id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17020 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open > /Users/hhokamoto/Downloads/cryosparc_P67_J415_class_03_00186_volume_sharp.mrc Opened cryosparc_P67_J415_class_03_00186_volume_sharp.mrc as #1, grid size 480,480,480, pixel 0.819, shown at level 0.0702, step 2, values float32 > volume #1 level 0.0522 > open > /Users/hhokamoto/Downloads/cryosparc_P67_J415_class_03_00187_volume_sharp.mrc Opened cryosparc_P67_J415_class_03_00187_volume_sharp.mrc as #2, grid size 480,480,480, pixel 0.819, shown at level 0.0703, step 2, values float32 > lighting simple > set bgColor white > lighting soft > volume #2 level 0.1726 > close #1 > close #2 > open /Users/hhokamoto/Downloads/cryosparc_P67_J407_004_volume_map.mrc > /Users/hhokamoto/Downloads/cryosparc_P67_J413_002_volume_map_sharp.mrc Opened cryosparc_P67_J407_004_volume_map.mrc as #1.1, grid size 480,480,480, pixel 0.819, shown at level 0.0802, step 2, values float32 Opened cryosparc_P67_J413_002_volume_map_sharp.mrc as #1.2, grid size 480,480,480, pixel 0.819, shown at level 0.0755, step 2, values float32 > windowsize 1000 1000 > volume #1.1 level 0.219 > volume #1.1 level 0.1762 > volume #1.2 level 0.2222 > volume #1.2 level 0.2521 > volume #1.2 level 0.1533 > hide #!1.2 models > close #1.2 > open ""/Users/hhokamoto/Downloads/cryosparc_P67_J407_004_volume_map_sharp > (1).mrc"" Opened cryosparc_P67_J407_004_volume_map_sharp (1).mrc as #2, grid size 480,480,480, pixel 0.819, shown at level 0.0778, step 2, values float32 Drag select of 2 cryosparc_P67_J407_004_volume_map_sharp (1).mrc > volume #2 level 0.1995 > hide #!2 models > show #!2 models > volume #2 level 0.1547 > open /Users/hhokamoto/Downloads/cryosparc_P67_J414_map_sharp.mrc Opened cryosparc_P67_J414_map_sharp.mrc as #3, grid size 480,480,480, pixel 0.819, shown at level 0.0824, step 2, values float32 > ui tool show ""Side View"" > open pdb:7k65 Summary of feedback from opening 7k65 fetched from pdb --- notes | Fetching compressed mmCIF 7k65 from http://files.rcsb.org/download/7k65.cif Fetching CCD Q7G from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/Q7G/Q7G.cif 7k65 title: Hedgehog receptor Patched (PTCH1) in complex with conformation selective nanobody TI23 [more info...] Chain information for 7k65 #4 --- Chain | Description | UniProt A | Protein patched homolog 1 | PTC1_MOUSE 1-1291 B | nanobody TI23 | Non-standard residues in 7k65 #4 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) Q7G — 2-{[(4-O-alpha-D-glucopyranosyl-alpha-D- glucopyranosyl)oxy]methyl}-4-{[(3beta,9beta,14beta,17beta,25R)-spirost-5-en-3-yl]oxy}butyl 4-O-alpha-D-glucopyranosyl-alpha-D-glucopyranoside > hide #4/B > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > select add #4 8796 atoms, 9038 bonds, 1 pseudobond, 1131 residues, 5 models selected > select subtract #2 8796 atoms, 9038 bonds, 1 pseudobond, 1131 residues, 3 models selected > view matrix models #4,1,0,0,20.612,0,1,0,34.563,0,0,1,-11.01 > view matrix models #4,1,0,0,23.646,0,1,0,84.822,0,0,1,34.527 > view matrix models #4,1,0,0,30.247,0,1,0,48.293,0,0,1,78.721 > view matrix models #4,1,0,0,33.295,0,1,0,32.055,0,0,1,93.207 > view matrix models #4,1,0,0,21.343,0,1,0,15.796,0,0,1,124.06 > open > /Users/hhokamoto/Downloads/cryosparc_P67_J415_class_03_00190_volume_sharp.mrc Opened cryosparc_P67_J415_class_03_00190_volume_sharp.mrc as #5, grid size 480,480,480, pixel 0.819, shown at level 0.0708, step 2, values float32 > hide #4 target ar > show #4/A target r > view matrix models #4,1,0,0,29.995,0,1,0,13.159,0,0,1,126.64 > view matrix models #4,1,0,0,48.927,0,1,0,3.5068,0,0,1,128.72 > graphics silhouettes true width 1 > view matrix models #4,1,0,0,70.665,0,1,0,-14.628,0,0,1,124.65 > view matrix models #4,1,0,0,45.128,0,1,0,17.587,0,0,1,110.91 > view matrix models #4,1,0,0,56.844,0,1,0,17.969,0,0,1,116.41 > volume #2 level 0.2448 > view matrix models #4,1,0,0,57.888,0,1,0,39.719,0,0,1,106.15 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.15314,-0.081951,-0.9848,310.01,-0.97583,0.14469,-0.16378,315.7,0.15591,0.98608,-0.057813,78.29 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.15314,-0.081951,-0.9848,310.93,-0.97583,0.14469,-0.16378,313.71,0.15591,0.98608,-0.057813,66.569 > transparency #2 50 > view matrix models > #4,0.15314,-0.081951,-0.9848,313.57,-0.97583,0.14469,-0.16378,315.67,0.15591,0.98608,-0.057813,57.642 > view matrix models > #4,0.15314,-0.081951,-0.9848,315.68,-0.97583,0.14469,-0.16378,315.68,0.15591,0.98608,-0.057813,58.002 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 448 shifted from previous position = 4.49 rotated from previous position = 42.8 degrees atoms outside contour = 6829, contour level = 0.24477 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36862113 -0.52443212 -0.76752161 421.46017226 -0.92869643 0.17177853 0.32865647 241.43183594 -0.04051428 0.83394430 -0.55035943 174.37950066 Axis 0.51915673 -0.74696189 -0.41536037 Axis point 266.76554319 0.00000000 96.40552375 Rotation angle (degrees) 150.87983581 Shift along axis -33.96683035 > color #4/a red > view matrix models > #4,-0.36862,-0.52443,-0.76752,420.48,-0.9287,0.17178,0.32866,239.27,-0.040514,0.83394,-0.55036,175.95 > volume #2 level 0.1854 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 88 shifted from previous position = 2.84 rotated from previous position = 0.0203 degrees atoms outside contour = 5507, contour level = 0.18544 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36847569 -0.52420703 -0.76774517 421.43751213 -0.92876140 0.17173829 0.32849387 241.46820786 -0.04034755 0.83409409 -0.55014464 174.30904219 Axis 0.51917141 -0.74692224 -0.41541331 Axis point 266.76617874 0.00000000 96.40010383 Rotation angle (degrees) 150.86100478 Shift along axis -33.96996388 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 48 shifted from previous position = 0.0195 rotated from previous position = 0.0126 degrees atoms outside contour = 5508, contour level = 0.18544 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36857929 -0.52407406 -0.76778622 421.43788404 -0.92871705 0.17168109 0.32864913 241.43403127 -0.04042211 0.83418942 -0.54999461 174.27364805 Axis 0.51912017 -0.74690265 -0.41551255 Axis point 266.75460032 0.00000000 96.37357466 Rotation angle (degrees) 150.86163841 Shift along axis -33.96369953 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 44 shifted from previous position = 0.00979 rotated from previous position = 0.0556 degrees atoms outside contour = 5512, contour level = 0.18544 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36894540 -0.52471305 -0.76717371 421.49784766 -0.92855134 0.17177357 0.32906877 241.35283479 -0.04088651 0.83376859 -0.55059808 174.47756509 Axis 0.51909666 -0.74700495 -0.41535800 Axis point 266.76019170 0.00000000 96.39076318 Rotation angle (degrees) 150.91328360 Shift along axis -33.96428918 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 76 shifted from previous position = 0.00905 rotated from previous position = 0.0399 degrees atoms outside contour = 5509, contour level = 0.18544 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36860182 -0.52434639 -0.76758945 421.45356097 -0.92870606 0.17176990 0.32863377 241.43676107 -0.04046917 0.83399998 -0.55027837 174.35454845 Axis 0.51914943 -0.74695156 -0.41538806 Axis point 266.76280618 0.00000000 96.40111713 Rotation angle (degrees) 150.87443600 Shift along axis -33.96898890 > view matrix models > #4,-0.3686,-0.52435,-0.76759,418.65,-0.92871,0.17177,0.32863,234.47,-0.040469,0.834,-0.55028,178.25 > view matrix models > #4,-0.3686,-0.52435,-0.76759,412.98,-0.92871,0.17177,0.32863,234.28,-0.040469,0.834,-0.55028,173.85 > view matrix models > #4,-0.3686,-0.52435,-0.76759,413.5,-0.92871,0.17177,0.32863,239.41,-0.040469,0.834,-0.55028,174.95 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 132 shifted from previous position = 8.23 rotated from previous position = 0.0118 degrees atoms outside contour = 5505, contour level = 0.18544 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36851605 -0.52421767 -0.76771854 421.44101994 -0.92874464 0.17175326 0.32853344 241.45561337 -0.04036487 0.83408432 -0.55015818 174.31320956 Axis 0.51915797 -0.74693066 -0.41541496 Axis point 266.76221477 0.00000000 96.39944300 Rotation angle (degrees) 150.86329476 Shift along axis -33.96845107 > volume #2 level 0.214 > transparency #2 70 > transparency #2 20 > view matrix models > #4,-0.36852,-0.52422,-0.76772,419.02,-0.92874,0.17175,0.32853,238.38,-0.040365,0.83408,-0.55016,176.4 > fitmap #4 inMap #2 Fit molecule 7k65 (#4) to map cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) using 8796 atoms average map value = 0.1558, steps = 88 shifted from previous position = 4.44 rotated from previous position = 0.0132 degrees atoms outside contour = 6206, contour level = 0.21401 Position of 7k65 (#4) relative to cryosparc_P67_J407_004_volume_map_sharp (1).mrc (#2) coordinates: Matrix rotation and translation -0.36860757 -0.52430361 -0.76761591 421.45296020 -0.92869966 0.17167058 0.32870375 241.44144191 -0.04056349 0.83404732 -0.55019966 174.34967800 Axis 0.51915142 -0.74691815 -0.41544564 Axis point 266.76990936 0.00000000 96.38440910 Rotation angle (degrees) 150.87598775 Shift along axis -33.97190649 > save /Users/hhokamoto/Desktop/image45.png supersample 3 > open ""/Users/hhokamoto/Downloads/cryosparc_P67_J418_006_volume_map_sharp > (1).mrc"" Opened cryosparc_P67_J418_006_volume_map_sharp (1).mrc as #6, grid size 480,480,480, pixel 0.819, shown at level 0.087, step 2, values float32 > volume #6 level 0.2602 > transparency #6 20 > fitmap #4 inMap #6 Fit molecule 7k65 (#4) to map cryosparc_P67_J418_006_volume_map_sharp (1).mrc (#6) using 8796 atoms average map value = 0.1686, steps = 76 shifted from previous position = 1.61 rotated from previous position = 3.65 degrees atoms outside contour = 6028, contour level = 0.26016 Position of 7k65 (#4) relative to cryosparc_P67_J418_006_volume_map_sharp (1).mrc (#6) coordinates: Matrix rotation and translation -0.32768508 -0.56593133 -0.75653435 422.94801383 -0.94164438 0.13037470 0.31033578 252.55869210 -0.07699580 0.81407872 -0.57562790 185.28835356 Axis 0.54424839 -0.73417954 -0.40592375 Axis point 276.19374296 0.00000000 96.25571768 Rotation angle (degrees) 152.43285936 Shift along axis -30.44759286 > view matrix models > #4,-0.32769,-0.56593,-0.75653,420.07,-0.94164,0.13037,0.31034,250.7,-0.076996,0.81408,-0.57563,187.31 > view matrix models > #4,-0.32769,-0.56593,-0.75653,418.44,-0.94164,0.13037,0.31034,249.87,-0.076996,0.81408,-0.57563,188.01 > fitmap #4 inMap #6 Fit molecule 7k65 (#4) to map cryosparc_P67_J418_006_volume_map_sharp (1).mrc (#6) using 8796 atoms average map value = 0.1686, steps = 88 shifted from previous position = 5.91 rotated from previous position = 0.0125 degrees atoms outside contour = 6027, contour level = 0.26016 Position of 7k65 (#4) relative to cryosparc_P67_J418_006_volume_map_sharp (1).mrc (#6) coordinates: Matrix rotation and translation -0.32778688 -0.56606069 -0.75639345 422.96656831 -0.94160552 0.13045850 0.31041848 252.52375828 -0.07703774 0.81397535 -0.57576845 185.33248924 Axis 0.54422598 -0.73422298 -0.40587521 Axis point 276.18503632 0.00000000 96.27079609 Rotation angle (degrees) 152.44267635 Shift along axis -30.44121398 > save /Users/hhokamoto/Desktop/image46.png supersample 3 > color #4/a yellow > color #4/a cyan > transparency #6 70 > view matrix models > #4,-0.32779,-0.56606,-0.75639,421.59,-0.94161,0.13046,0.31042,250.81,-0.077038,0.81398,-0.57577,186.81 > transparency #6 50 > fitmap #4 inMap #6 Fit molecule 7k65 (#4) to map cryosparc_P67_J418_006_volume_map_sharp (1).mrc (#6) using 8796 atoms average map value = 0.1686, steps = 76 shifted from previous position = 2.65 rotated from previous position = 0.0318 degrees atoms outside contour = 6027, contour level = 0.26016 Position of 7k65 (#4) relative to cryosparc_P67_J418_006_volume_map_sharp (1).mrc (#6) coordinates: Matrix rotation and translation -0.32755428 -0.56572566 -0.75674479 422.93517217 -0.94168803 0.13018469 0.31028311 252.59530661 -0.07701853 0.81425207 -0.57537963 185.24355534 Axis 0.54427969 -0.73409521 -0.40603430 Axis point 276.20912601 0.00000000 96.23515800 Rotation angle (degrees) 152.42115910 Shift along axis -30.44921733 > open /Users/hhokamoto/Downloads/cryosparc_P67_J423_003_volume_map_sharp.mrc Opened cryosparc_P67_J423_003_volume_map_sharp.mrc as #7, grid size 480,480,480, pixel 0.819, shown at level 0.0752, step 2, values float32 > hide #!4 models > select subtract #4 Nothing selected > hide #!6 models > volume #7 level 0.2145 > volume #7 level 0.168 > open /Users/hhokamoto/Downloads/cryosparc_P67_J424_map.mrc Opened cryosparc_P67_J424_map.mrc as #8, grid size 480,480,480, pixel 0.819, shown at level 0.0802, step 2, values float32 > show #!4 models > select add #4 8796 atoms, 9038 bonds, 1 pseudobond, 1131 residues, 3 models selected > volume #8 style mesh > volume #8 > volume #8 style surface > view matrix models > #4,-0.32755,-0.56573,-0.75674,418.79,-0.94169,0.13018,0.31028,239.51,-0.077019,0.81425,-0.57538,146.67 > view matrix models > #4,-0.32755,-0.56573,-0.75674,391.28,-0.94169,0.13018,0.31028,298.6,-0.077019,0.81425,-0.57538,99.312 > ui mousemode right ""rotate selected models"" > view matrix models > #4,-0.11759,-0.67914,-0.72453,377.91,0.94475,-0.30129,0.12909,151.99,-0.30597,-0.66932,0.67705,186.33 > view matrix models > #4,-0.62469,-0.18511,0.75861,165.55,0.18168,-0.97929,-0.089355,381.41,0.75944,0.082002,0.64539,-58.565 > view matrix models > #4,-0.672,-0.3325,0.66171,207.19,0.16584,-0.93841,-0.30312,406.02,0.72175,-0.093961,0.68575,-32.301 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.672,-0.3325,0.66171,233.74,0.16584,-0.93841,-0.30312,366.37,0.72175,-0.093961,0.68575,7.7846 > view matrix models > #4,-0.672,-0.3325,0.66171,242.95,0.16584,-0.93841,-0.30312,355.78,0.72175,-0.093961,0.68575,5.7838 > ui tool show ""Selection Inspector"" > fitmap #4 inMap #8 Fit molecule 7k65 (#4) to map cryosparc_P67_J424_map.mrc (#8) using 8796 atoms average map value = 0.1749, steps = 124 shifted from previous position = 2.3 rotated from previous position = 8.25 degrees atoms outside contour = 1772, contour level = 0.08023 Position of 7k65 (#4) relative to cryosparc_P67_J424_map.mrc (#8) coordinates: Matrix rotation and translation -0.56741469 -0.31893831 0.75915673 212.91070558 0.14417348 -0.94618067 -0.28975190 358.54016586 0.81071240 -0.05495922 0.58285925 2.67107640 Axis 0.44998096 -0.09880661 0.88755529 Axis point 78.50261282 193.22888080 0.00000000 Rotation angle (degrees) 164.87701510 Shift along axis 62.75035483 > transparency #8 50 > volume #8 level 0.1314 > view matrix models > #4,-0.56741,-0.31894,0.75916,216.69,0.14417,-0.94618,-0.28975,361.8,0.81071,-0.054959,0.58286,3.7942 > fitmap #4 inMap #8 Fit molecule 7k65 (#4) to map cryosparc_P67_J424_map.mrc (#8) using 8796 atoms average map value = 0.1749, steps = 104 shifted from previous position = 5.11 rotated from previous position = 0.0116 degrees atoms outside contour = 3178, contour level = 0.13138 Position of 7k65 (#4) relative to cryosparc_P67_J424_map.mrc (#8) coordinates: Matrix rotation and translation -0.56744258 -0.31890643 0.75914928 212.91233669 0.14431604 -0.94620176 -0.28961202 358.50789722 0.81066751 -0.05478078 0.58293848 2.64993439 Axis 0.44995837 -0.09871370 0.88757708 Axis point 78.50619786 193.21392212 -0.00000000 Rotation angle (degrees) 164.87369499 Shift along axis 62.76406836 > volume #8 level 0.2002 > volume #8 level 0.1561 > volume #8 level 0.1684 > save /Users/hhokamoto/Desktop/image47.png supersample 3 > volume #8 level 0.2072 > volume #8 level 0.1614 > save /Users/hhokamoto/Desktop/image48.png supersample 3 > rotate 180 Unknown command: rotate 180 > turn x 180 > turn y 180 > save /Users/hhokamoto/Desktop/image49.png supersample 3 > open /Users/hhokamoto/Downloads/cryosparc_P67_J425_003_volume_map_sharp.mrc Opened cryosparc_P67_J425_003_volume_map_sharp.mrc as #9, grid size 480,480,480, pixel 0.819, shown at level 0.0777, step 2, values float32 > volume #9 level 0.2198 > save /Users/hhokamoto/Downloads/2025-03-04_Hiro_2in1-Krios.cxs includeMaps > true > save /Users/hhokamoto/Downloads/250304.cxs includeMaps true > close #1.1 > close #2 > show #!5 models > show #!6 models > show #!7 models > show #!8 models > hide #1 models > show #1 models > close #1 > close #3 > close #5 > close #6 > close #7 > close #9 > save /Users/hhokamoto/Downloads/250304.cxs includeMaps true > hide #!4 models > hide #!8 models > close #8 > close #4 > open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- > Mapping/smo_mtr_1.defattr format defattr Summary of feedback from opening /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- Mapping/smo_mtr_1.defattr --- note | Assigned attribute 'mtr' to 0 residues using match mode: any > open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- > Mapping/smo_mtr_1.defattr format defattr Summary of feedback from opening /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- Mapping/smo_mtr_1.defattr --- note | Assigned attribute 'mtr' to 0 residues using match mode: any > open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- > Mapping/smo_mtr_1.defattr format defattr Summary of feedback from opening /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- Mapping/smo_mtr_1.defattr --- note | Assigned attribute 'mtr' to 0 residues using match mode: any > open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- > Mapping/smo_mtr_1.defattr format defattr Summary of feedback from opening /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- Mapping/smo_mtr_1.defattr --- note | Assigned attribute 'mtr' to 0 residues using match mode: any > open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO- > PTCH1/AF3/fold_smo_ptch1b/fold_smo_ptch1b_model_4.cif Chain information for fold_smo_ptch1b_model_4.cif #1 --- Chain | Description A | . B | . Computing secondary structure > lighting soft > open /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- > Mapping/smo_mtr_1.defattr /Users/hhokamoto/Library/CloudStorage/OneDrive- > UCSF/SMO-PTCH1/Variants-Mapping/ptch1_mtr_1.defattr Summary of feedback from opening /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- Mapping/smo_mtr_1.defattr --- note | Assigned attribute 'mtr' to 632 residues using match mode: any Summary of feedback from opening /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- Mapping/ptch1_mtr_1.defattr --- note | Assigned attribute 'mtr' to 1266 residues using match mode: any > color #1 by attribute Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #1 byattribute Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byattribute Missing or invalid ""attrName"" argument: Expected a text string > color byattribute mtr palette red:yellow:green 14895 atoms, 1900 residues, atom mtr range 0.596 to 1.17 > save /Users/hhokamoto/Library/CloudStorage/OneDrive-UCSF/SMO-PTCH1/Variants- > Mapping/Generon_color_byattribute_mtr_palette_red:yellow:green.cxs > save /Users/hhokamoto/Desktop/image50.png supersample 3 > open /Users/hhokamoto/Downloads/cryosparc_P67_J425_006_volume_map_sharp.mrc Opened cryosparc_P67_J425_006_volume_map_sharp.mrc as #2, grid size 480,480,480, pixel 0.819, shown at level 0.0779, step 2, values float32 > hide #!2 models > show #!2 models > hide #1 models > show #1 models > volume #2 level 0.2306 > volume #2 level 0.1853 > ui mousemode right ""translate selected models"" > select add #1 14895 atoms, 15281 bonds, 1900 residues, 1 model selected > view matrix models #1,1,0,0,1.5457,0,1,0,5.1242,0,0,1,4.8305 > view matrix models #1,1,0,0,61.819,0,1,0,206.37,0,0,1,220.08 > view matrix models #1,1,0,0,90.361,0,1,0,187.27,0,0,1,229.95 > view matrix models #1,1,0,0,85.947,0,1,0,167.79,0,0,1,181.59 > view matrix models #1,1,0,0,178.44,0,1,0,159.78,0,0,1,221.03 > view matrix models #1,1,0,0,169.22,0,1,0,161.68,0,0,1,218.16 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.17871,0.34169,-0.92266,193.82,0.18072,0.93321,0.31059,155.68,0.96716,-0.11124,-0.22852,224.22 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.17871,0.34169,-0.92266,194.86,0.18072,0.93321,0.31059,196.23,0.96716,-0.11124,-0.22852,191.83 > fitmap #1 inMap #2 Fit molecule fold_smo_ptch1b_model_4.cif (#1) to map cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) using 14895 atoms average map value = 0.1377, steps = 272 shifted from previous position = 3.88 rotated from previous position = 18.8 degrees atoms outside contour = 9925, contour level = 0.18526 Position of fold_smo_ptch1b_model_4.cif (#1) relative to cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.00639741 0.11184534 -0.99370503 193.84570252 0.02342669 0.99346940 0.11166800 193.80140545 0.99970509 -0.02256483 -0.00897580 193.99111741 Axis -0.06712044 -0.99676484 -0.04421198 Axis point -1.14163012 0.00000000 181.72364887 Rotation angle (degrees) 90.62751041 Shift along axis -214.76216753 > volume #2 level 0.2163 > select subtract #1 Nothing selected > transparency #2 20 > fitmap #1 inMap #2 Fit molecule fold_smo_ptch1b_model_4.cif (#1) to map cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) using 14895 atoms average map value = 0.1377, steps = 24 shifted from previous position = 0.00534 rotated from previous position = 0.00559 degrees atoms outside contour = 10984, contour level = 0.21628 Position of fold_smo_ptch1b_model_4.cif (#1) relative to cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.00644873 0.11188558 -0.99370017 193.84555061 0.02335451 0.99346663 0.11170772 193.79745453 0.99970645 -0.02248701 -0.00901963 193.98752207 Axis -0.06710142 -0.99676363 -0.04426821 Axis point -1.12752304 0.00000000 181.71407165 Rotation angle (degrees) 90.63031569 Shift along axis -214.76504671 > surface dust #2 size 8.19 > volume #2 level 0.1876 > fitmap #1 inMap #2 Fit molecule fold_smo_ptch1b_model_4.cif (#1) to map cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) using 14895 atoms average map value = 0.1377, steps = 24 shifted from previous position = 0.00398 rotated from previous position = 0.00362 degrees atoms outside contour = 9999, contour level = 0.18764 Position of fold_smo_ptch1b_model_4.cif (#1) relative to cryosparc_P67_J425_006_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation -0.00647074 0.11186222 -0.99370266 193.84906215 0.02330000 0.99347054 0.11168436 193.79570991 0.99970758 -0.02243059 -0.00903488 193.98660209 Axis -0.06706155 -0.99676562 -0.04428380 Axis point -1.11812123 0.00000000 181.71666739 Rotation angle (degrees) 90.63127131 Shift along axis -214.75918181 > hide #!2 models > show #1/A:367 atoms ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,3 Model Number: Z1C80001DLL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 2 days, 18 hours, 18 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: LG HDR WQHD: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 100.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX