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Opened 6 years ago
Closed 6 years ago
#2122 closed defect (fixed)
"volume zone" can create duplicate model IDs
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
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 volume zone #2 nearAtoms V0PRR range 3 minimalBounds true modelId #6; volume #6 level 0.4 color #edd400; surface dust #6 size 20 using the above command multiple times in a row (testing different parameters) created multiple volumes with model id #6, when I expected each command to overwrite the previous volumee. Trying to delete the volumes using volume viewer results in the error 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. 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 → Volume Data |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → "volume zone" can create duplicate model IDs |
comment:2 by , 6 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
Now issues an error message "Tried to create model #6 which already exists".