id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7671 Crash during color drop chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. 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""treatmentId"" : ""5b729754-3882-4560-826f-9c0bc27d77c6"", ""experimentId"" : ""6192fb082171a2330e561df0"", ""deploymentId"" : 400000035 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kunwoong/Desktop/hBEST1_KKW/Analysis/hB_1uM_BRIL_Close_J869.pdb Chain information for hB_1uM_BRIL_Close_J869.pdb #1 --- Chain | Description A B C D E | No description available > lighting soft > set bgColor white > style stick Changed 15460 atom styles > style sphere Changed 15460 atom styles > style ball Changed 15460 atom styles > style sphere Changed 15460 atom styles > show cartoons > hide cartoons > show cartoons > show atoms > hide atoms > hide cartoons > show cartoons > show atoms > hide atoms > lighting full > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > color byhetero > color bychain > show atoms > color byhetero > color bychain > color bypolymer > color bychain > rainbow > color bychain > coulombic Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for hB_1uM_BRIL_Close_J869.pdb_A SES surface #1.1: minimum, -18.17, mean -1.05, maximum 12.92 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_B SES surface #1.2: minimum, -17.96, mean -1.03, maximum 12.99 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_C SES surface #1.3: minimum, -18.22, mean -1.03, maximum 13.48 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_D SES surface #1.4: minimum, -17.73, mean -1.03, maximum 13.38 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_E SES surface #1.5: minimum, -18.21, mean -1.02, maximum 13.00 To also show corresponding color key, enter the above coulombic command and add key true > color bypolymer > coulombic Coulombic values for hB_1uM_BRIL_Close_J869.pdb_A SES surface #1.1: minimum, -18.17, mean -1.05, maximum 12.92 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_B SES surface #1.2: minimum, -17.96, mean -1.03, maximum 12.99 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_C SES surface #1.3: minimum, -18.22, mean -1.03, maximum 13.48 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_D SES surface #1.4: minimum, -17.73, mean -1.03, maximum 13.38 Coulombic values for hB_1uM_BRIL_Close_J869.pdb_E SES surface #1.5: minimum, -18.21, mean -1.02, maximum 13.00 To also show corresponding color key, enter the above coulombic command and add key true Drag select of hB_1uM_BRIL_Close_J869.pdb_A SES surface, 5700 of 414034 triangles, hB_1uM_BRIL_Close_J869.pdb_B SES surface, 4238 of 413800 triangles, hB_1uM_BRIL_Close_J869.pdb_E SES surface, 135 of 415282 triangles, 27 atoms, 14 residues > mlp sel Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_A SES surface"": minimum -28.94, mean -1.652, maximum 23.9 Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_B SES surface"": minimum -28.56, mean -1.689, maximum 24.25 To also show corresponding color key, enter the above mlp command and add key true > select clear > mlp Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_A SES surface"": minimum -28.94, mean -1.652, maximum 23.9 Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_B SES surface"": minimum -28.56, mean -1.689, maximum 24.25 Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_C SES surface"": minimum -28.83, mean -1.673, maximum 24.11 Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_D SES surface"": minimum -28.85, mean -1.655, maximum 24.16 Map values for surface ""hB_1uM_BRIL_Close_J869.pdb_E SES surface"": minimum -30.12, mean -1.648, maximum 24.54 To also show corresponding color key, enter the above mlp command and add key true > color bfactor 15460 atoms, 1870 residues, 5 surfaces, atom bfactor range 30 to 117 > color bynucleotide > lighting soft > color byhetero > interfaces ~solvent 10 buried areas: D E 5222, A E 5212, A B 5203, C D 5196, B C 5192, A D 730, B E 725, B D 724, A C 719, C E 718 > color bychain > color byhetero > color bychain > style stick Changed 15460 atom styles > hide atoms > show cartoons > hide atoms > show atoms > hide atoms > hide cartoons > style stick Changed 15460 atom styles > style stick Changed 15460 atom styles > style stick Changed 15460 atom styles > style sphere Changed 15460 atom styles > style ball Changed 15460 atom styles > close #1 > open > ""/Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hBEST1_1uM_Ca2+_2_84_3_Rifined_add > 365-376-more-5-coot-0.pdb"" Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb #1 --- Chain | Description A | No description available B C D E | No description available > color byhetero > color bychain > lighting soft > show atoms > hide cartoons > show cartoons > hide atoms > open > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values float32 Drag select of 13 residues, 2 hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc > select clear Drag select of 2 hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc > select clear > ui tool show ""Hide Dust"" > surface dust #2 size 4.12 > toolshed show > help help:user/preferences.html#startup > surface dust #2 size 8.55 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1616, steps = 72 shifted from previous position = 0.366 rotated from previous position = 5.82 degrees atoms outside contour = 11856, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99485217 -0.10132814 -0.00132629 11.81503200 0.10132736 0.99485293 -0.00064249 -10.44701308 0.00138457 0.00050479 0.99999891 0.15827496 Axis 0.00566060 -0.01337527 0.99989452 Axis point 108.69485305 111.05922478 0.00000000 Rotation angle (degrees) 5.81624885 Shift along axis 0.36487008 > volume show > volume hide > volume show > volume hide > volume show > transparency 50 > volume style image > volume style mesh > volume step 2 > volume step 1 > volume style surface > volume step 1 > volume step 2 > volume step 1 > volume step 2 > volume step 1 > volume style surface > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1615, steps = 28 shifted from previous position = 0.0142 rotated from previous position = 0.0126 degrees atoms outside contour = 11849, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99486629 -0.10119103 -0.00120322 11.78944005 0.10119016 0.99486681 -0.00076096 -10.40674069 0.00127404 0.00063530 0.99999899 0.15475061 Axis 0.00689847 -0.01223934 0.99990130 Axis point 108.42931063 110.98106554 0.00000000 Rotation angle (degrees) 5.80830946 Shift along axis 0.36343612 > select add #2 3 models selected > select add #2 3 models selected > select add #2 3 models selected > select add #2 3 models selected > select add #1 15585 atoms, 16043 bonds, 1887 residues, 4 models selected > select subtract #1 3 models selected > select add #2 3 models selected > select add #2 3 models selected > select clear > select /E:369 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > ui mousemode right ""translate selected models"" > ui mousemode right select > ui mousemode right translate > hide #!2 models > show #!2 models Drag select of 1 residues > select clear > volume show > ui tool show ""Color Zone"" > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1616, steps = 40 shifted from previous position = 0.0187 rotated from previous position = 0.0128 degrees atoms outside contour = 11860, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99485745 -0.10127572 -0.00136974 11.81284953 0.10127492 0.99485827 -0.00063925 -10.44672821 0.00142744 0.00049724 0.99999886 0.15456740 Axis 0.00561027 -0.01380825 0.99988892 Axis point 108.74286941 111.09855465 0.00000000 Rotation angle (degrees) 5.81326182 Shift along axis 0.36507454 > volume style surface > volume style mesh > volume style surface > transparency 0 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1616, steps = 44 shifted from previous position = 0.00164 rotated from previous position = 0.00177 degrees atoms outside contour = 11859, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99485583 -0.10129133 -0.00139519 11.81600456 0.10129050 0.99485668 -0.00064735 -10.44728670 0.00145358 0.00050270 0.99999882 0.15106904 Axis 0.00567627 -0.01406071 0.99988503 Axis point 108.73313571 111.11110157 0.00000000 Rotation angle (degrees) 5.81418271 Shift along axis 0.36501880 > volume showOutlineBox true > volume showOutlineBox false > transparency 50 > volume showOutlineBox true > volume showOutlineBox false > volume showOutlineBox true > volume showOutlineBox false > volume showOutlineBox true > volume showOutlineBox false > volume showOutlineBox true > transparency 0 > volume style image > volume showOutlineBox false > volume style mesh > volume style image > volume style mesh > transparency 50 > transparency 0 > transparency 50 > transparency 0 > volume style mesh > volume style surface > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1616, steps = 44 shifted from previous position = 0.0122 rotated from previous position = 0.00751 degrees atoms outside contour = 11852, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99486096 -0.10124137 -0.00136096 11.81476790 0.10124040 0.99486170 -0.00076347 -10.42056744 0.00143126 0.00062176 0.99999878 0.14108959 Axis 0.00684044 -0.01378833 0.99988154 Axis point 108.52119988 111.16574517 0.00000000 Rotation angle (degrees) 5.81132155 Shift along axis 0.36557337 > lighting flat > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting flat > lighting soft > graphics silhouettes false > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > graphics silhouettes true > lighting full > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting soft > lighting flat > lighting soft > view #1 clip false > log metadata #1 The model has no metadata > log chains #1 Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb #1 --- Chain | Description A | No description available B C D E | No description available > toolshed show > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-0.9663,0,1,0,-0.40548,0,0,1,-0.27405 > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-0.56269,0,1,0,-1.1395,0,0,1,-0.28211 > view matrix models #2,1,0,0,-0.44695,0,1,0,-2.3303,0,0,1,-0.29952 > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,-10.933,0,1,0,-11.918,0,0,1,-0.77204 > view matrix models #2,1,0,0,-16.965,0,1,0,-20.242,0,0,1,0.17308 > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > turn z models #2 > view matrix models > #2,-0.98209,0.013321,0.18796,192.5,0.013321,-0.99009,0.13977,200.42,0.18796,0.13977,0.97218,-35.429 > turn z models #2 > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1541, steps = 264 shifted from previous position = 1.44 rotated from previous position = 7.98 degrees atoms outside contour = 11800, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00277062 0.99930394 0.03720674 -8.20892403 -0.99710842 -0.00006494 0.07599458 211.74042453 0.07594406 -0.03730965 0.99641431 -0.21328296 Axis -0.05665211 -0.01936866 -0.99820609 Axis point 101.88221282 110.07940750 0.00000000 Rotation angle (degrees) 90.02521039 Shift along axis -3.42317485 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1541, steps = 40 shifted from previous position = 0.00918 rotated from previous position = 0.0212 degrees atoms outside contour = 11799, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00277185 0.99930923 0.03706424 -8.19015256 -0.99708243 -0.00006557 0.07633482 211.69106841 0.07628448 -0.03716763 0.99639362 -0.26767757 Axis -0.05675122 -0.01961012 -0.99819574 Axis point 101.86810172 110.04595197 0.00000000 Rotation angle (degrees) 90.02578605 Shift along axis -3.41929166 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1542, steps = 28 shifted from previous position = 0.0209 rotated from previous position = 0.0203 degrees atoms outside contour = 11792, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00276122 0.99930950 0.03705764 -8.18898023 -0.99705534 -0.00008884 0.07668785 211.64333090 0.07663815 -0.03716022 0.99636675 -0.32379426 Axis -0.05692403 -0.01979025 -0.99818235 Axis point 101.84450432 110.02172645 0.00000000 Rotation angle (degrees) 90.02752702 Shift along axis -3.39911987 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1541, steps = 28 shifted from previous position = 0.0227 rotated from previous position = 0.0199 degrees atoms outside contour = 11797, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00274432 0.99931173 0.03699886 -8.17786900 -0.99708155 -0.00008847 0.07634625 211.68978144 0.07629694 -0.03710034 0.99639517 -0.27422570 Axis -0.05672329 -0.01964904 -0.99819657 Axis point 101.87101298 110.03914825 0.00000000 Rotation angle (degrees) 90.02718605 Shift along axis -3.42189440 > transparency 50 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1541, steps = 28 shifted from previous position = 0.00414 rotated from previous position = 0.00305 degrees atoms outside contour = 11800, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00277538 0.99931138 0.03700588 -8.18348868 -0.99708472 -0.00005647 0.07630485 211.69359395 0.07625436 -0.03710972 0.99639808 -0.26569602 Axis -0.05670728 -0.01962424 -0.99819796 Axis point 101.87322551 110.04397532 0.00000000 Rotation angle (degrees) 90.02529618 Shift along axis -3.42504471 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1542, steps = 40 shifted from previous position = 0.0129 rotated from previous position = 0.0111 degrees atoms outside contour = 11799, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00270160 0.99930510 0.03718067 -8.19578682 -0.99708216 -0.00014468 0.07633816 211.70188390 0.07629045 -0.03727836 0.99638902 -0.26276099 Axis -0.05680826 -0.01955489 -0.99819358 Axis point 101.86280727 110.05369919 0.00000000 Rotation angle (degrees) 90.03019643 Shift along axis -3.41193255 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1542, steps = 44 shifted from previous position = 0.0102 rotated from previous position = 0.00553 degrees atoms outside contour = 11787, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.00276758 0.99930241 0.03724794 -8.21475666 -0.99708359 -0.00008329 0.07631965 211.69617522 0.07626948 -0.03735048 0.99638793 -0.26156908 Axis -0.05683506 -0.01951076 -0.99819292 Axis point 101.85736242 110.06036678 0.00000000 Rotation angle (degrees) 90.02657905 Shift along axis -3.40237161 > view matrix models > #1,0.99604,0.0028939,0.088817,-10.607,-0.0040597,0.99991,0.012949,-0.50458,-0.088772,-0.013258,0.99596,9.7526 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 2.323, steps = 116 shifted from previous position = 3.27 rotated from previous position = 13.4 degrees atoms outside contour = 1151, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.21412230 0.97680705 -0.00005397 25.97424766 -0.97680705 -0.21412230 0.00005753 239.77396814 0.00004459 0.00006509 1.00000049 0.30676796 Axis 0.00000387 -0.00005045 -1.00000000 Axis point 109.44071440 109.43834532 0.00000000 Rotation angle (degrees) 102.36402352 Shift along axis -0.31876368 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 2.324, steps = 44 shifted from previous position = 0.0171 rotated from previous position = 0.00412 degrees atoms outside contour = 1160, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.21415744 0.97679934 -0.00011503 25.99021348 -0.97679935 -0.21415743 0.00006929 239.76962632 0.00004299 0.00012725 1.00000049 0.28468522 Axis 0.00002967 -0.00008089 -1.00000000 Axis point 109.44339968 109.43012990 0.00000000 Rotation angle (degrees) 102.36608434 Shift along axis -0.30330872 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 2.324, steps = 40 shifted from previous position = 0.014 rotated from previous position = 0.00651 degrees atoms outside contour = 1152, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.21404976 0.97682294 -0.00011968 25.97380748 -0.97682295 -0.21404975 0.00004238 239.76481986 0.00001572 0.00012602 1.00000049 0.30147511 Axis 0.00004282 -0.00006931 -1.00000000 Axis point 109.44415118 109.43314614 0.00000000 Rotation angle (degrees) 102.35976839 Shift along axis -0.31698015 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 2.324, steps = 40 shifted from previous position = 0.0156 rotated from previous position = 0.00689 degrees atoms outside contour = 1163, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.21416027 0.97679872 -0.00016018 25.99459578 -0.97679873 -0.21416026 0.00004470 239.77329215 0.00000930 0.00016609 1.00000048 0.28224211 Axis 0.00006214 -0.00008675 -0.99999999 Axis point 109.44678264 109.43022645 0.00000000 Rotation angle (degrees) 102.36625080 Shift along axis -0.30142808 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 2.324, steps = 40 shifted from previous position = 0.0118 rotated from previous position = 0.0149 degrees atoms outside contour = 1157, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.21411422 0.97680882 0.00009257 25.96085653 -0.97680882 -0.21411421 0.00000978 239.77341081 0.00002932 -0.00008828 1.00000049 0.31958252 Axis -0.00005019 0.00003237 -1.00000000 Axis point 109.43461385 109.44338472 0.00000000 Rotation angle (degrees) 102.36354932 Shift along axis -0.31312302 > reset Unknown command: reset > ui mousemode right ""move picked models"" > ui mousemode right rotate > ui mousemode right select > volume zone #2 nearAtoms #1 range 5.13 > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all > mousemode rightMode ""move planes"" > volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all > mousemode rightMode ""move planes"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 109.4 tiltedSlabSpacing 0.855 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all > mousemode rightMode ""move planes"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume zone #2 nearAtoms #1 range 5.13 > volume style surface > volume zone #2 nearAtoms #1 range 5.13 > surface dust #2 size 8.55 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume style surface > volume hide > volume show > surface dust #2 size 8.55 > volume style surface > transparency 0 > transparency 50 > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume planes z style image imageMode ""full region"" > mousemode rightMode ""move planes"" > volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 109.4 tiltedSlabSpacing 0.855 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #2 style image region all imageMode ""tilted slab"" tiltedSlabAxis > 0,0,1 tiltedSlabOffset 109.4 tiltedSlabSpacing 0.855 tiltedSlabPlaneCount 10 > mousemode rightMode ""rotate slab"" > volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all > mousemode rightMode ""move planes"" > volume #2 orthoplanes xyz positionPlanes 128,128,128 style image region all > mousemode rightMode ""move planes"" > volume region all imageMode ""full region"" > volume unzone > mousemode rightMode ""crop volume"" > volume zone #2 nearAtoms #1 range 5.13 > volume #2 region 0,0,1,255,255,255 > volume #2 region 0,0,64,255,255,255 > volume style surface > volume #2 region 0,0,126,255,255,255 > close #1#2 > open > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc > ""/Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hBEST1_1uM_Ca2+_2_84_3_Rifined_add > 365-376-more-5-coot-0.pdb"" Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values float32 Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb #2 --- Chain | Description A | No description available B C D E | No description available > surface dust #1 size 8.55 > lighting soft > color bychain > volume #1 region 0,0,0,255,255,255 > volume #1 region 0,0,24,255,255,255 > volume #1 region 0,0,16,255,255,255 > select clear > volume #1 region 0,0,16,255,255,255 > volume #1 region 0,0,59,255,255,255 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (chain colors)"" Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" ""space-filling (single color)"" Using preset: Initial Styles / Space-Filling (Single Color) Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 15578 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""molecular surfaces"" ""chain id coloring (opaque)"" Using preset: Molecular Surfaces / Chain ID Coloring (Opaque) Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color bychain targ s trans 0 > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > preset ""overall look"" interactive Using preset: Overall Look / Interactive Preset expands to these ChimeraX commands: ~set bg graphics silhouettes f lighting depthCue t > close session > open > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc > format mrc Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as #1, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values float32 > ui tool show ""Color Actions"" > set bgColor white > close session > open > ""/Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hBEST1_1uM_Ca2+_2_84_3_Rifined_add > 365-376-more-5-coot-0.pdb"" > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc Chain information for hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb #1 --- Chain | Description A | No description available B C D E | No description available Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values float32 > surface dust #2 size 8.55 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1616, steps = 72 shifted from previous position = 0.366 rotated from previous position = 5.82 degrees atoms outside contour = 11856, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99485217 -0.10132814 -0.00132629 11.81503200 0.10132736 0.99485293 -0.00064249 -10.44701308 0.00138457 0.00050479 0.99999891 0.15827496 Axis 0.00566060 -0.01337527 0.99989452 Axis point 108.69485305 111.05922478 0.00000000 Rotation angle (degrees) 5.81624885 Shift along axis 0.36487008 > color byhetero > color bychain > graphics silhouettes true > rainbow > color bypolymer > color bychain > hide cartoons > show atoms > hide atoms > show cartoons > volume #2 region 0,0,85,255,255,255 > volume #2 region 0,0,172,255,255,255 > volume #2 region 0,0,0,255,255,255 > transparency 50 > ui mousemode right ""translate selected models"" > ui mousemode right rotate > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,1.7761,0,1,0,0.93388,0,0,1,0.19071 > view matrix models #2,1,0,0,0.00032648,0,1,0,-2.987,0,0,1,1.3749 > view matrix models #2,1,0,0,0.91576,0,1,0,-0.91704,0,0,1,1.5981 > ui mousemode right ""rotate selected models"" > ui mousemode right ""move picked models"" > view matrix models #2,1,0,0,1.7393,0,1,0,1.1656,0,0,1,1.4784 > view matrix models #2,1,0,0,1.7088,0,1,0,-2.6028,0,0,1,1.22 > view matrix models #2,1,0,0,3.5404,0,1,0,-7.3298,0,0,1,1.2143 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1373, steps = 120 shifted from previous position = 2.44 rotated from previous position = 4.19 degrees atoms outside contour = 12139, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99313810 -0.10779553 0.04535248 3.96071680 0.10524710 0.99290942 0.05526248 -11.94811310 -0.05098796 -0.05011006 0.99744133 11.51926146 Axis -0.41087231 0.37565403 0.83070331 Axis point 128.66082497 41.71562623 0.00000000 Rotation angle (degrees) 7.36733852 Shift along axis 3.45338291 > view matrix models #2,1,0,0,0.086309,0,1,0,-2.8764,0,0,1,1.1026 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1615, steps = 68 shifted from previous position = 0.653 rotated from previous position = 4.19 degrees atoms outside contour = 11850, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.99486445 -0.10120975 -0.00114681 11.78399238 0.10120889 0.99486489 -0.00078731 -10.40320970 0.00122061 0.00066720 0.99999903 0.15667417 Axis 0.00718497 -0.01169456 0.99990580 Axis point 108.37469673 110.90651497 0.00000000 Rotation angle (degrees) 5.80936170 Shift along axis 0.36298801 > turn z models #2 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1228, steps = 76 shifted from previous position = 2.96 rotated from previous position = 0.888 degrees atoms outside contour = 12115, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.08873665 -0.99008412 -0.10889999 236.34273135 0.99243426 -0.07857025 -0.09434470 23.72648838 0.08485289 -0.11644791 0.98956549 7.49165273 Axis -0.01109551 -0.09726129 0.99519703 Axis point 107.19597112 120.86101346 0.00000000 Rotation angle (degrees) 95.09864272 Shift along axis 2.52565913 > turn z models #2 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1279, steps = 96 shifted from previous position = 2.94 rotated from previous position = 2.81 degrees atoms outside contour = 12304, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.99858661 0.04773022 -0.02337864 207.24390802 -0.04164017 -0.97596023 -0.21393381 248.63994883 -0.03302773 -0.21265795 0.97656836 32.68438574 Axis 0.01419213 0.10733273 -0.99412186 Axis point 106.67072921 123.74011059 0.00000000 Rotation angle (degrees) 177.42372036 Shift along axis -2.86382565 > view matrix models > #2,-0.99966,0.002547,-0.025814,223.54,0.002547,-0.98072,-0.1954,236.74,-0.025814,-0.1954,0.98038,30.285 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1586, steps = 68 shifted from previous position = 1.68 rotated from previous position = 5.05 degrees atoms outside contour = 11717, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.99782829 -0.03196519 -0.05759231 228.77280239 0.04264137 -0.97989000 -0.19492882 235.09076777 -0.05020319 -0.19696132 0.97912506 29.57757493 Axis -0.02710021 -0.09852276 0.99476572 Axis point 112.57290594 121.16686199 0.00000000 Rotation angle (degrees) 177.85092936 Shift along axis 0.06117521 > view matrix models > #2,-0.99966,0.002547,-0.025814,220.3,0.002547,-0.98072,-0.1954,236.61,-0.025814,-0.1954,0.98038,30.194 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1171, steps = 64 shifted from previous position = 1.27 rotated from previous position = 3.52 degrees atoms outside contour = 12116, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.99769166 0.01962392 -0.06500925 219.74760688 -0.00417607 -0.97325259 -0.22969960 242.53414363 -0.06777802 -0.22889790 0.97108799 35.90746425 Axis 0.03344054 0.11549116 -0.99274545 Axis point 111.21082277 122.69233005 0.00000000 Rotation angle (degrees) 179.31318150 Shift along axis -0.28794250 > view matrix models > #2,-0.99966,0.002547,-0.025814,223.92,0.002547,-0.98072,-0.1954,236.92,-0.025814,-0.1954,0.98038,28.94 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 0.1449, steps = 84 shifted from previous position = 1.81 rotated from previous position = 3.23 degrees atoms outside contour = 11867, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.99420632 -0.01896635 -0.10580182 231.69210513 0.04282517 -0.97270654 -0.22805250 236.75776086 -0.09858879 -0.23126222 0.96788327 39.53681246 Axis -0.05152556 -0.11579029 0.99193635 Axis point 115.01402666 122.50565444 0.00000000 Rotation angle (degrees) 178.21512428 Shift along axis -0.13431315 > view matrix models > #2,-0.99966,0.002547,-0.025814,221.85,0.002547,-0.98072,-0.1954,232.97,-0.025814,-0.1954,0.98038,28.661 > fitmap #1 inMap #2 Fit molecule hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15585 atoms average map value = 2.323, steps = 156 shifted from previous position = 5.39 rotated from previous position = 16.3 degrees atoms outside contour = 1166, contour level = 0.66583 Position of hBEST1_1uM_Ca2+_2_84_3_Rifined_add 365-376-more-5-coot-0.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.99516389 0.09822817 0.00002831 207.59840355 -0.09822818 -0.99516389 -0.00007824 229.10798570 0.00002049 -0.00008064 0.99999999 0.32145125 Axis -0.00001221 0.00003979 -1.00000000 Axis point 109.43905253 109.44363903 0.00000000 Rotation angle (degrees) 174.36284979 Shift along axis -0.31487072 > ui mousemode right rotate > ui mousemode right zoom > ui mousemode right pivot > ui mousemode right ""translate selected atoms"" > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > ui mousemode right translate > ui mousemode right rotate > ui mousemode right translate > ui mousemode right zoom > lighting flat > lighting soft > view > view orient > ui tool show ""Side View"" > view > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > color byhetero > color bychain > hide atoms > show cartoons > ui mousemode right windowing > toolshed show > ui mousemode right translate > ui mousemode right zoom > ui windowfill toggle > help help:user > open > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/RealSpaceRefine_4/hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb Chain information for hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb #3 --- Chain | Description A B C D E | No description available > close session > open > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/RealSpaceRefine_4/hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb Chain information for hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb #1 --- Chain | Description A B C D E | No description available > open > /Users/kunwoong/Desktop/hBEST1_KKW/22.04.14_hBEST1_Bril_twin_1uM_Ca/hBEST1_2.84/hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc Opened hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc as #2, grid size 256,256,256, pixel 0.855, shown at level 0.666, step 1, values float32 > lighting soft > hide atoms > hide cartoons > show cartoons > surface dust #2 size 8.55 > fitmap #1 inMap #2 Fit molecule hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb (#1) to map hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) using 15460 atoms average map value = 2.301, steps = 44 shifted from previous position = 0.0101 rotated from previous position = 0.00636 degrees atoms outside contour = 1090, contour level = 0.66583 Position of hB1_1uM_220614_3d(0.3.4.6_real_space_refined_004.pdb (#1) relative to hB1_1uM_220614_3d(0.3.4.6.8.9)_(2_82A)_J869_009_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 1.00000000 0.00002600 -0.00006674 0.01063972 -0.00002601 1.00000000 -0.00008476 0.02061419 0.00006673 0.00008476 0.99999999 -0.01849326 Axis 0.76381772 -0.60138485 -0.23434749 Axis point 0.00000000 218.02504749 243.65302120 Rotation angle (degrees) 0.00635797 Shift along axis 0.00006360 > transparency 50 > volume style surface > volume style image > volume style surface > volume hide > volume show > transparency 0 > transparency 50 > lighting soft > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting flat > lighting full > lighting soft > view orient > ui tool show ""Side View"" > view > view orient > color bychain > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > ui tool show ""Selection Inspector"" > view > view orient > ui tool show ""Side View"" > view > set bgColor gray > set bgColor #80808000 > set bgColor gray > set bgColor white > set bgColor #ffffff00 > volume hide > hide atoms > show atoms > lighting soft > lighting full > lighting soft > hide atoms > volume show > ui tool show ""Side View"" > view orient > ui tool show ""Side View"" > view orient > volume #2 color #f9fff780 > volume #2 color #90938f80 > volume #2 color #bec2bc80 > volume #2 color #c5c9c380 > volume #2 color #b8b8b880 > volume #2 color #b4b4b480 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.7.101 OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,1 Processor Name: 6-Core Intel Core i9 Processor Speed: 2.9 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 12 MB Hyper-Threading Technology: Enabled Memory: 32 GB System Firmware Version: 1715.60.5.0.0 (iBridge: 19.16.10647.0.0,0) OS Loader Version: 540.60.2~89 Software: System Software Overview: System Version: macOS 12.1 (21C52) Kernel Version: Darwin 21.2.0 Time since boot: 25 days 25 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Radeon Pro 560X: Chipset Model: Radeon Pro 560X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00c2 ROM Revision: 113-C980AL-075 VBIOS Version: 113-C97501U-005 EFI Driver Version: 01.A1.075 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: 2476 IPS: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 202024760068 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: Yes Connection Type: DVI or HDMI Adapter Firmware Version: 3.0d Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.0 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX