id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 3212 Drawing silhouette: glFramebufferTexture2D: invalid operation chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Linux-4.4.0-178-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.92 (2020-03-05) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.92 (2020-03-05) © 2016-2020 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/disk3/modeling/gp17-2020/Figure4-20200512-fiber-ET-color- > change.cxs opened ChimeraX session > select clear > show #!26 models > transparency #26 50 > hide #!83 models > surface dust #50 size 30 > surface dust #26 size 30 > surface dust #34 size 30 > view name J6 > view name J7 > view J6 > open /data/disk3/modeling/nochan-new-trim-gp17-c1-short.mrc Opened nochan-new-trim-gp17-c1-short.mrc, grid size 160,160,160, pixel 5.4, shown at level 2.05e-05, step 1, values float32 > select #1 2 models selected > lighting flat > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > hide #!1 models > show #!1 models > show #!9 models > hide #!9 models > show #!9 models > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > fitmap #1 inMap #9 Fit map nochan-new-trim-gp17-c1-short.mrc in map nochan-new-trim.mrc using 934 points correlation = 0.9922, correlation about mean = 0.9617, overlap = 34.87 steps = 60, shift = 9.74, angle = 32 degrees Position of nochan-new-trim-gp17-c1-short.mrc (#1) relative to nochan-new- trim.mrc (#9) coordinates: Matrix rotation and translation -0.50611525 0.86236772 -0.01301046 1.38911285 -0.86245305 -0.50613234 0.00218729 -1.21911776 -0.00469876 0.01232793 0.99991297 -1.06579535 Axis 0.00587907 -0.00481873 -0.99997111 Axis point 0.34386807 -1.00288964 0.00000000 Rotation angle (degrees) 120.40887188 Shift along axis 1.07980585 > show #!17 models > fitmap #9 inMap #17 Fit map nochan-new-trim.mrc in map nochan-new-fiber.mrc using 14061 points correlation = 0.6271, correlation about mean = 0.3689, overlap = 211.1 steps = 40, shift = 0.0406, angle = 0.0249 degrees Position of nochan-new-trim.mrc (#9) relative to nochan-new-fiber.mrc (#17) coordinates: Matrix rotation and translation 0.49952609 0.86629883 0.00000834 -0.00416588 -0.86629884 0.49952609 -0.00000026 -0.00265282 -0.00000438 -0.00000709 0.99999999 -0.04873786 Axis -0.00000395 0.00000734 -1.00000000 Axis point -0.00437911 0.00227873 0.00000000 Rotation angle (degrees) 60.03134871 Shift along axis 0.04873786 > hide #!17 models > hide #!9 models > select clear > show #!17 models > volume #1 level 0.05692 > volume #1 color #d3d7cfb3 > hide #!17 models > select clear > view name test Unknown command: viewm J7 > view J7 > view J6 > volume #1 color white > transparency #6 50 > transparency #1 50 > select clear > view J6 > lighting soft > lighting full > view J7 > save image /data/disk3/Paper-use/Figure4-20200514-6.tif pixelSize 0.1 > supersample 3 transparentBackground true > transparency #1 70 > volume #1 color #44cccc > transparency #1 70 > volume #1 color white > transparency #1 70 > save image /data/disk3/Paper-use/Figure4-20200514-7.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!9 models > hide #!9 models > show #!17 models > hide #!17 models > show #!9 models > select #9 2 models selected > hide #!9 models > ~select #9 Nothing selected > select #9 2 models selected > ~select #9 Nothing selected > view J6 > save image /data/disk3/Paper-use/Figure4-20200514-8.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!47 models > hide #!47 models > show #!46 models > hide #!46 models > show #!45 models > hide #!45 models > show #!44 models > hide #!44 models > hide #!97 models > show #!97 models > select #97 2 models selected > show #!103 models > hide #!103 models > show #!102 models > hide #!102 models > show #!100 models > hide #!100 models > show #!100 models > hide #!67 models > show #!67 models > hide #!67 models > hide #!100 models > select clear > save image /data/disk3/Paper-use/Figure4-20200514-9.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!100 models > show #!9 models > hide #!9 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > hide #!97 models > show #!97 models > view J7 > select #97 2 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > view J7 > open /data/disk3/modeling/gp17/fiber-6-fromtail-clean-link-C1.mrc Opened fiber-6-fromtail-clean-link-C1.mrc, grid size 400,400,400, pixel 1.05, shown at level 9.12e-07, step 2, values float32 > select #94 2 models selected > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""rotate selected models"" > volume #94 level 0.007616 > volume #94 color #44cccc > volume #94 color #2cd5cc > select clear > view J7 > view J6 > open /data/disk3/modeling/gp17-2020/gp17-shaft-full-right.pdb Chain information for gp17-shaft-full-right.pdb #107 --- Chain | Description A B C | No description available > hide #!68 models > show #!68 models > hide #!69 models > show #!69 models > select #107 2886 atoms, 2922 bonds, 1 model selected > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > fitmap #107 inMap #100 Fit molecule gp17-shaft-full-right.pdb (#107) to map shaft-C-4.6-c1-cut.mrc (#100) using 2886 atoms average map value = 0.01205, steps = 268 shifted from previous position = 3.91 rotated from previous position = 24.7 degrees atoms outside contour = 1208, contour level = 0.011 Position of gp17-shaft-full-right.pdb (#107) relative to shaft-C-4.6-c1-cut.mrc (#100) coordinates: Matrix rotation and translation -0.36507994 0.18551431 -0.91230543 412.71672054 -0.29347167 0.90705012 0.30188507 184.92295630 0.88351071 0.37794795 -0.27670259 75.21949736 Axis 0.04089066 -0.96541320 -0.25749818 Axis point 200.19679794 0.00000000 160.94842252 Rotation angle (degrees) 111.55327465 Shift along axis -181.01968607 > select clear > select #107 2886 atoms, 2922 bonds, 1 model selected > ui mousemode rightMode ""rotate selected models"" > fitmap #107 inMap #100 Fit molecule gp17-shaft-full-right.pdb (#107) to map shaft-C-4.6-c1-cut.mrc (#100) using 2886 atoms average map value = 0.01205, steps = 92 shifted from previous position = 0.348 rotated from previous position = 5.15 degrees atoms outside contour = 1199, contour level = 0.011 Position of gp17-shaft-full-right.pdb (#107) relative to shaft-C-4.6-c1-cut.mrc (#100) coordinates: Matrix rotation and translation -0.35647978 0.17524692 -0.91772044 414.65031055 -0.27522767 0.91896846 0.28239480 182.61820863 0.89284492 0.35325007 -0.27936086 79.40951598 Axis 0.03794919 -0.96971612 -0.24126854 Axis point 198.19244484 -0.00000000 166.34318212 Rotation angle (degrees) 111.00418063 Shift along axis -180.51119438 > select clear > view J6 > hide #!97 models > hide #!95 models > hide #!34 models > show #!34 models > hide #!69 models > show #!69 models > hide #!68 models > open > /data/disk3/modeling/gp11-gp12-gp17-new-2020/gp17_cycle00_real_space_refined.pdb Chain information for gp17_cycle00_real_space_refined.pdb #108 --- Chain | Description C E F | No description available > hide #108 models > show #108 models > hide #!69 models > show #!69 models > matchmaker #108 to #69 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp17-refined-good.pdb, chain B (#69) with gp17_cycle00_real_space_refined.pdb, chain C (#108), sequence alignment score = 526 RMSD between 111 pruned atom pairs is 0.952 angstroms; (across all 116 pairs: 1.063) > view J6 > hide #!69 models > select #108 2787 atoms, 2829 bonds, 1 model selected > show #!69 models > hide #!69 models > show sel surfaces > color #108:96-120 #44CCCC > color #108:74-95 pink > select clear > show #!17 models > hide #!17 models > show #!17 models > fitmap #108 inMap #17 Fit molecule gp17_cycle00_real_space_refined.pdb (#108) to map nochan-new- fiber.mrc (#17) using 2787 atoms average map value = 0.1912, steps = 64 shifted from previous position = 6.84 rotated from previous position = 5.01 degrees atoms outside contour = 340, contour level = 0.067399 Position of gp17_cycle00_real_space_refined.pdb (#108) relative to nochan-new- fiber.mrc (#17) coordinates: Matrix rotation and translation -0.71944904 -0.69452681 -0.00505747 305.11209213 -0.69136290 0.71682988 -0.09040054 19.41620194 0.06641095 -0.06154203 -0.99589265 500.58704096 Axis 0.37410626 -0.92647841 0.04101527 Axis point 151.31406158 0.00000000 253.44548729 Rotation angle (degrees) 177.78955720 Shift along axis 116.68736621 > hide #107 models > hide #!100 models > transparency #17 30 > save image /data/disk3/Paper-use/Figure4-20200514-10.tif pixelSize 0.1 > supersample 3 transparentBackground true > hide #!34 models > show #!34 models > hide #!17 models > view name J8 > fitmap #94 inMap #1 Fit map fiber-6-fromtail-clean-link-C1.mrc in map nochan-new-trim- gp17-c1-short.mrc using 664 points correlation = 0.9588, correlation about mean = 0.08613, overlap = 1.645 steps = 252, shift = 28.1, angle = 111 degrees Position of fiber-6-fromtail-clean-link-C1.mrc (#94) relative to nochan-new- trim-gp17-c1-short.mrc (#1) coordinates: Matrix rotation and translation -0.21654387 0.97263279 0.08422717 -314.89959974 0.73244650 0.10481502 0.67270792 -232.88374737 0.64546950 0.20736267 -0.73509853 252.05197211 Axis -0.60622434 -0.73115341 -0.31290053 Axis point -107.35239874 0.00000000 156.24074184 Rotation angle (degrees) 157.43035619 Shift along axis 282.30635056 > view J8 > select #94 2 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > view J7 > view J6 > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > view J6 > ui mousemode rightMode ""translate selected models"" > view J6 > hide #!94 models > show #!94 models > view J7 > view J7 > hide #!108 models > show #!108 models > hide #!108 models > show #!108 models > fitmap #108 inMap #94 Fit molecule gp17_cycle00_real_space_refined.pdb (#108) to map fiber-6-fromtail-clean-link-C1.mrc (#94) using 2787 atoms average map value = 0.001075, steps = 224 shifted from previous position = 13.1 rotated from previous position = 9.66 degrees atoms outside contour = 2614, contour level = 0.0076162 Position of gp17_cycle00_real_space_refined.pdb (#108) relative to fiber-6-fromtail-clean-link-C1.mrc (#94) coordinates: Matrix rotation and translation 0.49194187 0.08724896 0.86624524 -186.27023198 -0.42673686 0.89141517 0.15256036 200.67904219 -0.75887341 -0.44470960 0.47575679 270.80705413 Axis -0.33069969 0.89980457 -0.28458647 Axis point 223.29305107 0.00000000 282.96425381 Rotation angle (degrees) 64.56055610 Shift along axis 165.10340288 > view J8 > view J7 > view J6 > volume #1 color #2cd5cc > volume #1 color #ffffff4c > view J8 > view J8 > view J7 > view J6 > view J8 > view J5 > view J6 > show #!96 models > hide #!96 models > show #!92 models > hide #!92 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > view J6 > view J8 > view J7 > show #!17 models > hide #!17 models > show #!54 models > hide #!54 models > show #!55 models > volume #55 level 0.0008263 > volume #55 step 1 > volume #55 level 0.0008976 > volume #55 color #ffffff4c > view J6 > view J1 > view J4 > view J6 > view J7 > show #!81 models > hide #!81 models > show #!9 models > hide #!9 models > show #!17 models > hide #!17 models > show #!17 models > select #17 2 models selected > hide #!17 models > hide #17.1 models > show #17.1 models > hide #!17 models > show #!17 models > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs > hide #!1 models > show #!1 models > hide #!34 models > hide #!26 models > hide #!108 models > view J7 > open /data/disk3/modeling/gp17-2020/free-fiber-C1.mrc Opened free-fiber-C1.mrc, grid size 360,360,360, pixel 1.05, shown at level 9.98e-07, step 2, values float32 > hide #!67.2 models > hide #!67.1 models > show #!67.2 models > hide #!67.2 models > hide #!67 models > hide #!109 models > show #!109 models > select #109 2 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > volume #109 level 0.001403 > volume #109 step 1 > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > show #!92 models > hide #!92 models > show #!91 models > hide #!91 models > show #!91 models > fitmap #109 inMap #91 Fit map free-fiber-C1.mrc in map shaft-C-4.6-c6.mrc using 23884 points correlation = 0, correlation about mean = 0, overlap = 0 steps = 84, shift = 15.4, angle = 19.7 degrees Position of free-fiber-C1.mrc (#109) relative to shaft-C-4.6-c6.mrc (#91) coordinates: Matrix rotation and translation 0.00139109 0.73296791 0.68026175 154.49950216 -0.57282837 -0.55700999 0.60133810 450.86289091 0.81967412 -0.39050974 0.41908996 155.59587546 Axis -0.60269351 -0.08471353 -0.79346339 Axis point 160.08955027 216.81081922 0.00000000 Rotation angle (degrees) 124.62929111 Shift along axis -254.76966471 > hide #!91 models > volume #109 level 0.005456 > show #!97 models > hide #!97 models > show #!86 models > hide #!86 models > show #!89 models > hide #!89 models > close #109 > open /data/disk3/modeling/gp17-2020/free-fiber-C1.mrc Opened free-fiber-C1.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > toolshed show ""Side View"" > open /data/disk3/modeling/gp17-2020/free-fiber-C1.mrc Opened free-fiber-C1.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > volume #109 level 0.0001,0 level 9.001e-05,0.8 level 0,1 > volume #110 region 0,0,0,679,679,679 step 4 > volume #110 region 0,0,0,679,679,679 step 4 > volume #110 change image level 0.0001,0 level 9.001e-05,0.8 level 0,1 > volume #110 level 0.002883 > select #110 3 models selected > ui mousemode rightMode ""rotate selected models"" > volume #110 step 1 > volume #110 level 0.002337 > open /data/disk3/modeling/gp17-2020/free-fiber-C1.mrc Opened free-fiber-C1.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > volume #109 region 0,0,0,679,679,679 step 4 > volume #109 region 0,0,0,679,679,679 step 4 > volume #109 step 1 > volume #109 change image level -2.414e-22,0 level 4.588e-19,0.8 level > 4.59e-18,1 > volume #109 level 0.002555 > select #109 3 models selected > ui mousemode rightMode ""rotate selected models"" > volume #109 level 0.0006767 > ui mousemode rightMode ""translate selected models"" > lighting flat > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > volume #109 level 0.001278 > hide #!17 models > show #!17 models > hide #!17 models > show #!27 models > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > hide #!27 models > show #!10 models > fitmap #109 inMap #10 Fit map free-fiber-C1.mrc in map fiber-c6-flip-trim.mrc using 94402 points correlation = 0.9888, correlation about mean = 0.9274, overlap = 2.64 steps = 176, shift = 13.5, angle = 17.4 degrees Position of free-fiber-C1.mrc (#109) relative to fiber-c6-flip-trim.mrc (#10) coordinates: Matrix rotation and translation 0.99999884 -0.00018523 0.00153708 -0.36970164 0.00018436 0.99999985 0.00055040 -0.27833222 -0.00153718 -0.00055011 0.99999868 0.83609747 Axis -0.33489358 0.93551978 0.11246791 Axis point 546.81189732 0.00000000 250.21720667 Rotation angle (degrees) 0.09414132 Shift along axis -0.04254046 > hide #!10 models > select clear > show #!108 models > hide #!108 models > show #!108 models > show #!1 models > show #!62 models > hide #!62 models > show #!69 models > hide #!69 models > show #!69 models > hide #!108 models > hide #!109 models > show #!109 models > hide #!109 models > hide #!1 models > show #!1 models > show #!108 models > show #!109 models > hide #!108 models > hide #!69 models > show #!69 models > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs > hide #!69 models > show #!69 models > hide #!109 models > show #!108 models > hide #!108 models > hide #!1 models > select #69 2787 atoms, 2829 bonds, 1 model selected > show sel surfaces > hide #!69 models > show #!69 models > hide #69.1 models > show #69.1 models > hide #69.3 models > show #69.3 models > show #!1 models > show #!108 models > show #!109 models > matchmaker #69 to #108 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp17_cycle00_real_space_refined.pdb, chain C (#108) with gp17-refined-good.pdb, chain B (#69), sequence alignment score = 526 RMSD between 111 pruned atom pairs is 0.952 angstroms; (across all 116 pairs: 1.063) > hide #!108 models > show #!108 models > hide #!108 models > hide #!109 models > show #!109 models > show #!108 models > hide #!108 models > hide #!1 models > hide #!109 models > show #!109 models > fitmap #69 inMap #109 Fit molecule gp17-refined-good.pdb (#69) to map free-fiber-C1.mrc (#109) using 2787 atoms average map value = 0.004, steps = 96 shifted from previous position = 5.41 rotated from previous position = 7.91 degrees atoms outside contour = 627, contour level = 0.0012778 Position of gp17-refined-good.pdb (#69) relative to free-fiber-C1.mrc (#109) coordinates: Matrix rotation and translation 0.82760955 -0.26266447 -0.49605415 437.65948765 0.54514984 0.58663312 0.59889331 143.11501459 0.13369382 -0.76607370 0.62869470 268.99035291 Axis -0.79984436 -0.36902017 0.47336361 Axis point 0.00000000 415.81491740 217.81756995 Rotation angle (degrees) 58.56917929 Shift along axis -275.54155529 > lighting flat > ui mousemode rightMode ""rotate selected models"" > fitmap #69 inMap #109 Fit molecule gp17-refined-good.pdb (#69) to map free-fiber-C1.mrc (#109) using 2787 atoms average map value = 0.004188, steps = 116 shifted from previous position = 3.21 rotated from previous position = 21 degrees atoms outside contour = 478, contour level = 0.0012778 Position of gp17-refined-good.pdb (#69) relative to free-fiber-C1.mrc (#109) coordinates: Matrix rotation and translation -0.20593789 -0.73229163 0.64910589 494.21981877 0.95668599 -0.29014663 -0.02380817 365.85024705 0.20577043 0.61608753 0.76032537 -46.20041028 Axis 0.34407678 0.23838485 0.90817610 Axis point 138.14702317 346.23057688 -0.00000000 Rotation angle (degrees) 111.58490511 Shift along axis 215.30461138 > matchmaker #108 to #69 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker gp17-refined-good.pdb, chain B (#69) with gp17_cycle00_real_space_refined.pdb, chain C (#108), sequence alignment score = 526 RMSD between 111 pruned atom pairs is 0.952 angstroms; (across all 116 pairs: 1.063) > show #!108 models > fitmap #108 inMap #1 Fit molecule gp17_cycle00_real_space_refined.pdb (#108) to map nochan-new- trim-gp17-c1-short.mrc (#1) using 2787 atoms average map value = 0.1813, steps = 52 shifted from previous position = 5.27 rotated from previous position = 6.65 degrees atoms outside contour = 435, contour level = 0.056916 Position of gp17_cycle00_real_space_refined.pdb (#108) relative to nochan-new- trim-gp17-c1-short.mrc (#1) coordinates: Matrix rotation and translation -0.16522467 0.80677202 0.56729158 -289.82076006 -0.01977205 0.57237196 -0.81975571 159.48415871 -0.98605775 -0.14666038 -0.07861843 489.22967694 Axis 0.35728586 0.82453366 -0.43873802 Axis point -5.28012506 0.00000000 382.45879374 Rotation angle (degrees) 109.61727403 Shift along axis -186.69246237 > hide #!108 models > show #!108 models > hide #!109 models > show #!109 models > hide #!108 models > lighting soft > view name J10 > select clear > volume #109 level 0.002236 > volume #109 level 0.001672 > volume #109 level 0.001278 > volume #109 level 0.00124 > view J10 > view name J11 > view J10 > save image /data/disk3/Paper-use/Figure4-20200514-A1.tif pixelSize 0.1 > supersample 3 transparentBackground true > hide #!109 models > show #!108 models > hide #!69 models > show #!1 models > hide #69.3 models > hide #!108 models > show #!69 models > volume #94 step 1 > volume #1 level 0.0554 > volume #1 color #ffffff4c > show #69.3 models > save image /data/disk3/Paper-use/Figure4-20200514-A2.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!101 models > hide #!101 models > show #!101 models > hide #!101 models > show #!104 models > hide #!104 models > show #!103 models > hide #!103 models > show #!102 models > hide #!102 models > show #!101 models > hide #!101 models > show #!105 models > show #!100 models > hide #!105 models > show #!101 models > hide #!101 models > show #!101 models > hide #!101 models > show #!101 models > show #!102 models > show #!103 models > show #!104 models > show #!105 models > hide #!100 models > show #!100 models > hide #!100 models > hide #!101 models > hide #!102 models > hide #!103 models > hide #!104 models > hide #!105 models > hide #!90 models > show #!90 models > show #!108 models > hide #!108 models > show #!108 models > show #!109 models > hide #!108 models > select #108 2787 atoms, 2829 bonds, 1 model selected > show #!108 models > hide #!108 models > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs > show #!108 models > hide #!108 models > show #!108 models > hide #!109 models > hide #!69 models > show #!69 models > hide #!69 models > show #!69 models > hide #!69 models > show #!69 models > hide #!69 models > show #!69 models > hide #!108 models > show #!108 models > show #!109 models > hide #!69 models > show #!69 models > hide #!108 models > show #!108 models > hide #!108 models > hide #!109 models > show #!109 models > hide #!109 models > show #!108 models > hide #!108 models > show #!108 models > hide #!108 models > show #!108 models > hide #!108 models > show #!109 models > show #!97 models > hide #!97 models > show #!97 models > fitmap #97 inMap #92 Fit map fiber-6-fromtail-clean-link-C1.mrc in map fiber-5.4-seg-c6.mrc using 5406 points correlation = 0.8479, correlation about mean = 0.2135, overlap = 0.4846 steps = 48, shift = 0.00923, angle = 0.0319 degrees Position of fiber-6-fromtail-clean-link-C1.mrc (#97) relative to fiber-5.4-seg-c6.mrc (#92) coordinates: Matrix rotation and translation 0.21628094 0.60261668 -0.76816385 225.35643588 -0.96262041 0.00022601 -0.27085400 569.15151662 -0.16304752 0.79803076 0.58014000 -79.80942989 Axis 0.53722655 -0.30413434 -0.78669558 Axis point 413.95329284 173.98181280 0.00000000 Rotation angle (degrees) 95.83572035 Shift along axis 10.75466726 > hide #!109 models > show #!109 models > hide #!1 models > show #!95 models > fitmap #95 inMap #92 Fit map shaft-C-4.6.mrc in map fiber-5.4-seg-c6.mrc using 70731 points correlation = 0.9157, correlation about mean = 0.5212, overlap = 14.35 steps = 44, shift = 0.0392, angle = 0.0383 degrees Position of shaft-C-4.6.mrc (#95) relative to fiber-5.4-seg-c6.mrc (#92) coordinates: Matrix rotation and translation -0.19604015 0.03454125 -0.97998730 437.19127359 0.00062180 0.99938357 0.03510051 160.37128780 0.98059565 0.00627176 -0.19594080 122.15269742 Axis -0.01470039 -0.99974234 -0.01729624 Axis point 168.53987427 0.00000000 237.88916305 Rotation angle (degrees) 101.32059982 Shift along axis -168.86962900 > hide #!95 models > show #!70 models > hide #!70 models > show #!70 models > select #70 2787 atoms, 2829 bonds, 1 model selected > fitmap #70 inMap #92 Fit molecule gp17_real_space_refined-coot-4.pdb (#70) to map fiber-5.4-seg-c6.mrc (#92) using 2787 atoms average map value = 0.006346, steps = 88 shifted from previous position = 5.37 rotated from previous position = 1.69 degrees atoms outside contour = 1268, contour level = 0.002996 Position of gp17_real_space_refined-coot-4.pdb (#70) relative to fiber-5.4-seg-c6.mrc (#92) coordinates: Matrix rotation and translation -0.86091270 0.50788871 0.02963773 424.84172141 -0.50828642 -0.86115651 -0.00737465 643.84806886 0.02177722 -0.02141339 0.99953351 27.36641270 Axis -0.01381354 0.00773442 -0.99987467 Axis point 300.16227920 264.08212689 0.00000000 Rotation angle (degrees) 149.45923624 Shift along axis -28.25176151 > hide #!70 models > show #!70 models > hide #!70 models > show #!70 models > hide #!70 models > close #70 > show #!71 models > hide #!71 models > show #!71 models > fitmap #71 inMap #92 Fit molecule gp17_real_space_refined-coot-4-c6.pdb (#71) to map fiber-5.4-seg-c6.mrc (#92) using 16722 atoms average map value = 0.006028, steps = 76 shifted from previous position = 2.41 rotated from previous position = 1.36 degrees atoms outside contour = 7984, contour level = 0.002996 Position of gp17_real_space_refined-coot-4-c6.pdb (#71) relative to fiber-5.4-seg-c6.mrc (#92) coordinates: Matrix rotation and translation -0.84616000 0.53290997 -0.00449530 423.41401875 -0.53292617 -0.84609842 0.01035045 644.99482400 0.00171239 0.01115380 0.99993632 28.11846062 Axis 0.00075372 -0.00582415 -0.99998276 Axis point 304.78730585 261.29804255 0.00000000 Rotation angle (degrees) 147.79654753 Shift along axis -31.55538840 > hide #!71 models > save image /data/disk3/Paper-use/Figure4-20200514-A1.tif pixelSize 0.1 > supersample 3 transparentBackground true > select #97 2 models selected > ui mousemode rightMode ""translate selected models"" > fitmap #97 inMap #92 Fit map fiber-6-fromtail-clean-link-C1.mrc in map fiber-5.4-seg-c6.mrc using 5406 points correlation = 0.8479, correlation about mean = 0.2135, overlap = 0.4846 steps = 88, shift = 7.04, angle = 12 degrees Position of fiber-6-fromtail-clean-link-C1.mrc (#97) relative to fiber-5.4-seg-c6.mrc (#92) coordinates: Matrix rotation and translation 0.21639546 0.60305635 -0.76778646 225.14300036 -0.96256676 0.00031634 -0.27104450 569.15919342 -0.16321223 0.79769853 0.58055046 -79.77927727 Axis 0.53713836 -0.30385229 -0.78686477 Axis point 413.90369154 174.07624366 0.00000000 Rotation angle (degrees) 95.81800153 Shift along axis 10.76812333 > select clear > show #107 models > hide #107 models > show #107 models > hide #107 models > show #!89 models > hide #!89 models > show #!68 models > fitmap #68 inMap #92 Fit molecule gp17-shaft-full-right.pdb (#68) to map fiber-5.4-seg-c6.mrc (#92) using 2886 atoms average map value = 0.009752, steps = 68 shifted from previous position = 1.84 rotated from previous position = 0.201 degrees atoms outside contour = 741, contour level = 0.002996 Position of gp17-shaft-full-right.pdb (#68) relative to fiber-5.4-seg-c6.mrc (#92) coordinates: Matrix rotation and translation -0.19306896 0.01797353 -0.98102056 440.92451515 0.01824718 0.99972506 0.01472510 160.82443250 0.98101550 -0.01505790 -0.19334385 127.73475631 Axis -0.01517789 -0.99988480 0.00013946 Axis point 166.71616013 0.00000000 244.11174499 Rotation angle (degrees) 101.14799363 Shift along axis -167.48039563 > fitmap #68 inMap #109 Fit molecule gp17-shaft-full-right.pdb (#68) to map free-fiber-C1.mrc (#109) using 2886 atoms average map value = 0.004709, steps = 308 shifted from previous position = 42.3 rotated from previous position = 9.63 degrees atoms outside contour = 503, contour level = 0.0012402 Position of gp17-shaft-full-right.pdb (#68) relative to free-fiber-C1.mrc (#109) coordinates: Matrix rotation and translation -0.03199957 0.87514369 0.48280375 146.36188321 0.08918726 -0.47862394 0.87347851 357.30940126 0.99550069 0.07101089 -0.06273592 54.34846318 Axis -0.64991733 -0.41523249 -0.63654493 Axis point 0.00000000 99.29127264 -108.78926909 Rotation angle (degrees) 141.87630089 Shift along axis -278.08483340 > show #!108 models > hide #!108 models > show #!1 models > show #!89 models > hide #!89 models > show #107 models > fitmap #107 inMap #1 Fit molecule gp17-shaft-full-right.pdb (#107) to map nochan-new-trim- gp17-c1-short.mrc (#1) using 2886 atoms average map value = 0.1817, steps = 256 shifted from previous position = 57.3 rotated from previous position = 26.9 degrees atoms outside contour = 429, contour level = 0.055398 Position of gp17-shaft-full-right.pdb (#107) relative to nochan-new-trim- gp17-c1-short.mrc (#1) coordinates: Matrix rotation and translation -0.83887173 -0.17162536 -0.51656472 190.71825093 -0.52998756 0.04111938 0.84700797 -33.05706746 -0.12412722 0.98430385 -0.12545319 86.90437586 Axis 0.25013343 -0.71496496 -0.65288466 Axis point 80.14083924 0.00000000 76.84865895 Rotation angle (degrees) 164.07104231 Shift along axis 14.60112165 > show #!102 models > show #!101 models > show #!100 models > hide #!100 models > hide #!101 models > hide #!102 models > select #107 2886 atoms, 2922 bonds, 1 model selected > select clear Drag select of 114 residues > hide sel cartoons > select #107 2886 atoms, 2922 bonds, 1 model selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" Drag select of 43 residues, 109 free-fiber-C1.mrc > select clear Drag select of 28 residues Drag select of 22 residues > hide sel cartoons Drag select of 19 residues > hide sel cartoons Drag select of 1 residues, 109 free-fiber-C1.mrc > select clear > select clear > fitmap #107 inMap #1 Fit molecule gp17-shaft-full-right.pdb (#107) to map nochan-new-trim- gp17-c1-short.mrc (#1) using 2886 atoms average map value = 0.1822, steps = 132 shifted from previous position = 59.2 rotated from previous position = 11 degrees atoms outside contour = 426, contour level = 0.055398 Position of gp17-shaft-full-right.pdb (#107) relative to nochan-new-trim- gp17-c1-short.mrc (#1) coordinates: Matrix rotation and translation -0.84225433 -0.13285118 -0.52245416 184.00319139 -0.53898500 0.18928569 0.82077173 -59.58758927 -0.01014740 0.97289343 -0.23103147 88.83844089 Axis 0.22663272 -0.76324071 -0.60506300 Axis point 70.80722383 0.00000000 88.01233932 Rotation angle (degrees) 160.39019237 Shift along axis 33.42796418 > select #107 2886 atoms, 2922 bonds, 1 model selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > select clear > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs > hide #107 models > hide #!109 models > show #!109 models > hide #!109 models > open /data/disk3/modeling/gp17/fiber-6-fromtail-clean-link-C1.mrc Opened fiber-6-fromtail-clean-link-C1.mrc, grid size 400,400,400, pixel 1.05, shown at level 9.12e-07, step 2, values float32 > select #70 2 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > volume #70 level 0.007414 > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > hide #!97 models > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > volume #70 step 1 > fitmap #70 inMap #1 Fit map fiber-6-fromtail-clean-link-C1.mrc in map nochan-new-trim- gp17-c1-short.mrc using 5599 points correlation = 0.9579, correlation about mean = 0.0551, overlap = 13.65 steps = 96, shift = 11.7, angle = 55.2 degrees Position of fiber-6-fromtail-clean-link-C1.mrc (#70) relative to nochan-new- trim-gp17-c1-short.mrc (#1) coordinates: Matrix rotation and translation 0.36091389 -0.86661750 -0.34455069 164.59863348 0.78075595 0.07871174 0.61985850 -219.73489364 -0.51006006 -0.49272557 0.70502497 328.08228260 Axis -0.55775276 0.08297198 0.82584957 Axis point 344.81018145 39.21328111 0.00000000 Rotation angle (degrees) 85.85244404 Shift along axis 160.90943096 > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > show #107 models > select #107 2886 atoms, 2922 bonds, 1 model selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > select #70 2 models selected > ui mousemode rightMode ""rotate selected models"" > ui mousemode rightMode ""translate selected models"" > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs > select clear > volume #70 color #2cd5cc > volume #70 color #4096bf > volume #70 color #2cd5cc > volume #70 color #40bfbf > volume #70 color #44cccc > show #!97 models > hide #107 models > show #107 models > show #!109 models > hide #107 models > hide #!109 models > show #!109 models > hide #!1 models > hide #!70 models > view name J10 > save image /data/disk3/Paper-use/Figure4-20200514-A1.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!1 models > hide #!109 models > show #!109 models > hide #!1 models > view J10 > lighting full > lighting full > save image /data/disk3/Paper-use/Figure4-20200514-A1.tif pixelSize 0.1 > supersample 3 transparentBackground true > view name J10 > save image /data/disk3/Paper-use/Figure4-20200514-A1.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!108 models > hide #!108 models > show #!108 models > hide #!108 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!109 models Drag select of 16 residues > hide sel cartoons > show #!109 models > hide #!109 models > show #!70 models > show #107 models > hide #!1 models Drag select of 39 residues > hide sel cartoons Drag select of 2 residues > hide sel cartoons > show #!1 models Drag select of 2 residues Drag select of 5 residues > hide sel cartoons > select #68/B:260 9 atoms, 8 bonds, 1 model selected > hide sel cartoons > show #!11 models > hide #!11 models > show #!109 models > view J10 > hide #!109 models > show #!109 models > hide #!1 models > hide #107 models > hide #!70 models > view J11 > view J10 > lighting flat > view J10 > select clear > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs > lighting soft > hide #!109 models > show #!109 models > transparency #109 70 > transparency #109 80 > transparency #109 90 > lighting soft > lighting full > view J10 > save image /data/disk3/Paper-use/Figure4-20200514-A1.tif pixelSize 0.1 > supersample 3 transparentBackground true > hide #!109 models > show #!108 models > hide #!97 models > show #!94 models > hide #!69 models > hide #!108 models > show #!108 models > show #107 models > hide #107 models > show #107 models > view name J11 > fitmap #107 inMap #1 Fit molecule gp17-shaft-full-right.pdb (#107) to map nochan-new-trim- gp17-c1-short.mrc (#1) using 2886 atoms average map value = 0.1824, steps = 144 shifted from previous position = 72.1 rotated from previous position = 13.9 degrees atoms outside contour = 417, contour level = 0.055398 Position of gp17-shaft-full-right.pdb (#107) relative to nochan-new-trim- gp17-c1-short.mrc (#1) coordinates: Matrix rotation and translation -0.84220659 -0.08996679 -0.53159588 175.94842368 -0.52662414 0.34860865 0.77533164 -88.81898455 0.11556482 0.93294057 -0.34097916 95.82858825 Axis 0.19789014 -0.81256006 -0.54825691 Axis point 61.09582678 0.00000000 98.98886229 Rotation angle (degrees) 156.53284560 Shift along axis 54.45053220 > view J11 > hide #!68 models > show #!109 models > hide #!109 models > show #!109 models > show #!1 models > hide #!109 models > lighting soft > transparency #1 90 > save image /data/disk3/Paper-use/Figure4-20200514-A2.tif pixelSize 0.1 > supersample 3 transparentBackground true > save image /data/disk3/Paper-use/Figure4-20200514-A3.tif pixelSize 0.1 > supersample 3 transparentBackground true > hide #!108 models > hide #107 models > show #!109 models > hide #!70 models > view name J12 > view J11 > hide #!109 models > show #!109 models > volume #1 level 0.06829 > volume #109 level 0.001653 > volume #109 level 0.002086 > volume #109 color #ffffff4c > volume #109 color #ffffff19 > volume #109 color #ffffff4c > volume #109 color #44cccc > volume #109 color #ffffff4c > show #!108 models > hide #!108 models > show #!69 models > save image /data/disk3/Paper-use/Figure4-20200514-A3.tif pixelSize 0.1 > supersample 3 transparentBackground true > hide #!109 models > show #!108 models > hide #!69 models > show #!1 models > volume #1 level 0.05843 > save image /data/disk3/Paper-use/Figure4-20200514-A4.tif pixelSize 0.1 > supersample 3 transparentBackground true > show #!70 models > save image /data/disk3/Paper-use/Figure4-20200514-A5.tif pixelSize 0.1 > supersample 3 transparentBackground true > hide #!70 models > hide #!1 models > hide #!94 models > hide #!108 models > show #!109 models > show #107 models > hide #107 models > show #!69 models > show #107 models > hide #107 models > fitmap #94 inMap #109 Fit map fiber-6-fromtail-clean-link-C1.mrc in map free-fiber-C1.mrc using 5271 points correlation = 0.9144, correlation about mean = 0.1405, overlap = 0.2745 steps = 144, shift = 12.2, angle = 18.2 degrees Position of fiber-6-fromtail-clean-link-C1.mrc (#94) relative to free- fiber-C1.mrc (#109) coordinates: Matrix rotation and translation 0.86388881 0.19657941 0.46373761 146.33764130 -0.47729758 0.02541986 0.87837396 313.93790623 0.16088210 -0.98015832 0.11578682 449.74173981 Axis -0.92926917 0.15142825 -0.33693959 Axis point 0.00000000 367.87790094 9.39038982 Rotation angle (degrees) 89.85402500 Shift along axis -239.98379087 > view J11 > show #!70 models > hide #!70 models > show #!97 models > save image /data/disk3/Paper-use/Figure4-20200514-A6.tif pixelSize 0.1 > supersample 3 transparentBackground true > save session /data/disk3/modeling/gp17-2020/Figure4-20200514-fiber-ET-color- > change.cxs An error occurred in drawing the scene. Redrawing graphics is now stopped to avoid a continuous stream of error messages. To restart graphics use the command ""graphics restart"" after changing the settings that caused the error. Traceback (most recent call last): File ""/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site- packages/chimerax/core/updateloop.py"", line 73, in draw_new_frame view.draw(check_for_changes = False) File ""/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 166, in draw self._draw_scene(camera, drawings) File ""/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site- packages/chimerax/core/graphics/view.py"", line 239, in _draw_scene silhouette.draw_silhouette(r) File ""/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 1668, in draw_silhouette fb.attach_depth_texture(None) # Detach depth texture File ""/home/cwang/software/chimerax-2020.03.05/lib/python3.7/site- packages/chimerax/core/graphics/opengl.py"", line 2038, in attach_depth_texture tid, level) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1282, description = b'invalid operation', baseOperation = glFramebufferTexture2D, cArguments = ( GL_FRAMEBUFFER, GL_DEPTH_ATTACHMENT, GL_TEXTURE_2D, 0, 0, ) ) OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K2200/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation }}} " defect closed normal Graphics 0.92 can't reproduce all ChimeraX