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Opened 6 years ago
Closed 6 years ago
#2705 closed defect (duplicate)
Problem with item chooser
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | General Controls | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Linux-4.4.0-170-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-29) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 0.91 (2019-06-29) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /data/disk3/modeling/gp17/Figure4-20191221.cxs opened ChimeraX session > hide #!4 models > hide #!5 models > hide #!21 models > hide #!22 models > show #!5 models > show #!3 models > show #!1 models > hide #!5 models > open /data/disk3/modeling/gp17/tail-fiber-c6-refined.mrc Opened tail-fiber-c6-refined.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > hide #!1 models > hide #!3 models > hide #!7 models > lighting soft > lighting flat > view cofr false > view cofr false > view cofr false > lighting simple > lighting soft > lighting soft > lighting full > lighting shadows false > show #!26 models > show #!27 models > show #!58 models > select #7 3 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" > hide #!7 models > select #7 3 models selected > select #7 3 models selected > close #7 > open /data/disk3/modeling/gp17/tail-fiber-c6-refined.mrc Opened tail-fiber-c6-refined.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > select #7 3 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 "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!27 models > show #!27 models > hide #!27 models > hide #!7 models > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > surface dust #58 size 50 > show #!7 models > hide #!7 models > show #!7 models > hide #!58 models > show #!58 models > fitmap #7 inMap #58 Fit map tail-fiber-c6-refined.mrc in map gp17-trimer-clean.mrc using 1361379 points correlation = 0.229, correlation about mean = -0.05609, overlap = 18.41 steps = 148, shift = 9.55, angle = 5.3 degrees Position of tail-fiber-c6-refined.mrc (#7) relative to gp17-trimer-clean.mrc (#58) coordinates: Matrix rotation and translation -0.88536761 0.46487563 -0.00384924 151.45339527 -0.46478934 -0.88531620 -0.01364108 486.03485005 -0.00974920 -0.01028829 0.99989954 -233.02316843 Axis 0.00360635 0.00634617 -0.99997336 Axis point 135.03909156 223.71224110 0.00000000 Rotation angle (degrees) 152.29981718 Shift along axis 236.64761410 > fitmap #7 inMap #58 Fit map tail-fiber-c6-refined.mrc in map gp17-trimer-clean.mrc using 1361379 points correlation = 0.2289, correlation about mean = -0.05608, overlap = 18.41 steps = 40, shift = 0.0114, angle = 0.00266 degrees Position of tail-fiber-c6-refined.mrc (#7) relative to gp17-trimer-clean.mrc (#58) coordinates: Matrix rotation and translation -0.88535824 0.46489355 -0.00384024 151.43553282 -0.46480774 -0.88530716 -0.01360032 486.03401662 -0.00972250 -0.01025618 0.99990013 -233.05055126 Axis 0.00359691 0.00632687 -0.99997352 Axis point 135.03427558 223.71510666 0.00000000 Rotation angle (degrees) 152.29864647 Shift along axis 236.66415415 > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > view cofr false > lighting soft > lighting simple > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > lighting full > show #!10 models > hide #!10 models > show #!11 models > hide #!11 models > show #!11 models > hide #!11 models > show #!17 models > show #!23 models > hide #!23 models > show #!23 models > open /data/disk3/modeling/gp17/tail-fiber-c6-refined-trimmed.mrc Opened tail-fiber-c6-refined-trimmed.mrc, grid size 680,680,680, pixel 1.05, shown at step 1, values float32 > lighting flat > select #8 3 models selected > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > fitmap #8 inMap #7 Fit map tail-fiber-c6-refined-trimmed.mrc in map tail-fiber-c6-refined.mrc using 163050 points correlation = 0.7669, correlation about mean = 0.3559, overlap = 13.41 steps = 260, shift = 31.9, angle = 8.94 degrees Position of tail-fiber-c6-refined-trimmed.mrc (#8) relative to tail- fiber-c6-refined.mrc (#7) coordinates: Matrix rotation and translation -0.49699671 -0.86775171 0.00111265 845.79304017 0.86771276 -0.49696133 0.01019804 222.85387366 -0.00829642 0.00603385 0.99994738 0.71024093 Axis -0.00239943 0.00542155 0.99998242 Axis point 358.30681742 356.56356841 0.00000000 Rotation angle (degrees) 119.80207130 Shift along axis -0.11097515 > hide #!8 models > hide #!7 models > show #!8 models > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > lighting soft > lighting flat > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > toolshed show "Side View" > view cofr false > lighting full > lighting simple > lighting soft > lighting shadows true intensity 0.5 > hide #!8 models > show #!8 models > select #8 3 models selected > select #8 3 models selected > select clear > hide #!17 models > show #!17 models > surface dust #17 size 50 > surface dust #17 size 80 > lighting full > lighting soft > lighting simple > lighting shadows true > set silhouettes false > lighting flat > lighting full > lighting soft > lighting full > lighting simple > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting shadows false > lighting simple > lighting simple > lighting simple > lighting soft > lighting full > lighting flat > lighting shadows true intensity 0.5 > set silhouettes false > lighting soft > lighting simple > lighting simple > lighting full > lighting soft > lighting flat > lighting full > lighting simple > set silhouettes false > lighting shadows true > lighting flat > lighting full > lighting soft > lighting simple > lighting full > lighting flat > open /data/disk3/modeling/gp17/phage-adsorb.mrc Opened phage-adsorb.mrc, grid size 128,128,128, pixel 5.2, shown at level 0.0808, step 1, values float32 > select #9 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" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > hide #!9 models > show #!9 models > fitmap #9 inMap #17 Fit map phage-adsorb.mrc in map gp8-C12-clean.mrc using 20977 points correlation = 0.02429, correlation about mean = -0.03777, overlap = 0.1276 steps = 444, shift = 1.97, angle = 2.25 degrees Position of phage-adsorb.mrc (#9) relative to gp8-C12-clean.mrc (#17) coordinates: Matrix rotation and translation 0.08812352 -0.99556893 -0.03281414 201.51932427 0.99579619 0.08887423 -0.02216641 205.95304388 0.02498453 -0.03072281 0.99921564 242.72820939 Axis -0.00429490 -0.02901216 0.99956983 Axis point -14.99195209 217.16507431 0.00000000 Rotation angle (degrees) 84.94530416 Shift along axis 235.78314650 > lighting flat > ui mousemode rightMode "rotate selected models" > fitmap #9 inMap #17 Fit map phage-adsorb.mrc in map gp8-C12-clean.mrc using 20977 points correlation = 0.03839, correlation about mean = -0.02662, overlap = 0.2263 steps = 324, shift = 7.03, angle = 2.01 degrees Position of phage-adsorb.mrc (#9) relative to gp8-C12-clean.mrc (#17) coordinates: Matrix rotation and translation 0.22334184 -0.97415353 -0.03381334 200.82076044 0.97205963 0.22516448 -0.06634047 195.23675588 0.07223937 -0.01805198 0.99722395 246.54499408 Axis 0.02476716 -0.05439441 0.99821232 Axis point -33.53971331 226.77553479 0.00000000 Rotation angle (degrees) 77.12262809 Shift along axis 240.45822117 > lighting flat internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on mapped window > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate 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 "translate selected models" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > hide #!9 models > show #!9 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!17 models > show #!17 models > hide #!23 models > show #!23 models > fitmap #9 inMap #23 Fit map phage-adsorb.mrc in map gp12-new.mrc using 20977 points correlation = 0.4091, correlation about mean = 0.2015, overlap = 9.32 steps = 136, shift = 3.32, angle = 2.95 degrees Position of phage-adsorb.mrc (#9) relative to gp12-new.mrc (#23) coordinates: Matrix rotation and translation -0.94376386 0.33061783 0.00127941 2.19668870 -0.33061623 -0.94376437 0.00130872 0.99650521 0.00164015 0.00081213 0.99999832 36.46065053 Axis -0.00075101 -0.00054555 -0.99999957 Axis point 1.16770985 0.30381713 0.00000000 Rotation angle (degrees) 160.69376037 Shift along axis -36.46282820 > lighting flat > lighting soft > lighting flat > fitmap #9 inMap #23 Fit map phage-adsorb.mrc in map gp12-new.mrc using 20977 points correlation = 0.409, correlation about mean = 0.2014, overlap = 9.321 steps = 60, shift = 0.0032, angle = 0.00678 degrees Position of phage-adsorb.mrc (#9) relative to gp12-new.mrc (#23) coordinates: Matrix rotation and translation -0.94380270 0.33050697 0.00127217 2.19642900 -0.33050540 -0.94380321 0.00129557 0.99360947 0.00162888 0.00080231 0.99999834 36.46208797 Axis -0.00074623 -0.00053963 -0.99999958 Axis point 1.16740916 0.30254969 0.00000000 Rotation angle (degrees) 160.70048992 Shift along axis -36.46424774 > lighting flat > lighting soft > transparency #17 50 > transparency #17 0 > transparency #9 0 > transparency #9 60 > transparency #9 50 > transparency #9 30 > transparency #9 80 > transparency #9 50 > transparency #9 30 > transparency #9 40 > select clear > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > open /data/disk3/modeling/gp17/phage-adsorb-trimmed.mrc Opened phage-adsorb-trimmed.mrc, grid size 128,128,128, pixel 5.2, shown at level 0.0533, step 1, values float32 > view cofr false > select #12 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > hide #!12 models > show #!12 models > hide #!9 models > show #!9 models > fitmap #12 inMap #9 Fit map phage-adsorb-trimmed.mrc in map phage-adsorb.mrc using 20976 points correlation = 1, correlation about mean = 1, overlap = 651.7 steps = 68, shift = 9.42, angle = 4.6 degrees Position of phage-adsorb-trimmed.mrc (#12) relative to phage-adsorb.mrc (#9) coordinates: Matrix rotation and translation 0.99999996 -0.00020022 0.00002598 0.00201664 0.00020023 0.99999998 0.00004296 0.00321015 -0.00002598 -0.00004295 1.00000001 -0.06157352 Axis -0.20811395 0.12587071 0.96997173 Axis point -53.59419906 -52.01693056 0.00000000 Rotation angle (degrees) 0.01182710 Shift along axis -0.05974020 > hide #!9 models > close #9 > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > transparency #12 40 > lighting flat > lighting soft > transparency #12 40 > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > open /data/disk3/modeling/gp17/tail-fiber-c6-refined-trimmed-down.mrc Opened tail-fiber-c6-refined-trimmed-down.mrc, grid size 128,128,128, pixel 5.2, shown at level 0.000139, step 1, values float32 > view cofr false > select #9 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" > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > ~select #9 Nothing selected > select #9 2 models selected > ~select #9 Nothing selected > select #9 2 models selected > ~select #9 Nothing selected > select #9 2 models selected > ~select #9 Nothing selected > select #9 2 models selected > hide #!12 models > show #!12 models > fitmap #9 inMap #12 Fit map tail-fiber-c6-refined-trimmed-down.mrc in map phage-adsorb-trimmed.mrc using 20966 points correlation = 0.489, correlation about mean = 0.1292, overlap = 10.75 steps = 60, shift = 12.2, angle = 2.96 degrees Position of tail-fiber-c6-refined-trimmed-down.mrc (#9) relative to phage- adsorb-trimmed.mrc (#12) coordinates: Matrix rotation and translation 0.99999571 0.00293975 0.00009399 -0.00022331 -0.00293973 0.99999569 -0.00015517 -0.07305683 -0.00009445 0.00015489 1.00000000 0.03176600 Axis 0.05263735 0.03199048 -0.99810116 Axis point -24.48010217 -0.56981865 0.00000000 Rotation angle (degrees) 0.16875534 Shift along axis -0.03405455 > surface dust #9 size 50 > ~select #9 Nothing selected > select #9 2 models selected > hide #!9 models > show #!9 models > hide #!12 models > show #!12 models > surface dust #12 size 50 > hide #!9 models > show #!9 models > hide #!17 models > show #!17 models > hide #!17 models > hide #!58 models > show #!58 models > hide #!8 models > show #!17 models > show #!8 models > select clear > hide #!17 models > show #!17 models > hide #!9 models > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > hide #!8 models > show #!9 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!58 models > show #!58 models > save /data/disk3/modeling/gp17/fiber-6-clean.mrc models #23 > select #58 3 models selected > save /data/disk3/modeling/gp17/gp17-trimmer-clean.mrc models #58 > show #!10 models > select #10 19602 atoms, 19872 bonds, 1 pseudobond, 2 models selected > ~select #10 18 models selected > hide #!10 models > show #!5 models > hide #!5 models > hide #!9 models > show #!9 models > select #9 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "rotate selected models" > show #!8 models > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > hide #!8 models > show #!8 models > hide #!9 models > lighting soft > lighting simple > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting flat > lighting soft > lighting simple > lighting soft > lighting full > lighting shadows false > view name p1 > save image /data/disk3/Paper-use/Fiber-20191230.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Fiber-20191230-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!8 models > show #!9 models > select clear > open /data/disk3/modeling/gp17/gp17-trimmer-clean-trimmed.mrc Opened gp17-trimmer-clean-trimmed.mrc, grid size 400,400,400, pixel 1.05, shown at level 0.00448, step 2, values float32 > hide #!13 models > show #!13 models > select #13 2 models selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > lighting flat > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > fitmap #13 inMap #58 Fit map gp17-trimmer-clean-trimmed.mrc in map gp17-trimmer-clean.mrc using 7517 points correlation = 0.9917, correlation about mean = 0.8412, overlap = 2.293 steps = 224, shift = 23, angle = 8.55 degrees Position of gp17-trimmer-clean-trimmed.mrc (#13) relative to gp17-trimmer- clean.mrc (#58) coordinates: Matrix rotation and translation -0.49959562 0.86625877 0.00002396 -76.49091940 -0.86625874 -0.49959561 0.00021738 287.31213680 0.00020028 0.00008784 0.99999999 -209.61848724 Axis -0.00007477 -0.00010177 -0.99999999 Axis point 44.75312766 165.75514064 0.00000000 Rotation angle (degrees) 119.97324957 Shift along axis 209.59496559 > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > lighting soft > surface dust #13 size 50 > select clear > show #!58 models > hide #!58 models > show #!58 models > hide #!58 models > view p1 > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > save image /data/disk3/Paper-use/Fiber-20191230-2.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > hide #!9 models > show #!9 models > show #!12 models > fitmap #12 inMap #9 Fit map phage-adsorb-trimmed.mrc in map tail-fiber-c6-refined-trimmed-down.mrc using 20976 points correlation = 0.4382, correlation about mean = -0.0008006, overlap = 9.585 steps = 80, shift = 0.892, angle = 7.27 degrees Position of phage-adsorb-trimmed.mrc (#12) relative to tail-fiber-c6-refined- trimmed-down.mrc (#9) coordinates: Matrix rotation and translation 0.99999431 0.00334923 -0.00030272 -0.03008891 -0.00334923 0.99999437 0.00001783 0.08640328 0.00030278 -0.00001681 0.99999994 -0.20513882 Axis -0.00514988 -0.09002564 -0.99592613 Axis point 31.06996375 8.73384749 0.00000000 Rotation angle (degrees) 0.19268230 Shift along axis 0.19667956 > hide #!9 models > show #!9 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > hide #!23 models > show #!23 models > fitmap #9 inMap #23 Fit map tail-fiber-c6-refined-trimmed-down.mrc in map fiber-6-clean.mrc using 5742 points correlation = 0, correlation about mean = 0, overlap = 0 steps = 24, shift = 0, angle = 0 degrees Position of tail-fiber-c6-refined-trimmed-down.mrc (#9) relative to fiber-6-clean.mrc (#23) coordinates: Matrix rotation and translation -0.97664700 0.21380420 -0.02117613 -0.86065118 -0.21392431 -0.97684380 0.00355263 1.36292523 -0.01992620 0.00799976 0.99976946 36.39992806 Axis 0.01039647 -0.00292207 -0.99994169 Axis point -0.17312315 0.65435913 0.00000000 Rotation angle (degrees) 167.65036452 Shift along axis -36.41073572 > hide #!9 models > show #!9 models > fitmap #12 inMap #23 Fit map phage-adsorb-trimmed.mrc in map fiber-6-clean.mrc using 20976 points correlation = 0.4219, correlation about mean = 0.2022, overlap = 9.527 steps = 248, shift = 0.891, angle = 7.12 degrees Position of phage-adsorb-trimmed.mrc (#12) relative to fiber-6-clean.mrc (#23) coordinates: Matrix rotation and translation -0.94455049 0.32836513 0.00082539 2.13128707 -0.32836370 -0.94455018 0.00149730 1.02298155 0.00127128 0.00114325 0.99999854 36.48188758 Axis -0.00053911 -0.00067897 -0.99999962 Axis point 1.14009063 0.32081759 0.00000000 Rotation angle (degrees) 160.83046034 Shift along axis -36.48371743 > fitmap #9 inMap #12 Fit map tail-fiber-c6-refined-trimmed-down.mrc in map phage-adsorb-trimmed.mrc using 5742 points correlation = 0.6549, correlation about mean = 0.06653, overlap = 7.467 steps = 88, shift = 0.213, angle = 6.92 degrees Position of tail-fiber-c6-refined-trimmed-down.mrc (#9) relative to phage- adsorb-trimmed.mrc (#12) coordinates: Matrix rotation and translation 1.00000000 0.00024610 0.00000419 0.04544686 -0.00024610 0.99999997 -0.00021604 -0.12141001 -0.00000425 0.00021603 0.99999999 0.06625896 Axis 0.65965460 0.01288036 -0.75145852 Axis point -492.16247906 -242.02232272 -0.00000000 Rotation angle (degrees) 0.01876428 Shift along axis -0.02137543 > hide #!9 models > hide #!17 models > show #!17 models > hide #!17 models > hide #!12 models > show #!12 models > show #!22 models > hide #!22 models > show #!9 models > hide #!9 models > show #!8 models > show #!9 models > hide #!8 models > show #!8 models > select #8 3 models selected > ui mousemode rightMode "rotate selected models" > select clear > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!12 models > hide #!8 models > show #!8 models > hide #!9 models > show #!17 models > hide #!17 models > save image /data/disk3/Paper-use/Fiber-20191231.tif pixelSize 0.1 supersample 10 transparentBackground true > save image /data/disk3/Paper-use/Fiber-20191231-1.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!8 models > show #!8 models > hide #!8 models > show #!9 models > save image /data/disk3/Paper-use/Fiber-20191231-2.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!12 models > save image /data/disk3/Paper-use/Fiber-20191231-3.tif pixelSize 0.1 supersample 10 transparentBackground true > show #!8 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > hide #!9 models > show #!9 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > save image /data/disk3/Paper-use/Fiber-20191231-4.tif pixelSize 0.1 supersample 10 transparentBackground true > hide #!8 models > show #!8 models > hide #!8 models > lighting soft > hide #!9 models > show #!8 models > hide #!12 models > hide #!13 models > show #!11 models > hide #!11 models > show #!58 models > show #!9 models > hide #!9 models > show #!12 models > hide #!12 models > show #!13 models > hide #!8 models > show #!8 models > select #8 3 models selected > lighting simple > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!8 models > show #!8 models > ui mousemode rightMode "rotate selected models" > hide #!8 models > show #!8 models > select #8 3 models selected > select #8 3 models selected > select #8 3 models selected > ui mousemode rightMode "rotate selected models" > select #8 3 models selected > hide #!8 models > show #!8 models > ui mousemode rightMode "rotate selected models" > hide #!58 models > show #!58 models > hide #!58 models > show #!58 models > hide #!8 models > show #!9 models > hide #!58 models > hide #!13 models > show #!13 models > hide #!12 models > select #9 2 models selected > ui mousemode rightMode "rotate selected models" > show #!8 models > lighting soft > lighting flat > lighting shadows true intensity 0.5 > lighting simple > ~select #9 Nothing selected > hide #!9 models > save session /data/disk3/modeling/gp17/Figure4-20191230.cxs > save image /data/disk3/Paper-use/Fiber-20191231.tif pixelSize 0.1 supersample 10 transparentBackground true > open /data/disk3/modeling/gp17/4A0T.pdb 4A0T.pdb title: Structure of the carboxy-terminal domain of bacteriophage T7 fibre GP17 containing residues 371-553. [more info...] Chain information for 4A0T.pdb #14 --- Chain | Description A B C | bacteriophage T7 fibre GP17 Non-standard residues in 4A0T.pdb #14 --- 1PE — pentaethylene glycol (PEG400) TMO — trimethylamine oxide TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) > select #14/C:426 5 atoms, 4 bonds, 1 model selected > select #14 5115 atoms, 4473 bonds, 1 model selected > ui mousemode rightMode "rotate selected models" > ui mousemode rightMode "translate selected models" > ui mousemode rightMode "rotate selected models" > hide #!13 models > show #!13 models > hide #!8 models > show #!8 models > fitmap #14 inMap #8 Fit molecule 4A0T.pdb (#14) to map tail-fiber-c6-refined-trimmed.mrc (#8) using 5115 atoms average map value = 0.01101, steps = 108 shifted from previous position = 11.3 rotated from previous position = 10.8 degrees atoms outside contour = 1652, contour level = 0.009 Position of 4A0T.pdb (#14) relative to tail-fiber-c6-refined-trimmed.mrc (#8) coordinates: Matrix rotation and translation 0.99357797 -0.06933845 0.08941493 437.59930594 0.00342228 -0.77145872 -0.63627019 623.10365056 0.11309792 0.63249004 -0.76626708 310.98803375 Axis 0.99818634 -0.01863239 0.05724389 Axis point 0.00000000 264.32422719 256.36641215 Rotation angle (degrees) 140.54049111 Shift along axis 442.99790626 > ~select #14 Nothing selected > select #14 5115 atoms, 4473 bonds, 1 model selected > ~select #14 Nothing selected > select #14 5115 atoms, 4473 bonds, 1 model selected > open /data/disk3/modeling/gp17/4A0T.pdb 4A0T.pdb title: Structure of the carboxy-terminal domain of bacteriophage T7 fibre GP17 containing residues 371-553. [more info...] Chain information for 4A0T.pdb #15 --- Chain | Description A B C | bacteriophage T7 fibre GP17 Non-standard residues in 4A0T.pdb #15 --- 1PE — pentaethylene glycol (PEG400) TMO — trimethylamine oxide TRS — 2-amino-2-hydroxymethyl-propane-1,3-diol (tris buffer) > transparency #8 40 > select clear > transparency #8 30 > transparency #8 80 > transparency #8 60 > select clear > hide #!15 models > show #!15 models > select #15 5115 atoms, 4473 bonds, 1 model selected > close #15 > sym #14 C6 > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > hide #!14 models > show #!14 models > split #14 Chain information for 4A0T.pdb A #14.1 --- Chain | Description A | No description available Chain information for 4A0T.pdb B #14.2 --- Chain | Description B | No description available Chain information for 4A0T.pdb C #14.3 --- Chain | Description C | No description available Split 4A0T.pdb (#14) into 3 models > hide #!14.1 models > show #!14.1 models > hide #!14.1 models > show #!14.1 models > hide #!14.2 models > hide #!14.3 models > show #!14.3 models > select #14 5115 atoms, 4473 bonds, 4 models selected > hide #!8 models > show #!8 models > hide #!13 models > show #!13 models > hide #!13 models > show #!58 models > select clear > hide #!14 models > lighting soft > lighting simple > lighting shadows true > lighting full > lighting soft > lighting simple Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/save_dialog.py", line 154, in _format_selected fmt.update(self.session, self) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/savemap.py", line 67, in update self._map_menu.value = m File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py", line 262, in value or (val is not None and self.value == val): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py", line 255, in value return self.item_map[text] KeyError: 'gp17-trimer-clean.mrc #58' KeyError: 'gp17-trimer-clean.mrc #58' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/ui/widgets/item_chooser.py", line 255, in value return self.item_map[text] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 384.130 OpenGL renderer: Quadro K2200/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → General Controls |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Problem with item chooser |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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