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Opened 5 years ago
Closed 5 years ago
#3212 closed defect (can't reproduce)
Drawing silhouette: glFramebufferTexture2D: invalid operation
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | 0.92 |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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
Change History (2)
comment:1 by , 5 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Drawing silhouette: glFramebufferTexture2D: invalid operation |
| Version: | → 0.92 |
comment:2 by , 5 years ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
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OpenGL InvalidOperation error in glFramebufferTexture2D when drawing silhouettes. OpenGL docs say this can be caused by
GL_INVALID_OPERATION is generated if the default framebuffer object name 0 is bound.
GL_INVALID_OPERATION is generated if texture is neither 0 nor the name of an existing texture object.
GL_INVALID_OPERATION is generated if texture is the name of an existing two-dimensional texture object but textarget is not GL_TEXTURE_2D or if texture is the name of an existing cube map texture object but textarget is GL_TEXTURE_2D.
The texture id is 0 in this call, removing the depth texture so the second two causes for the error can be ruled out. An offscreen framebuffer has been enabled that seems to rule out cause 1, although some incorrect code could have popped that framebuffer.
Possible graphics driver bug. Have seen several reports with Quadro K2200 (might be this same user).
No other bug reports with glFramebufferTexture2D.