390838 222.77778194 Axis -0.47472837 0.84492963 0.24642827 Axis point 158.28884611 0.00000000 56.44756915 Rotation angle (degrees) 107.64015346 Shift along axis 8.55329959 > hide #!6 models > undo > view matrix models > #5,0.62203,-0.78139,0.050116,55.689,0.78284,0.62192,-0.019621,81.26,-0.015836,0.051437,0.99855,105.32 > view matrix models > #5,0.62203,-0.78139,0.050116,58.483,0.78284,0.62192,-0.019621,78.791,-0.015836,0.051437,0.99855,101.3 > view matrix models > #5,0.62203,-0.78139,0.050116,61.9,0.78284,0.62192,-0.019621,81.582,-0.015836,0.051437,0.99855,101.33 > select add #6 7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 7 models selected > fitmap #6 inMap #5 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using 7202 atoms average map value = 0.07301, steps = 80 shifted from previous position = 2.31 rotated from previous position = 3.24 degrees atoms outside contour = 6001, contour level = 0.32651 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.93622815 0.34552280 -0.06395973 -20.30498607 -0.33791562 0.93520690 0.10583525 32.31214349 0.09638407 -0.07747295 0.99232457 -2.30568729 Axis -0.25265267 -0.22100097 -0.94197941 Axis point 81.59424250 73.70779532 0.00000000 Rotation angle (degrees) 21.27023524 Shift along axis 0.16100402 > hide #!4 models > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.57484,-0.81744,0.036626,72.078,0.81819,0.57483,-0.011917,81.867,-0.011312,0.036817,0.99926,102.28,#6,0.81794,-0.5687,-0.086936,33.908,0.57062,0.82121,-0.0033193,83.855,0.073281,-0.046892,0.99621,101.4 > view matrix models > #5,0.52462,-0.85089,0.027741,81.823,0.85121,0.52368,-0.034629,86.048,0.014938,0.04178,0.99902,99.002,#6,0.78136,-0.61664,-0.09608,43.613,0.61663,0.78655,-0.033382,85.765,0.096156,-0.033162,0.99481,97.745 > select subtract #5 7202 atoms, 7386 bonds, 28 pseudobonds, 924 residues, 4 models selected > view matrix models > #6,0.58782,-0.79612,-0.14373,88.654,0.79645,0.60066,-0.069746,90.432,0.14186,-0.073472,0.98716,98.017 > fitmap #6 inMap #5 Fit molecule NaCT_PF4_daneng.cif (#6) to map NaCT_PF4_daneng.map (#5) using 7202 atoms average map value = 0.6613, steps = 100 shifted from previous position = 3.43 rotated from previous position = 11.1 degrees atoms outside contour = 1504, contour level = 0.32651 Position of NaCT_PF4_daneng.cif (#6) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.99999928 0.00019541 -0.00118212 0.09624853 -0.00019524 0.99999997 0.00014340 0.00390135 0.00118215 -0.00014317 0.99999929 -0.09049126 Axis -0.11873948 -0.97964280 -0.16186696 Axis point 76.67943902 0.00000000 81.31311248 Rotation angle (degrees) 0.06913881 Shift along axis -0.00060288 > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!6 models > show #!7 models > select subtract #6 Nothing selected > select add #7 2 models selected > view matrix models > #7,-0.11445,0.75543,-0.64515,52.398,0.084644,0.65447,0.75133,93.088,0.98982,0.031385,-0.13885,121.31 > view matrix models > #7,0.071953,0.8597,-0.50571,13.441,0.05422,0.50291,0.86264,99.645,0.99593,-0.089489,-0.010427,120.22 > fitmap #7 inMap #5 Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_PF4_daneng.map using 219319 points correlation = 0.2179, correlation about mean = 0.05573, overlap = 1072 steps = 108, shift = 2.31, angle = 5.94 degrees Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.00052605 0.87578287 0.48270499 -16.15807808 0.03823494 -0.48236972 0.87513290 64.78700313 0.99926865 0.01799584 -0.03373925 9.70572934 Axis -0.65681319 -0.39583614 -0.64180229 Axis point 0.00000000 36.14910919 -3.18196835 Rotation angle (degrees) 139.26988212 Shift along axis -21.26135782 > hide #!5 models > hide #!7 models > show #!5 models > show #!4 models > select add #4 4 models selected > view matrix models > #7,-0.02912,0.65231,-0.75739,64.851,0.080278,0.75679,0.64871,95.555,0.99635,-0.041912,-0.074404,124.11,#4,0.24629,-0.84154,-0.48079,144.76,-0.19113,-0.5285,0.82714,219.66,-0.95016,-0.11183,-0.29101,329.48 > fitmap #4 inMap #5 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using 16959 points correlation = 0.2009, correlation about mean = 0.0192, overlap = 91.7 steps = 60, shift = 1.52, angle = 3.76 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation -0.05416137 -0.87813800 0.47533167 146.12958841 -0.40066211 0.45514067 0.79518353 33.00785917 -0.91462365 -0.14737916 -0.37648767 231.34571047 Axis -0.53985291 0.79609710 0.27347439 Axis point 168.44130562 -0.00000000 54.02964318 Rotation angle (degrees) 119.19307708 Shift along axis 10.65610329 > view matrix models > #7,0.1163,0.73397,-0.66915,36.001,-0.23254,0.67511,0.70011,126.33,0.96561,0.074183,0.24919,85.822,#4,0.12708,-0.92183,-0.36617,151.19,0.054535,-0.36211,0.93054,172.45,-0.99039,-0.13822,0.0042549,307.45 > view matrix models > #7,0.14363,0.69949,-0.70006,39.406,-0.21837,0.71236,0.66698,125.06,0.96524,0.057077,0.25506,86.746,#4,0.10813,-0.90416,-0.41329,155.63,0.05285,-0.40991,0.91059,178.82,-0.99273,-0.1203,0.0034614,306.1 > fitmap #4 inMap #5 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using 16959 points correlation = 0.2171, correlation about mean = 0.02131, overlap = 102 steps = 88, shift = 3.25, angle = 5.74 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.16634675 -0.78249500 0.60002528 108.30083016 -0.09921204 0.59213404 0.79970885 -5.07453912 -0.98106357 -0.19255870 0.02086665 204.93816356 Axis -0.49918107 0.79540000 0.34373987 Axis point 165.48787126 0.00000000 39.15681814 Rotation angle (degrees) 96.33412445 Shift along axis 12.34740450 > ui mousemode right ""move picked models"" > view matrix models > #4,0.14447,-0.91969,-0.3651,153.48,0.12361,-0.34931,0.92882,163.42,-0.98176,-0.17932,0.063221,308.08 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.034577,0.56533,-0.82414,73.111,-0.10668,0.82201,0.55939,114.82,0.99369,0.068576,0.088732,98.519,#4,0.26403,-0.81897,-0.50949,146.68,0.060617,-0.5131,0.85619,190.84,-0.96261,-0.25694,-0.085828,327.18 > fitmap #4 inMap #5 Fit map NaCT_inhibitor1_BI_NU_refine.mrc in map NaCT_PF4_daneng.map using 16959 points correlation = 0.2591, correlation about mean = 0.06695, overlap = 134 steps = 176, shift = 1.72, angle = 7.2 degrees Position of NaCT_inhibitor1_BI_NU_refine.mrc (#4) relative to NaCT_PF4_daneng.map (#5) coordinates: Matrix rotation and translation 0.15206260 -0.89697867 0.41509786 135.17317197 -0.11694582 0.40070302 0.90871380 -3.25614042 -0.98142786 -0.18672534 -0.04396597 212.20325818 Axis -0.56502562 0.72032555 0.40233959 Axis point 179.49458021 0.00000000 31.95919307 Rotation angle (degrees) 104.21730485 Shift along axis 6.65598668 > hide #!4 models > hide #!5 models > select subtract #4 2 models selected > select subtract #7 Nothing selected > volume #8 level 0.1162 > surface dust #8 size 11.5 > show #!7 models > select add #7 2 models selected > view matrix models > #7,-0.12196,0.7327,-0.66954,58.16,-0.22042,0.63773,0.73805,125.86,0.96775,0.23759,0.083722,85.926 > ui mousemode right ""move picked models"" > view matrix models > #7,-0.12196,0.7327,-0.66954,65.819,-0.22042,0.63773,0.73805,113.73,0.96775,0.23759,0.083722,83.622 > view matrix models > #7,-0.12196,0.7327,-0.66954,64.945,-0.22042,0.63773,0.73805,113.33,0.96775,0.23759,0.083722,88.927 > fitmap #7 inMap #8 Fit map NaCT_apo_NU_refine.mrc z flip in map NaCT_inhibitor2_PF4_NU_refine.mrc z flip using 219319 points correlation = 0.9678, correlation about mean = 0.7446, overlap = 2277 steps = 76, shift = 2.46, angle = 10.9 degrees Position of NaCT_apo_NU_refine.mrc z flip (#7) relative to NaCT_inhibitor2_PF4_NU_refine.mrc z flip (#8) coordinates: Matrix rotation and translation 0.99979866 -0.01060064 0.01703819 0.00080321 0.01071757 0.99991956 -0.00678627 1.28540241 -0.01696488 0.00696750 0.99983184 -0.71161149 Axis 0.32419360 0.80149553 0.50249719 Axis point -61.99720868 0.00000000 12.02417600 Rotation angle (degrees) 1.21546438 Shift along axis 0.67292190 > select subtract #7 Nothing selected > volume #8 level 0.1335 > save /Users/haoranfu/Desktop/PF4a.tif width 1140 height 765 supersample 3 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/haoranfu/Downloads/7jsk.cif 7jsk.cif title: Structure of the NaCT-Citrate complex [more info...] Chain information for 7jsk.cif #1 --- Chain | Description | UniProt A B | Solute carrier family 13 member 5 | S13A5_HUMAN 1-568 Non-standard residues in 7jsk.cif #1 --- CIT — citric acid NA — sodium 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) OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac mini Model Identifier: Mac16,10 Model Number: Z1CF0005RD/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 2 days, 15 hours, 39 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: DELL U2715H: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Dell S2716DG: Resolution: 1440 x 2560 UI Looks like: 720 x 1280 @ 60.00Hz Mirror: Off Online: Yes Rotation: 270 Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX