![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 6 years ago
Closed 6 years ago
#2123 closed defect (duplicate)
self._child_drawings.remove(d): not in list (after earlier KeyError)
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted: Platform: Linux-4.15.0-51-generic-x86_64-with-debian-stretch-sid ChimeraX Version: 0.91 (2019-06-25) Description Was resetting clipping in the side view panel when the error popped up Log: UCSF ChimeraX version: 0.91 (2019-06-25) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open maps_and_models/State1_composite.cif name State1 Summary of feedback from opening maps_and_models/State1_composite.cif --- warnings | skipping chem_comp category: Missing column 'type' near line 297 Unknown polymer entity '?' near line 342 Missing or incomplete entity_poly_seq table. Inferred polymer connectivity. skipping chem_comp category: Missing column 'type' near line 72840 skipping chem_comp category: Missing column 'type' near line 72867 Chain information for State1 #1 --- Chain | Description A1 A2 A3 | No description available B1 | No description available B2 | No description available B3 | No description available C | No description available D | No description available E1 E2 E3 | No description available F | No description available G1 | No description available G2 | No description available G3 | No description available K1 | No description available K2 | No description available K3 | No description available a | No description available ac | No description available b | No description available c1 c2 c3 c4 c5 c6 c7 c8 c9 | No description available d | No description available e | No description available f | No description available pr | No description available > open maps_and_models/J1509_state1_Vo.mrc Opened J1509_state1_Vo.mrc, grid size 340,340,340, pixel 1.06, shown at level 0.16, step 2, values float32 > set bgColor white > set silhouettes true > camera ortho > surface cap true > lighting soft shadows true intensity 0.1 > close #1.1 > split #1 chains Chain information for State1 A1 #1.1 --- Chain | Description A1 | No description available Chain information for State1 A2 #1.2 --- Chain | Description A2 | No description available Chain information for State1 A3 #1.3 --- Chain | Description A3 | No description available Chain information for State1 B1 #1.4 --- Chain | Description B1 | No description available Chain information for State1 B2 #1.5 --- Chain | Description B2 | No description available Chain information for State1 B3 #1.6 --- Chain | Description B3 | No description available Chain information for State1 C #1.7 --- Chain | Description C | No description available Chain information for State1 D #1.8 --- Chain | Description D | No description available Chain information for State1 E1 #1.9 --- Chain | Description E1 | No description available Chain information for State1 E2 #1.10 --- Chain | Description E2 | No description available Chain information for State1 E3 #1.11 --- Chain | Description E3 | No description available Chain information for State1 F #1.12 --- Chain | Description F | No description available Chain information for State1 G1 #1.13 --- Chain | Description G1 | No description available Chain information for State1 G2 #1.14 --- Chain | Description G2 | No description available Chain information for State1 G3 #1.15 --- Chain | Description G3 | No description available Chain information for State1 K1 #1.16 --- Chain | Description K1 | No description available Chain information for State1 K2 #1.17 --- Chain | Description K2 | No description available Chain information for State1 K3 #1.18 --- Chain | Description K3 | No description available Chain information for State1 a #1.19 --- Chain | Description a | No description available Chain information for State1 ac #1.20 --- Chain | Description ac | No description available Chain information for State1 b #1.21 --- Chain | Description b | No description available Chain information for State1 c1 #1.22 --- Chain | Description c1 | No description available Chain information for State1 c2 #1.23 --- Chain | Description c2 | No description available Chain information for State1 c3 #1.24 --- Chain | Description c3 | No description available Chain information for State1 c4 #1.25 --- Chain | Description c4 | No description available Chain information for State1 c5 #1.26 --- Chain | Description c5 | No description available Chain information for State1 c6 #1.27 --- Chain | Description c6 | No description available Chain information for State1 c7 #1.28 --- Chain | Description c7 | No description available Chain information for State1 c8 #1.29 --- Chain | Description c8 | No description available Chain information for State1 c9 #1.30 --- Chain | Description c9 | No description available Chain information for State1 d #1.31 --- Chain | Description d | No description available Chain information for State1 e #1.32 --- Chain | Description e | No description available Chain information for State1 f #1.33 --- Chain | Description f | No description available Chain information for State1 pr #1.34 --- Chain | Description pr | No description available Split State1 (#1) into 34 models > dssp > select #1.1-3 13993 atoms, 14279 bonds, 3 models selected > name frozen subunitA sel > select #1.4-6 10847 atoms, 11060 bonds, 3 models selected > name frozen subunitB sel > select #1.7 2927 atoms, 2981 bonds, 1 model selected > name frozen subunitC sel > select #1.8 1726 atoms, 1744 bonds, 1 model selected > name frozen subunitD sel > select #1.9-11 5040 atoms, 5079 bonds, 3 models selected > name frozen subunitE sel > select #1.12 876 atoms, 890 bonds, 1 model selected > name frozen subunitF sel > select #1.13-15 2392 atoms, 2401 bonds, 3 models selected > name frozen subunitG sel > select #1.16-18 5441 atoms, 5542 bonds, 3 models selected > name frozen SidK sel > select #1.19 5615 atoms, 5754 bonds, 1 model selected > name frozen V0a sel > select #1.21 1503 atoms, 1537 bonds, 1 model selected > name frozen V0b sel > select #1.22-30 9612 atoms, 9747 bonds, 9 models selected > name frozen V0cring sel > select #1.31 2833 atoms, 2899 bonds, 1 model selected > name frozen V0d sel > select #1.32 628 atoms, 653 bonds, 1 model selected > name frozen V0e sel > select #1.33 675 atoms, 691 bonds, 1 model selected > name frozen V0RNAseK sel > select #1.20 337 atoms, 347 bonds, 1 model selected > name frozen V0Ac45 sel > select #1.34 443 atoms, 456 bonds, 1 model selected > name frozen V0PRR sel > color subunitA #F2EA42 target cabp > color subunitB #D01F26 target cabp > color subunitC #996633 target cabp > color subunitD #3A53A3 target cabp > color subunitE #804F9F target cabp > color subunitF #B9529E target cabp > color subunitG #fce94f target cabp > color SidK #D2D2D2 target cabp > color V0a #8ef826 target cabp > color V0b #9d42bf target cabp > color V0cring #df9fda target cabp > color V0d #96cff7 target cabp > color V0e #3465a4 target cabp > color V0RNAseK #CC0000 target cabp > color V0Ac45 #B2B2FF target cabp > color V0PRR #edd400 target cabp > color subunitA #F2EA42 target s > color subunitB #D01F26 target s > color subunitC #996633 target s > color subunitD #3A53A3 target s > color subunitE #804F9F target s > color subunitF #B9529E target s > color subunitG #fce94f target s > color SidK #D2D2D2 target s > color V0a #8ef826 target s > color V0b #9d42bf target s > color V0cring #df9fda target s > color V0d #96cff7 target s > color V0e #3465a4 target s > color V0RNAseK #CC0000 target s > color V0Ac45 #B2B2FF target s > color V0PRR #edd400 target s > select clear > hide atoms > show cartoons > hide SidK target cs > hide subunitG target cs > hide subunitF target cs > hide subunitE target cs > hide subunitC target cs > hide subunitA target cs > hide subunitB target cs > hide subunitD target cs > hide subunitF target cs > volume #2 step 1 level 0.5 > volume zone #2 nearAtoms #1 range 2 invert true minimalBounds true modelId #3 Invalid "color" argument: Color constant should have 3 (4), 6 (8), or 12 (16) hexadecimal digits > volume #2 step 1 level 0.5 color #eeeeec surfaceSmoothing true subdivideSurface true smoothingIterations 4 > surface dust #2 size 10 > color zone #2 near #1 distance 3 sharpEdges true update false > cartoon style V0cring modeHelix tube > cartoon style V0b modeHelix tube > volume zone #2 nearAtoms V0RNAseK range 3.5 minimalBounds true modelId #4 > volume #4 level 0.4 color #CC0000 > surface dust #4 size 10 > volume zone #2 nearAtoms V0PRR range 3 minimalBounds true modelId #6 > volume #6 level 0.4 color #edd400 > surface dust #6 size 20 > volume zone #2 nearAtoms #1 & ~V0Ac45 range 2 invert true minimalBounds true modelId #5 Expected a keyword > surface dust #5 size 40 > select #1.19:476-514 287 atoms, 296 bonds, 1 model selected > name frozen loop34 sel Expected a keyword Invalid "surfaceSmoothing" argument: Expected true or false (or 1 or 0) > surface dust #3 size 20 Invalid "models" argument: No models specified by "#1.8.1" > view matrix camera -0.54093,-0.18668,-0.82009,-168.87,0.83482,-0.00050518,-0.55053,-56.055,0.10236,-0.98242,0.15612,336.09 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > volume #3 level 0.56 color #D3D7CF > volume #3 level 0.56 color #B2B2FF > volume #5 level 0.45 color #B2B2FF > surface dust #5 size 40 > volume #3 level 0.56 color #D3D7CF > surface dust #3 size 20 > volume #3 level 0.56 color #D3D7CF > surface dust #3 size 20 > surface dust #4 size 10 > save session /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure3/Fig3a_Vo.cxs Invalid "models" argument: Expected model id and 12 comma-separated numbers > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > volume zone #2 nearAtoms V0e range 3 minimalBounds true modelId #7 > volume #7 level 0.4 color #3465a4 > surface dust #7 size 20 > turn y -100 > name glu (#1.21:98 | #1.22-29:139) & sidechain > show glu bonds > style glu ball Changed 54 atom styles > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > color glu #ef2929 target abp > hide #!4 models > hide V0e target c > save session /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure3/Fig3b_Vo.cxs > size glu stickRadius 0.3 Changed 45 bond radii > size glu stickRadius 0.4 Changed 45 bond radii > size glu stickRadius 0.5 Changed 45 bond radii > style glu stick Changed 54 atom styles > style glu ball Changed 54 atom styles > style glu stick Changed 54 atom styles > style glu ball Changed 54 atom styles > size glu ballScale 0.5 Changed 9 ball scales > size glu ballScale 0.4 Changed 9 ball scales > size glu ballScale 0.3 Changed 9 ball scales > size glu ballScale 0.35 Changed 9 ball scales > size glu ballScale 0.4 Changed 9 ball scales > style glu ball Changed 54 atom styles > style glu stick Changed 54 atom styles Unknown command: sie glu stick 0.2 > size glu stickRadius 0.2 Changed 45 bond radii > size glu stickRadius 0.3 Changed 45 bond radii > size glu stickRadius 0.4 Changed 45 bond radii > size glu stickRadius 0.5 Changed 45 bond radii > size glu stickRadius 0.4 Changed 45 bond radii Missing "ballScale" keyword's argument > style glu ball Changed 54 atom styles > size glu ballScale 0.3 Changed 9 ball scales > size glu ballScale 0.35 Changed 9 ball scales > size glu ballScale 0.3 Changed 9 ball scales > style glu stick Changed 54 atom styles > surface dust #7 size 20 > save session /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure3/Fig3b_Vo.cxs > save image output/Vo_side.png pixelSize 0.106 transparentBackground true > select clear > save image output/Vo_side.png width 2000 pixelSize 0.106 transparentBackground true Cannot specify width or height if pixel_size is given > save image output/Vo_side_test.png width 2000 height 2000 transparentBackground true > save image output/Vo_side.png width 4000 height 4000 transparentBackground true > view matrix camera -0.54093,-0.18668,-0.82009,-168.87,0.83482,-0.00050518,-0.55053,-56.055,0.10236,-0.98242,0.15612,336.09 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > hide #!7 models > show #!4 models > show V0e target c > hide V0RNAseK target c > select up Nothing selected > select down Nothing selected > save image output/Vo_front.png width 4000 height 4000 transparentBackground true > set selectionWidth 2 > select loop34 287 atoms, 296 bonds, 1 model selected > set silhouetteWidth 2 > set silhouetteWidth 1.2 > set silhouetteWidth 1 > set silhouetteWidth 1.5 > set silhouetteWidth 1 > set silhouetteWidth 1.2 > set silhouetteWidth 2 > save image output/Vo_front.png width 4000 height 4000 transparentBackground true > hide V0PRR target c > hide #!6 models > show #!6 models > surface dust #6 size 20 > select clear > volume zone #2 nearAtoms V0PRR range 2.5 minimalBounds true modelId #6 > volume #6 level 0.4 color #edd400 > surface dust #6 size 20 > volume zone #2 nearAtoms V0PRR range 2 minimalBounds true modelId #6 > volume #6 level 0.4 color #edd400 > surface dust #6 size 20 > volume zone #2 nearAtoms V0PRR range 3 minimalBounds true modelId #6 > volume #6 level 0.4 color #edd400 > surface dust #6 size 20 > surface dust #6 size 20 > surface dust #6 size 25 > surface dust #6 size 30 > surface dust #6 size 50 > surface dust #6 size 20 > volume zone #2 nearAtoms V0PRR range 3 minimalBounds true modelId #6 > volume #6 level 0.45 color #edd400 > surface dust #6 size 20 > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > surface dust #6 size 30 > surface dust #6 size 40 > surface dust #6 size 100 > surface dust #6 size 1 > surface undust #6 > hide #!6 models > show #!6 models > hide #!6.1 models > hide #!6 models Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/map/volume_viewer.py", line 2127, in close_map_cb self.dialog.session.models.close([v]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 587, in close mremoved = self.remove(models) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] KeyError: (6, 1) KeyError: (6, 1) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 570, in remove del self._models[model_id] See log for complete Python traceback. > save image output/Vo_front.png width 4000 height 4000 transparentBackground true Invalid "models" argument: No models specified by "#6" > volume zone #2 nearAtoms V0PRR range 3 minimalBounds true modelId #6 > volume #6 level 0.4 color #edd400 > surface dust #6 size 20 > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera -0.54093,-0.18668,-0.82009,-168.87,0.83482,-0.00050518,-0.55053,-56.055,0.10236,-0.98242,0.15612,336.09 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > hide glu target abp > save image output/Vo_front.png width 4000 height 4000 transparentBackground true > show #!7 models > hide #!4 models > hide V0e target c > show V0RNAseK target c > show glu target abp > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > save image output/Vo_side.png width 4000 height 4000 transparentBackground true > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > view matrix camera 0.83158,-0.12601,-0.54093,-43.799,0.54908,0.039884,0.83482,527.54,-0.083624,-0.99123,0.10236,312.36 models #2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#1.3,1,0,0,0,0,1,0,0,0,0,1,0,#1.4,1,0,0,0,0,1,0,0,0,0,1,0,#1.5,1,0,0,0,0,1,0,0,0,0,1,0,#1.6,1,0,0,0,0,1,0,0,0,0,1,0,#1.7,1,0,0,0,0,1,0,0,0,0,1,0,#1.8,1,0,0,0,0,1,0,0,0,0,1,0,#1.9,1,0,0,0,0,1,0,0,0,0,1,0,#1.10,1,0,0,0,0,1,0,0,0,0,1,0,#1.11,1,0,0,0,0,1,0,0,0,0,1,0,#1.12,1,0,0,0,0,1,0,0,0,0,1,0,#1.13,1,0,0,0,0,1,0,0,0,0,1,0,#1.14,1,0,0,0,0,1,0,0,0,0,1,0,#1.15,1,0,0,0,0,1,0,0,0,0,1,0,#1.16,1,0,0,0,0,1,0,0,0,0,1,0,#1.17,1,0,0,0,0,1,0,0,0,0,1,0,#1.18,1,0,0,0,0,1,0,0,0,0,1,0,#1.19,1,0,0,0,0,1,0,0,0,0,1,0,#1.20,1,0,0,0,0,1,0,0,0,0,1,0,#1.21,1,0,0,0,0,1,0,0,0,0,1,0,#1.22,1,0,0,0,0,1,0,0,0,0,1,0,#1.23,1,0,0,0,0,1,0,0,0,0,1,0,#1.24,1,0,0,0,0,1,0,0,0,0,1,0,#1.25,1,0,0,0,0,1,0,0,0,0,1,0,#1.26,1,0,0,0,0,1,0,0,0,0,1,0,#1.27,1,0,0,0,0,1,0,0,0,0,1,0,#1.28,1,0,0,0,0,1,0,0,0,0,1,0,#1.29,1,0,0,0,0,1,0,0,0,0,1,0,#1.30,1,0,0,0,0,1,0,0,0,0,1,0,#1.31,1,0,0,0,0,1,0,0,0,0,1,0,#1.32,1,0,0,0,0,1,0,0,0,0,1,0,#1.33,1,0,0,0,0,1,0,0,0,0,1,0,#1.34,1,0,0,0,0,1,0,0,0,0,1,0,#1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0,#4,1,0,0,0,0,1,0,0,0,0,1,0,#4.1,1,0,0,0,0,1,0,0,0,0,1,0,#5,1,0,0,0,0,1,0,0,0,0,1,0,#5.1,1,0,0,0,0,1,0,0,0,0,1,0,#6,1,0,0,0,0,1,0,0,0,0,1,0,#6.1,1,0,0,0,0,1,0,0,0,0,1,0 > save image output/Vo_side2.png width 4000 height 4000 transparentBackground true > save image output/Vo_side2.png width 4000 height 4000 transparentBackground true > zoom Pixel size at center of rotation is 0.0987 > zoom pixelSize 0.098 > zoom pixelSize 0.099 > save image output/Vo_side2.png width 4000 height 4000 transparentBackground true > zoom pixelSize 0.1 > zoom pixelSize 0.106 > zoom pixelSize 0.1 > save image output/Vo_side2.png width 4000 height 4000 transparentBackground true > zoom pixelSize 0.102 > zoom pixelSize 0.101 > save image output/Vo_side2.png width 4000 height 4000 transparentBackground true > zoom pixelSize 0.1015 > save image output/Vo_side.png width 4000 height 4000 transparentBackground true > save session /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure3/Fig3b_Vo.cxs > zoom pixelSize 0.101 > save image output/Vo_side.png width 4000 height 4000 transparentBackground true > save session /home/yazan/Dropbox/Abbas_etal_2019_brainV- ATPase/Figures/Figure3/Fig3b_Vo.cxs > hide V0cring target c > hide glu target abp > save image output/Vo_side_subunita.png width 4000 height 4000 transparentBackground true > show V0e target c > hide V0RNAseK target c > hide #!5 models > show #!4 models > hide #!7 models > show #!5 models > show V0cring target c > hide V0d target c > turn x 90 > show V0d target c > show V0d target c > hide V0d target c > hide #!4 models > show V0RNAseK target c > show glu target abp > name antdtohide #1.19:10-358 | #1.19:823-833 > hide antdtohide target c > name antdtohide #1.19:2-358 | #1.19:823-833 > hide antdtohide target c > select glu 54 atoms, 45 bonds, 9 models selected > select glu 54 atoms, 45 bonds, 9 models selected > style glu sphere Changed 54 atom styles > select clear > save image output/Vo_top.png width 4000 height 4000 transparentBackground true > cartoon style V0cring modeHelix wrap > cartoon style V0b modeHelix tube > cartoon style V0cring modeHelix wrap > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix tube > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix wrap > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix tube > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix wrap > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix tube > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix wrap > cartoon style V0b modeHelix wrap > cartoon style V0cring modeHelix wrap > cartoon style V0b modeHelix tube > select glu 54 atoms, 45 bonds, 9 models selected > name glu (#1.21:98 | #1.22-30:139) & sidechain > show glu bonds > style glu stick Changed 60 atom styles > size glu stickRadius 0.4 Changed 50 bond radii > color glu #ef2929 target abp > show glu bonds Expected a keyword > show glu bonds > style glu sphere Changed 60 atom styles > select clear > hide #!5 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!7 models > hide #!7 models > show #!6 models > hide #!6 models > show #!5 models > save image output/Vo_top.png width 4000 height 4000 transparentBackground true > zoom pixelSize 0.101 > turn x 90 > turn x -90 > turn x -90 > turn x 90 > turn x 90 > turn x 90 > turn x -90 > turn x -90 > ui mousemode rightMode "pick blobs" > measure blob #!5.1 triangleNumber 114217 color #0000ccff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 133462 color #f1501aff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 115261 color #570cefff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 115257 color #c68b50ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 102134 color #d9327cff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 102134 color #9320ceff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 102134 color #87b27bff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 102134 color #d56f54ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 103164 color #ab8488ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 103166 color #a8bb29ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 104353 color #ee1d57ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 114217 color #e07427ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 104374 color #33df70ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 104374 color #26e961ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!6.1 triangleNumber 2626 color #a08890ff outline true Surface J1509_state1_Vo.mrc zone #6.1 blob: volume = 2591.7 area = 2699.8 size = 86.094 26.247 14.965 > measure blob #!6.1 triangleNumber 499 color #4453e7ff outline true Surface J1509_state1_Vo.mrc zone #6.1 blob: volume = 2591.7 area = 2699.8 size = 86.094 26.247 14.965 > measure blob #!6.1 triangleNumber 521 color #8c87a5ff outline true Surface J1509_state1_Vo.mrc zone #6.1 blob: volume = 2591.7 area = 2699.8 size = 86.094 26.247 14.965 > measure blob #!5.1 triangleNumber 218915 color #20f63bff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 > measure blob #!5.1 triangleNumber 218920 color #ff0e05ff outline true Surface J1509_state1_Vo.mrc zone #5.1 blob: volume = 10202 area = 10413 size = 106.58 48.645 44.782 Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback if not self.draw_new_frame(): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 61, in draw_new_frame surface.update_clip_caps(view) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 25, in update_clip_caps show_surface_clip_caps(planes, drawings, offset = settings.clipping_cap_offset) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 44, in show_surface_clip_caps cap.session.models.remove([cap]) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/models.py", line 576, in remove parent.remove_drawing(model, delete=False) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py", line 296, in remove_drawing self._child_drawings.remove(d) ValueError: list.remove(x): x not in list ValueError: list.remove(x): x not in list File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/graphics/drawing.py", line 296, in remove_drawing self._child_drawings.remove(d) See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback if not self.draw_new_frame(): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 61, in draw_new_frame surface.update_clip_caps(view) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 25, in update_clip_caps show_surface_clip_caps(planes, drawings, offset = settings.clipping_cap_offset) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 41, in show_surface_clip_caps del d._clip_cap_drawings[cap.clip_plane_name] KeyError: 'far' KeyError: 'far' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 41, in show_surface_clip_caps del d._clip_cap_drawings[cap.clip_plane_name] See log for complete Python traceback. Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback if not self.draw_new_frame(): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 61, in draw_new_frame surface.update_clip_caps(view) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 25, in update_clip_caps show_surface_clip_caps(planes, drawings, offset = settings.clipping_cap_offset) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 41, in show_surface_clip_caps del d._clip_cap_drawings[cap.clip_plane_name] KeyError: 'far' KeyError: 'far' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 41, in show_surface_clip_caps del d._clip_cap_drawings[cap.clip_plane_name] See log for complete Python traceback. [_many_ of these removed] Traceback (most recent call last): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 128, in _redraw_timer_callback if not self.draw_new_frame(): File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/core/updateloop.py", line 61, in draw_new_frame surface.update_clip_caps(view) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 25, in update_clip_caps show_surface_clip_caps(planes, drawings, offset = settings.clipping_cap_offset) File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 41, in show_surface_clip_caps del d._clip_cap_drawings[cap.clip_plane_name] KeyError: 'near' KeyError: 'near' File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site- packages/chimerax/surface/cap.py", line 41, in show_surface_clip_caps del d._clip_cap_drawings[cap.clip_plane_name] See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 418.56 OpenGL renderer: GeForce RTX 2070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Component: | Unassigned → Graphics |
|---|---|
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → self._child_drawings.remove(d): not in list (after earlier KeyError) |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
Note:
See TracTickets
for help on using tickets.
The last tracebacks appear to result from using "volume zone" with the modelId argument to make multiple volumes that have the same id number. Models cannot have the same id number and that volume zone bug was fixed yesterday.