id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7641 wrapped C/C++ object of type QScreen has been deleted paulino@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.15.6-x86_64-i386-64bit ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description tried to open .mrc map downloaded from cryosparc and got the error described Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/joanapaulino/Downloads/cryosparc_P64_J565_map.mrc format mrc Opened cryosparc_P64_J565_map.mrc as #1, grid size 320,320,320, pixel 1.33, shown at level 0.306, step 2, values float32 > volume #1 level 0.4745 > volume #1 level 0.4698 > close #1 > open /Users/joanapaulino/Downloads/cryosparc_P64_J567_map.mrc format mrc Opened cryosparc_P64_J567_map.mrc as #1, grid size 320,320,320, pixel 1.33, shown at level 0.302, step 2, values float32 > volume #1 level 0.4068 > open ""/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2 > structures/Nef.pdb"" format pdb Chain information for Nef.pdb #2 --- Chain | Description N | No description available > select #2 1047 atoms, 1081 bonds, 1 pseudobond, 133 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-3.1026,0,1,0,103.26,0,0,1,75.197 > view matrix models #2,1,0,0,24.587,0,1,0,77.14,0,0,1,109.33 > view matrix models #2,1,0,0,22.293,0,1,0,79.712,0,0,1,110.85 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.93307,-0.35405,0.063472,72.575,0.18142,0.31085,-0.93298,245.28,0.3106,0.88205,0.35428,16.822 > ui tool show ""Fit in Map"" Fit molecule Nef.pdb (#2) to map cryosparc_P64_J567_map.mrc (#1) using 1047 atoms average map value = 0.4278, steps = 216 shifted from previous position = 35.4 rotated from previous position = 48.8 degrees atoms outside contour = 339, contour level = 0.40677 Position of Nef.pdb (#2) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation 0.87433761 -0.44569008 -0.19207835 146.74048628 0.34929937 0.85267497 -0.38850398 90.36995714 0.33693277 0.27259079 0.90120506 61.51035367 Axis 0.56921020 -0.45548465 0.68449506 Axis point -246.21699054 290.78701746 -0.00000000 Rotation angle (degrees) 35.50066062 Shift along axis 84.46758583 > view matrix models > #2,-0.57024,0.49588,-0.65493,268.25,0.68964,0.72216,-0.053672,25.766,0.44635,-0.48227,-0.75378,321.6 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.57024,0.49588,-0.65493,264.04,0.68964,0.72216,-0.053672,29.732,0.44635,-0.48227,-0.75378,294.9 > volume #1 level 0.4889 > view matrix models > #2,-0.57024,0.49588,-0.65493,260.3,0.68964,0.72216,-0.053672,21.754,0.44635,-0.48227,-0.75378,291.99 > view matrix models > #2,-0.57024,0.49588,-0.65493,249.12,0.68964,0.72216,-0.053672,30.88,0.44635,-0.48227,-0.75378,298.73 Fit molecule Nef.pdb (#2) to map cryosparc_P64_J567_map.mrc (#1) using 1047 atoms average map value = 0.4078, steps = 116 shifted from previous position = 15.8 rotated from previous position = 21.6 degrees atoms outside contour = 916, contour level = 0.48891 Position of Nef.pdb (#2) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation -0.80417606 0.36002470 -0.47295144 288.31046373 0.55080217 0.75046024 -0.36527577 68.80885664 0.22342295 -0.55424871 -0.80180455 353.89929024 Axis -0.25319483 -0.93303513 0.25561262 Axis point 96.86720360 0.00000000 215.05586764 Rotation angle (degrees) 158.08831871 Shift along axis -46.73867394 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.49016,-0.49013,0.72078,98.619,-0.11841,-0.8567,-0.50203,392.15,0.86355,0.16073,-0.47796,135.12 Opened Nef.pdb map 5 as #3, grid size 46,37,45, pixel 1.67, shown at level 0.0848, step 1, values float32 Fit map Nef.pdb map 5 in map cryosparc_P64_J567_map.mrc using 4186 points correlation = 0.8546, correlation about mean = 0.1208, overlap = 567.7 steps = 180, shift = 5.53, angle = 49.1 degrees Position of Nef.pdb map 5 (#3) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation -0.19603024 -0.23578218 0.95182924 134.11342861 0.26326783 -0.94768006 -0.18053408 319.75337294 0.94459631 0.21519588 0.24784781 35.17876644 Axis 0.62128880 0.01135557 0.78349938 Axis point 19.88289311 166.19130797 0.00000000 Rotation angle (degrees) 161.42927284 Shift along axis 114.51669370 Average map value = 0.4042 for 1047 atoms, 891 outside contour > show #!3 models > select #3 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.19603,-0.23578,0.95183,85.784,0.26327,-0.94768,-0.18053,295.15,0.9446,0.2152,0.24785,40.671 > volume #1 level 0.4022 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.2611,0.035366,0.96466,-15.044,0.56521,-0.81572,-0.12308,229.62,0.78254,0.57737,-0.23297,66.015 > view matrix models > #3,0.19313,-0.022427,0.98092,0.34507,0.51754,-0.84702,-0.12126,240.21,0.83358,0.53109,-0.15198,56.495 > view matrix models > #3,0.1536,-0.052543,0.98674,9.2159,0.49037,-0.86289,-0.12228,246.19,0.85787,0.50265,-0.10677,52.109 > view matrix models > #3,0.21232,-0.30801,0.92739,41.378,-0.35504,-0.90849,-0.22045,379.9,0.91042,-0.28246,-0.30225,170.08 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.21232,-0.30801,0.92739,38.848,-0.35504,-0.90849,-0.22045,403.12,0.91042,-0.28246,-0.30225,162.53 > view matrix models > #3,0.21232,-0.30801,0.92739,76.95,-0.35504,-0.90849,-0.22045,417.79,0.91042,-0.28246,-0.30225,159.71 > view matrix models > #3,0.21232,-0.30801,0.92739,75.405,-0.35504,-0.90849,-0.22045,408.38,0.91042,-0.28246,-0.30225,155.59 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.055116,0.30423,0.951,13.211,-0.29955,-0.90354,0.3064,344.06,0.95249,-0.30176,0.041331,115.82 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.055116,0.30423,0.951,13.928,-0.29955,-0.90354,0.3064,348.43,0.95249,-0.30176,0.041331,118.57 > view matrix models > #3,0.055116,0.30423,0.951,14.881,-0.29955,-0.90354,0.3064,344.79,0.95249,-0.30176,0.041331,118.08 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.42549,0.5685,-0.7041,222.16,0.89764,0.16639,-0.40811,112.31,-0.11486,-0.80568,-0.58111,399.25 Opened Nef.pdb map 10 as #3, grid size 32,28,32, pixel 3.33, shown at level 0.044, step 1, values float32 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 834 points correlation = 0.8999, correlation about mean = 0.368, overlap = 69.89 steps = 52, shift = 0.932, angle = 2.55 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation -0.20408606 -0.24557672 0.94765022 137.41751491 0.30459029 -0.93590504 -0.17693644 312.47875440 0.93036209 0.25253480 0.26580545 30.91300169 Axis 0.61514681 0.02476240 0.78802362 Axis point 21.24389626 163.26286518 0.00000000 Rotation angle (degrees) 159.56892891 Shift along axis 116.62984521 Average map value = 0.4028 for 1047 atoms, 472 outside contour Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 834 points correlation = 0.8999, correlation about mean = 0.3672, overlap = 69.89 steps = 40, shift = 0.0233, angle = 0.0446 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation -0.20379792 -0.24492655 0.94788047 137.26173828 0.30467812 -0.93598777 -0.17634660 312.43700860 0.93039650 0.25285937 0.26537612 30.90026117 Axis 0.61529689 0.02506450 0.78789689 Axis point 21.20175468 163.21040328 0.00000000 Rotation angle (degrees) 159.58731375 Shift along axis 116.63401787 Average map value = 0.4027 for 1047 atoms, 472 outside contour > show #!3 models > select #3.1 1 model selected > select #3 2 models selected > view matrix models > #3,0.29672,-0.34104,0.89199,86.484,0.94531,0.23738,-0.2237,71.953,-0.13545,0.90959,0.39282,77.836 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.29672,-0.34104,0.89199,124.91,0.94531,0.23738,-0.2237,197.23,-0.13545,0.90959,0.39282,91.972 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.71554,-0.22913,-0.65992,216.79,-0.45618,0.56217,-0.68982,398.18,0.52905,0.79465,0.29773,25.091 > view matrix models > #3,0.79282,0.043306,0.60792,34.918,0.56887,-0.41052,-0.71265,387.93,0.2187,0.91082,-0.3501,121.59 > volume #3 level 0.3071 > view matrix models > #3,0.097984,-0.28112,0.95466,138.08,0.926,-0.32567,-0.19094,271.74,0.36458,0.90272,0.22841,41.152 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.097984,-0.28112,0.95466,91.141,0.926,-0.32567,-0.19094,147.73,0.36458,0.90272,0.22841,18.708 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 198 points correlation = 0.9781, correlation about mean = 0.031, overlap = 30.73 steps = 68, shift = 2.78, angle = 8.25 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation -0.19333828 -0.18586406 0.96336642 124.12678606 0.16990158 -0.97340075 -0.15370241 332.39489422 0.96630935 0.13396092 0.21977423 45.51117444 Axis 0.62873957 -0.00643230 0.77758934 Axis point 18.83480888 170.42196652 0.00000000 Rotation angle (degrees) 166.77580912 Shift along axis 111.29436167 Average map value = 0.4003 for 1047 atoms, 474 outside contour > view matrix models > #3,-0.19334,-0.18586,0.96337,91.571,0.1699,-0.9734,-0.1537,384.47,0.96631,0.13396,0.21977,47.321 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.7151,0.3776,0.58826,-70.304,0.63584,-0.0017394,-0.77182,254.85,-0.29041,0.92597,-0.24133,163.99 > view matrix models > #3,0.46178,0.20176,0.86375,-40.759,0.88698,-0.098376,-0.45122,199.04,-0.0060652,0.97448,-0.22438,116.26 > view matrix models > #3,0.93978,-0.31228,0.1389,38.849,0.088507,0.61489,0.78363,83.051,-0.33012,-0.72415,0.6055,301.44 > view matrix models > #3,0.28718,0.61974,0.73038,-58.575,-0.94143,0.041911,0.3346,350.38,0.17676,-0.78369,0.59547,240.23 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.28718,0.61974,0.73038,-52.094,-0.94143,0.041911,0.3346,299.95,0.17676,-0.78369,0.59547,229.69 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.4222,0.88086,0.2141,-51.179,-0.80046,0.25142,0.54411,230.07,0.42545,-0.4011,0.81124,120.96 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.4222,0.88086,0.2141,-48.31,-0.80046,0.25142,0.54411,233.44,0.42545,-0.4011,0.81124,126.49 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc using 198 points correlation = 0.9781, correlation about mean = 0.03124, overlap = 30.73 steps = 60, shift = 0.0225, angle = 0.125 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc (#1) coordinates: Matrix rotation and translation -0.19441784 -0.18625022 0.96307453 124.35131550 0.17172700 -0.97310856 -0.15352383 332.09840778 0.96576992 0.13553813 0.22117385 45.24266068 Axis 0.62822967 -0.00585799 0.77800589 Axis point 18.97574678 170.29447584 0.00000000 Rotation angle (degrees) 166.69935245 Shift along axis 111.37481370 Average map value = 0.4004 for 1047 atoms, 475 outside contour > view matrix models > #3,-0.19442,-0.18625,0.96307,54.115,0.17173,-0.97311,-0.15352,370.41,0.96577,0.13554,0.22117,41.273 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.066815,-0.40302,0.91275,52.357,-0.89387,0.38227,0.23422,294.95,-0.44331,-0.83153,-0.33471,425.43 > ~select #3 Nothing selected > open ""/Users/joanapaulino/Documents/postdoc_UCSF/Serinc/Nef_AP2 > structures/Ap2_deltacomp.pdb"" format pdb Chain information for Ap2_deltacomp.pdb #4 --- Chain | Description A | No description available B | No description available M | No description available S | No description available > select #4 10528 atoms, 10715 bonds, 1432 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,-2.251,0,1,0,30.007,0,0,1,105.93 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.72707,0.65895,0.19277,-83.672,0.66728,-0.61214,-0.42428,222.26,-0.16158,0.43711,-0.88477,347.09 > view matrix models > #4,0.71834,0.43279,0.54468,-101.82,0.53166,-0.84647,-0.028595,218.44,0.44868,0.31013,-0.83816,264.08 > volume #1 zflip Expected a keyword > volume #1 flipNormals Missing ""flipNormals"" keyword's argument > volume zflip #1 Expected a density maps specifier or a keyword > volume flip #1 Opened cryosparc_P64_J567_map.mrc z flip as #5, grid size 320,320,320, pixel 1.33, shown at step 1, values float32 > select #1 2 models selected > view matrix models > #1,0.94909,-0.30564,-0.076181,89.85,0.24296,0.86425,-0.4405,67.543,0.20047,0.39957,0.89451,-103.53 > ui mousemode right ""translate selected models"" > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.76541,-0.41752,-0.48971,237.07,-0.4846,0.12677,-0.8655,461.85,0.42344,0.89978,-0.1053,-48.454 > view matrix models > #1,0.60585,-0.36375,-0.70755,304.52,-0.68324,0.21773,-0.69697,450.26,0.40758,0.90569,-0.11662,-43.994 > select #5 2 models selected > view matrix models > #5,0.4477,0.89066,-0.079315,-50.979,0.76536,-0.42756,-0.48106,239.54,-0.46237,0.15467,-0.87309,473.64 > select #4 10528 atoms, 10715 bonds, 1432 residues, 1 model selected > view matrix models > #4,0.043991,0.99877,-0.022833,4.9317,0.98309,-0.047344,-0.17689,55.233,-0.17775,-0.014666,-0.98397,429.49 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.043991,0.99877,-0.022833,45.775,0.98309,-0.047344,-0.17689,43.719,-0.17775,-0.014666,-0.98397,358.47 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.87758,0.46162,-0.12949,10.104,0.44033,-0.88288,-0.16317,246.25,-0.18965,0.086178,-0.97806,344.89 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.87758,0.46162,-0.12949,8.5949,0.44033,-0.88288,-0.16317,266.39,-0.18965,0.086178,-0.97806,353.98 > view matrix models > #4,0.87758,0.46162,-0.12949,28.216,0.44033,-0.88288,-0.16317,266.62,-0.18965,0.086178,-0.97806,349.03 Fit molecule Ap2_deltacomp.pdb (#4) to map cryosparc_P64_J567_map.mrc z flip (#5) using 10528 atoms average map value = 0.504, steps = 152 shifted from previous position = 15.9 rotated from previous position = 10.6 degrees atoms outside contour = 2692, contour level = 0.40221 Position of Ap2_deltacomp.pdb (#4) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation 0.85886822 -0.36085971 0.36349092 85.14213916 0.46895092 0.83941481 -0.27471405 68.38652369 -0.20598643 0.40640257 0.89017220 96.75963346 Axis 0.56047877 0.46861279 0.68283643 Axis point 2.76337619 8.34934762 0.00000000 Rotation angle (degrees) 37.41763745 Shift along axis 145.83816461 > view matrix models > #4,0.81853,0.55384,-0.15254,40.643,0.55593,-0.83059,-0.032566,228.71,-0.14474,-0.058147,-0.98776,360.19 > select #3 2 models selected > view matrix models > #3,0.066815,-0.40302,0.91275,66.179,-0.89387,0.38227,0.23422,298.86,-0.44331,-0.83153,-0.33471,443.42 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.16534,-0.5302,0.83159,124.05,-0.8394,0.51832,0.16358,280.52,-0.51776,-0.67099,-0.53075,452.95 > view matrix models > #3,0.59472,0.30448,0.74404,-84.169,-0.78725,0.033017,0.61575,290.57,0.16292,-0.95195,0.25934,312.61 > view matrix models > #3,-0.71534,-0.35494,-0.60191,328.65,0.6534,-0.64509,-0.39613,289.19,-0.24768,-0.67666,0.69339,286.55 > view matrix models > #3,0.955,-0.28515,-0.081657,32.6,0.031432,-0.17646,0.98381,166.22,-0.29494,-0.9421,-0.15956,419.15 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.955,-0.28515,-0.081657,122.6,0.031432,-0.17646,0.98381,118.03,-0.29494,-0.9421,-0.15956,406.47 > view matrix models > #3,0.955,-0.28515,-0.081657,89.505,0.031432,-0.17646,0.98381,98.311,-0.29494,-0.9421,-0.15956,420.3 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.14796,-0.88965,-0.432,360.73,0.66349,-0.41322,0.62372,80.657,-0.73341,-0.19434,0.65142,294.69 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 198 points correlation = 0.9648, correlation about mean = 0.05386, overlap = 30.18 steps = 244, shift = 23.4, angle = 62.1 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation 0.91197230 0.37145202 0.17415484 -23.69769214 0.40935666 -0.85194738 -0.32651612 303.18567925 0.02708569 0.36906510 -0.92900877 250.83238238 Axis 0.97698296 0.20656690 0.05323920 Axis point 0.00000000 130.74021255 153.58738027 Rotation angle (degrees) 159.14621711 Shift along axis 52.82999988 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.77074,-0.62176,-0.13916,156.22,0.50993,0.47101,0.7198,-69.407,-0.382,-0.62574,0.68009,336.83 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.59228,-0.80278,0.068866,183.23,0.31618,0.31018,0.89656,-39.673,-0.7411,-0.50924,0.43754,396.66 > volume #3 level 0.2017 > view matrix models > #3,0.18126,-0.95508,0.23447,243.11,0.25529,0.27594,0.92665,-29.827,-0.94972,-0.1081,0.29384,387.07 > view matrix models > #3,0.18681,-0.93244,0.30929,231.37,-0.11658,0.29157,0.94942,17.255,-0.97545,-0.21342,-0.054237,441.67 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.18681,-0.93244,0.30929,268.22,-0.11658,0.29157,0.94942,23.97,-0.97545,-0.21342,-0.054237,408.93 > view matrix models > #3,0.18681,-0.93244,0.30929,261.32,-0.11658,0.29157,0.94942,46.929,-0.97545,-0.21342,-0.054237,416.74 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.55506,-0.60571,-0.57012,259.69,0.61514,-0.16247,0.7715,25.144,-0.55993,-0.77892,0.28242,399.2 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.55506,-0.60571,-0.57012,258.49,0.61514,-0.16247,0.7715,28.259,-0.55993,-0.77892,0.28242,399.66 > view matrix models > #3,0.55506,-0.60571,-0.57012,257.73,0.61514,-0.16247,0.7715,28.259,-0.55993,-0.77892,0.28242,400.26 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422 points correlation = 0.9244, correlation about mean = 0.1079, overlap = 52.42 steps = 100, shift = 1.78, angle = 28 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation 0.91427140 0.09203474 0.39450906 -16.52334862 0.26902592 -0.86603913 -0.42142765 336.22461469 0.30287430 0.49143242 -0.81655454 187.83271143 Axis 0.97698536 0.09807179 0.18942421 Axis point 0.00000000 146.36611613 137.53169526 Rotation angle (degrees) 152.14846685 Shift along axis 52.41114204 > hide #!3 models > select #2 1047 atoms, 1081 bonds, 1 pseudobond, 133 residues, 2 models selected > view matrix models > #2,-0.19442,-0.18625,0.96307,122.87,0.17173,-0.97311,-0.15352,340.19,0.96577,0.13554,0.22117,62.638 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.44461,0.89542,-0.023355,-7.7266,0.55046,-0.25257,0.79574,91.223,0.70662,-0.36665,-0.60519,252.77 > view matrix models > #2,0.48612,0.86829,-0.098813,-1.8995,0.75099,-0.35725,0.55533,102.8,0.44689,-0.34416,-0.82574,308.79 > view matrix models > #2,0.50968,0.85745,-0.070766,-6.6396,0.76575,-0.4146,0.49166,115.16,0.39223,-0.30478,-0.86791,315.47 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.50968,0.85745,-0.070766,23.456,0.76575,-0.4146,0.49166,104.24,0.39223,-0.30478,-0.86791,309.21 > view matrix models > #2,0.50968,0.85745,-0.070766,0.34037,0.76575,-0.4146,0.49166,74.535,0.39223,-0.30478,-0.86791,323.14 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422 points correlation = 0.9243, correlation about mean = 0.1078, overlap = 52.42 steps = 44, shift = 0.0165, angle = 0.019 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation 0.91430258 0.09215302 0.39440917 -16.53749166 0.26916167 -0.86589103 -0.42164522 336.22291980 0.30265948 0.49167115 -0.81649047 187.81632315 Axis 0.97699233 0.09814643 0.18934961 Axis point 0.00000000 146.35562024 137.54670997 Rotation angle (degrees) 152.13354858 Shift along axis 52.40502232 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422 points correlation = 0.9243, correlation about mean = 0.1078, overlap = 52.42 steps = 40, shift = 0.023, angle = 0.0235 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation 0.91429158 0.09182094 0.39451211 -16.49750921 0.26887499 -0.86602061 -0.42156201 336.25180272 0.30294740 0.49150504 -0.81648371 187.80987684 Axis 0.97699016 0.09797508 0.18944947 Axis point 0.00000000 146.37500340 137.53246006 Rotation angle (degrees) 152.14175105 Shift along axis 52.40687549 Fit map Nef.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 422 points correlation = 0.9491, correlation about mean = 0.2295, overlap = 53.81 steps = 248, shift = 14.9, angle = 76.3 degrees Position of Nef.pdb map 10 (#3) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation -0.04595522 0.08887634 0.99498196 55.61281617 -0.73146668 0.67535164 -0.09410974 230.24948794 -0.68032684 -0.73212099 0.03397415 400.00854804 Axis -0.32362265 0.84977792 -0.41610800 Axis point 272.54567402 0.00000000 226.96673308 Rotation angle (degrees) 99.68984739 Shift along axis 11.21660864 Average map value = 0.3896 for 1047 atoms, 491 outside contour > ~select #2 Nothing selected > open /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/dmSer_monomer.pdb > format pdb Chain information for dmSer_monomer.pdb #6 --- Chain | Description B | No description available > select #6 2967 atoms, 3040 bonds, 3 pseudobonds, 367 residues, 2 models selected > view matrix models #6,1,0,0,-104.98,0,1,0,-15.13,0,0,1,92.406 > set bgColor white > set bgColor black > ui mousemode right select > select #6/B:459 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/B:460 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #6/B:30 7 atoms, 7 bonds, 1 residue, 1 model selected > select #6/B:30 7 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select clear > select clear > select clear > select #6 2967 atoms, 3040 bonds, 3 pseudobonds, 367 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #6,1,0,0,-94.508,0,1,0,4.0449,0,0,1,107.67 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.97409,0.19028,-0.1222,-97.99,0.14873,-0.94611,-0.28767,365.01,-0.17035,0.26204,-0.9499,479.89 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.97409,0.19028,-0.1222,-34.607,0.14873,-0.94611,-0.28767,341.34,-0.17035,0.26204,-0.9499,496.39 > view matrix models > #6,0.97409,0.19028,-0.1222,14.241,0.14873,-0.94611,-0.28767,404.43,-0.17035,0.26204,-0.9499,488.54 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.88083,-0.11275,0.45981,-24.642,0.25029,-0.71349,-0.65443,411.86,0.40185,0.69153,-0.60024,214.58 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.88083,-0.11275,0.45981,-36.228,0.25029,-0.71349,-0.65443,436.15,0.40185,0.69153,-0.60024,219.86 > view matrix models > #6,0.88083,-0.11275,0.45981,-50.392,0.25029,-0.71349,-0.65443,395.89,0.40185,0.69153,-0.60024,192.63 > view matrix models > #6,0.88083,-0.11275,0.45981,-48.631,0.25029,-0.71349,-0.65443,418.77,0.40185,0.69153,-0.60024,173.38 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.64439,-0.76461,0.011298,501.76,-0.54415,0.44811,-0.7093,409.11,0.53727,-0.46321,-0.70482,363.9 > hide #4 models > hide #3.1 models > hide #!2 models > view matrix models > #6,-0.48153,-0.87362,-0.070063,499.23,-0.59058,0.38251,-0.71056,431.43,0.64756,-0.30078,-0.70014,309.4 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.48153,-0.87362,-0.070063,490.33,-0.59058,0.38251,-0.71056,425.17,0.64756,-0.30078,-0.70014,310.57 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.98972,0.059401,0.13007,-48.44,0.11729,-0.85758,-0.50079,438.26,0.0818,0.5109,-0.85574,329.03 Opened dmSer_monomer.pdb map 10 as #7, grid size 34,37,38, pixel 3.33, shown at level 0.0589, step 1, values float32 Fit map dmSer_monomer.pdb map 10 in map cryosparc_P64_J567_map.mrc z flip using 2124 points correlation = 0.9127, correlation about mean = 0.221, overlap = 201.5 steps = 256, shift = 13.1, angle = 64.2 degrees Position of dmSer_monomer.pdb map 10 (#7) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation -0.41172816 -0.83849172 0.35694756 361.44582445 0.63423323 0.01761232 0.77294115 -80.08988683 -0.65439143 0.54462964 0.52454782 129.12273817 Axis -0.12676441 0.56152135 0.81769466 Axis point 224.65711033 55.05861868 0.00000000 Rotation angle (degrees) 115.77155115 Shift along axis 14.79232778 Average map value = 0.4026 for 2967 atoms, 1351 outside contour > view matrix models > #6,0.89961,0.38657,-0.20313,-19.236,0.16105,-0.72607,-0.66849,426.59,-0.40591,0.56867,-0.71544,398.8 > volume #1 level 0.3129 > close #1 > volume #5 level 0.5707 > volume #5 level 0.4215 > view matrix models > #6,0.84409,0.52927,-0.085876,-54.16,0.1063,-0.32215,-0.9407,421.63,-0.52555,0.78491,-0.32819,313.3 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.84409,0.52927,-0.085876,-45.545,0.1063,-0.32215,-0.9407,444.12,-0.52555,0.78491,-0.32819,312.87 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.45272,-0.84137,-0.29521,323.72,-0.54073,0.0041952,-0.84118,516.24,0.70898,0.54045,-0.45305,96.724 > ui mousemode right ""translate selected models"" > view matrix models > #6,0.45272,-0.84137,-0.29521,313.25,-0.54073,0.0041952,-0.84118,508.16,0.70898,0.54045,-0.45305,90.555 > view matrix models > #6,0.45272,-0.84137,-0.29521,311.75,-0.54073,0.0041952,-0.84118,512.3,0.70898,0.54045,-0.45305,95.862 > view matrix models > #6,0.45272,-0.84137,-0.29521,320.25,-0.54073,0.0041952,-0.84118,516.66,0.70898,0.54045,-0.45305,93.974 > ui mousemode right ""rotate selected models"" > view matrix models > #6,-0.36245,0.75023,-0.55298,279.82,0.72194,-0.14925,-0.67567,221.79,-0.58944,-0.64411,-0.48752,604.77 > view matrix models > #6,-0.34339,0.89058,-0.29824,201.5,0.72617,0.050376,-0.68567,187.97,-0.59562,-0.45202,-0.66401,607 > ui mousemode right ""translate selected models"" > view matrix models > #6,-0.34339,0.89058,-0.29824,200.2,0.72617,0.050376,-0.68567,185.41,-0.59562,-0.45202,-0.66401,610.03 > view matrix models > #6,-0.34339,0.89058,-0.29824,197.96,0.72617,0.050376,-0.68567,185.19,-0.59562,-0.45202,-0.66401,610.34 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.20172,0.93302,-0.29796,65.543,0.81466,-0.32872,-0.47778,190.58,-0.54373,-0.14636,-0.8264,576.72 Fit molecule dmSer_monomer.pdb (#6) to map cryosparc_P64_J567_map.mrc z flip (#5) using 2967 atoms average map value = 0.4029, steps = 144 shifted from previous position = 19.2 rotated from previous position = 35.6 degrees atoms outside contour = 1788, contour level = 0.42147 Position of dmSer_monomer.pdb (#6) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation 0.88707098 0.42222441 -0.18663237 -49.03411228 -0.43050774 0.61070172 -0.66461004 336.46864139 -0.16663787 0.66990295 0.72350664 -42.22229793 Axis 0.84259283 -0.01262424 -0.53840315 Axis point 0.00000000 233.66118265 368.96301673 Rotation angle (degrees) 52.36423052 Shift along axis -22.83083530 > show #4 models > show #!2 models > hide #!5 models > ui mousemode right ""translate selected models"" > view matrix models > #6,0.026928,0.67982,-0.73288,236.15,0.94316,-0.26022,-0.20673,80.29,-0.33125,-0.68566,-0.64819,594.53 > ui mousemode right ""rotate selected models"" > view matrix models > #6,0.86552,0.49493,-0.076951,-51.307,0.47174,-0.85712,-0.2069,292.42,-0.16836,0.14277,-0.97533,476.36 > show #!5 models > view matrix models > #6,0.26069,0.95399,-0.14812,21.168,0.92172,-0.29158,-0.25574,100.19,-0.28717,-0.069857,-0.95533,536.77 > ~select #6 Nothing selected > close #6-7 > open /Users/joanapaulino/Downloads/AF-Q86VE9-F1-model_v2.pdb AF-Q86VE9-F1-model_v2.pdb title: Alphafold monomer V2.0 prediction for serine incorporator 5 (Q86VE9) [more info...] Chain information for AF-Q86VE9-F1-model_v2.pdb #1 --- Chain | Description A | serine incorporator 5 > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-28.552,0,1,0,95.1,0,0,1,344.87 > view matrix models #1,1,0,0,171.29,0,1,0,192.55,0,0,1,298.24 > ui mousemode right select > ~select #1 Nothing selected > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > ~select #1 Nothing selected > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > ~select #1 Nothing selected > select clear > select clear > select clear > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > select clear > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > select #1/A:422 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > view matrix models #1,1,0,0,142.67,0,1,0,185.31,0,0,1,319 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98562,0.1197,-0.11929,142.11,-0.14272,0.9676,-0.20827,186.44,0.090495,0.2223,0.97077,317.19 > view matrix models > #1,0.98548,0.12095,-0.11914,142.1,-0.14404,0.96709,-0.20973,186.45,0.089852,0.22385,0.97047,317.18 > ui mousemode right select > select #1/A:345 12 atoms, 12 bonds, 1 residue, 1 model selected > select clear > select #1/A:389 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:389 8 atoms, 7 bonds, 1 residue, 1 model selected > ui mousemode right ""translate selected models"" > select #1 3289 atoms, 3371 bonds, 423 residues, 1 model selected > view matrix models > #1,0.98548,0.12095,-0.11914,197.44,-0.14404,0.96709,-0.20973,220.55,0.089852,0.22385,0.97047,275.16 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.9161,0.40049,-0.019236,198.55,-0.39597,-0.89612,0.20045,234.28,0.063039,0.19124,0.97952,275.43 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.9161,0.40049,-0.019236,208.59,-0.39597,-0.89612,0.20045,227.41,0.063039,0.19124,0.97952,264.33 Fit molecule AF-Q86VE9-F1-model_v2.pdb (#1) to map cryosparc_P64_J567_map.mrc z flip (#5) using 3289 atoms average map value = 0.3863, steps = 260 shifted from previous position = 14.9 rotated from previous position = 32.5 degrees atoms outside contour = 2188, contour level = 0.42147 Position of AF-Q86VE9-F1-model_v2.pdb (#1) relative to cryosparc_P64_J567_map.mrc z flip (#5) coordinates: Matrix rotation and translation -0.79777253 -0.56951509 0.19801906 195.05644723 -0.50913117 0.81220747 0.28478849 214.44406485 -0.32302390 0.12637876 -0.93791469 174.16072666 Axis -0.28910658 0.95093242 0.11020402 Axis point 141.56576331 0.00000000 56.79200727 Rotation angle (degrees) 164.09970069 Shift along axis 166.72292314 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.90964,-0.2753,-0.31107,218.16,0.31088,-0.04552,0.94936,204.77,-0.27552,-0.96028,0.044179,277.88 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.90964,-0.2753,-0.31107,216.99,0.31088,-0.04552,0.94936,208.65,-0.27552,-0.96028,0.044179,282.21 > view matrix models > #1,0.90964,-0.2753,-0.31107,215.19,0.31088,-0.04552,0.94936,211.02,-0.27552,-0.96028,0.044179,284.96 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.91229,0.32269,-0.25218,213.8,-0.39329,-0.86201,0.31977,220.51,-0.11419,0.3909,0.91332,271.64 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.91229,0.32269,-0.25218,210.76,-0.39329,-0.86201,0.31977,216.51,-0.11419,0.3909,0.91332,268.27 > view matrix models > #1,-0.91229,0.32269,-0.25218,211.45,-0.39329,-0.86201,0.31977,216.46,-0.11419,0.3909,0.91332,268.11 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.8971,0.18256,-0.40234,212.95,-0.33985,-0.86703,0.36436,216.27,-0.28232,0.4636,0.83986,268.08 > view matrix models > #1,-0.89927,0.37458,-0.22584,210.95,-0.43546,-0.81532,0.38162,216,-0.041188,0.44152,0.89631,267.63 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.89927,0.37458,-0.22584,218.7,-0.43546,-0.81532,0.38162,220.31,-0.041188,0.44152,0.89631,264.4 > view matrix models > #1,-0.89927,0.37458,-0.22584,217.56,-0.43546,-0.81532,0.38162,220.67,-0.041188,0.44152,0.89631,264.27 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.95757,0.23018,-0.17345,218.64,-0.26541,-0.93885,0.21937,221.78,-0.11235,0.25609,0.9601,265.66 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.95757,0.23018,-0.17345,214.15,-0.26541,-0.93885,0.21937,219.72,-0.11235,0.25609,0.9601,265.84 > ~select #1 Nothing selected > volume #5 level 0.238 > ui tool show ""Side View"" > volume #5 level 0.3876 > hide #!5 models > show #!5 models > volume #5 level 0.1819 > volume #5 level 0.3783 > volume #5 level 0.2941 > save > /Users/joanapaulino/Documents/postdoc_UCSF/Serinc/chX_session_serinc5WTAP2Nef_GOKrios.cxs > includeMaps true > close session > open > /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_00_02800_volume.mrc Opened cryosparc_P73_J25_class_00_02800_volume.mrc as #1, grid size 48,48,48, pixel 5.31, shown at level 0.692, step 1, values float32 > surface dust #1 size 53.1 > volume #1 level 0.9069 > volume #1 level 0.6444 > surface dust #1 size 53.1 > surface dust #1 size 53.1 > volume #1 level 0.7876 Traceback (most recent call last): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/gui.py"", line 609, in closeEvent sbar.destroy() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/ui/statusbar.py"", line 51, in destroy v.delete() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 438, in delete self.make_current() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 99, in make_current qc = self._initialize_context() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) RuntimeError: wrapped C/C++ object of type QScreen has been deleted RuntimeError: wrapped C/C++ object of type QScreen has been deleted File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 125, in _initialize_context qc.setScreen(self._screen) See log for complete Python traceback. > open > /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #2, grid size 48,48,48, pixel 5.31, shown at level 0.682, step 1, values float32 Traceback (most recent call last): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 73, in t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb()) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 85, in capture_thumbnails_cb fs.capture_image(models, ses) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 173, in capture_image self.image = models_image(session, models, size) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 235, in models_image image = v.image(width, height, camera = c, drawings = models) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 413, in image if not self._use_opengl(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 104, in _use_opengl if not self._render.make_current(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") chimerax.graphics.opengl.OpenGLError: Could not make graphics context current Error processing trigger ""frame drawn"": chimerax.graphics.opengl.OpenGLError: Could not make graphics context current File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") See log for complete Python traceback. > open > /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #3, grid size 48,48,48, pixel 5.31, shown at level 0.682, step 1, values float32 Traceback (most recent call last): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 73, in t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb()) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 85, in capture_thumbnails_cb fs.capture_image(models, ses) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 173, in capture_image self.image = models_image(session, models, size) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 235, in models_image image = v.image(width, height, camera = c, drawings = models) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 413, in image if not self._use_opengl(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 104, in _use_opengl if not self._render.make_current(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") chimerax.graphics.opengl.OpenGLError: Could not make graphics context current Error processing trigger ""frame drawn"": chimerax.graphics.opengl.OpenGLError: Could not make graphics context current File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") See log for complete Python traceback. > open > /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #4, grid size 48,48,48, pixel 5.31, shown at level 0.682, step 1, values float32 Traceback (most recent call last): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 73, in t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb()) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 85, in capture_thumbnails_cb fs.capture_image(models, ses) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 173, in capture_image self.image = models_image(session, models, size) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 235, in models_image image = v.image(width, height, camera = c, drawings = models) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 413, in image if not self._use_opengl(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 104, in _use_opengl if not self._render.make_current(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") chimerax.graphics.opengl.OpenGLError: Could not make graphics context current Error processing trigger ""frame drawn"": chimerax.graphics.opengl.OpenGLError: Could not make graphics context current File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") See log for complete Python traceback. > open > /Users/joanapaulino/Downloads/cryosparc_P73_J25_class_03_03200_volume.mrc Opened cryosparc_P73_J25_class_03_03200_volume.mrc as #5, grid size 48,48,48, pixel 5.31, shown at level 0.682, step 1, values float32 Traceback (most recent call last): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/triggerset.py"", line 130, in invoke return self._func(self._name, data) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 73, in t.add_handler('frame drawn', lambda *args, s=self: s.capture_thumbnails_cb()) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 85, in capture_thumbnails_cb fs.capture_image(models, ses) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 173, in capture_image self.image = models_image(session, models, size) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/core/filehistory.py"", line 235, in models_image image = v.image(width, height, camera = c, drawings = models) File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 413, in image if not self._use_opengl(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/view.py"", line 104, in _use_opengl if not self._render.make_current(): File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 478, in make_current return self._opengl_context.make_current() File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") chimerax.graphics.opengl.OpenGLError: Could not make graphics context current Error processing trigger ""frame drawn"": chimerax.graphics.opengl.OpenGLError: Could not make graphics context current File ""/opt/sbgrid/i386-mac/chimerax/1.2.5/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site- packages/chimerax/graphics/opengl.py"", line 108, in make_current raise OpenGLError(""Could not make graphics context current"") See log for complete Python traceback. OpenGL version: unknown Could not make opengl context currentHardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 32 GB Boot ROM Version: 1037.147.1.0.0 (iBridge: 17.16.16065.0.0,0) Software: System Software Overview: System Version: macOS 10.15.6 (19G73) Kernel Version: Darwin 19.6.0 Time since boot: 7 days 6:41 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: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.01.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60 Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: YMYH14BR3UKL Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: DVI or HDMI Automatically Adjust Brightness: No Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-Clipper: 0.16.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 matplotlib-inline: 0.1.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 }}} " defect closed normal Window Toolkit duplicate Eric Pettersen all ChimeraX