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Opened 22 months ago
Closed 22 months ago
#10428 closed defect (fixed)
self._positions is None
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-64bit
ChimeraX Version: 1.8.dev202401040148 (2024-01-04 01:48:54 UTC)
Description
Holding down arrow key while using sequential model display controls
Log:
> camera ortho
> cofr centerOfView
> mousemode alt rightMode "contour level"
> mousemode rightMode clip
> mousemode alt leftMode "translate selected models"
> mousemode shift leftMode "rotate selected models"
> mousemode alt control leftMode "pick blobs"
> alias cofron cofr centerofview showpivot true
> alias cofroff cofr centerofview showpivot false
> alias symclip cofr centerofview; clip near -$1 far $1 position cofr
> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ##~num_residues
> cornflower blue
> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ##~num_residues #3d60ffff; transparency 50
> alias project_map set bgColor black; lighting depthcue false; volume $1
> style image sdlevel 0,0 color white sdlevel 100,0.15 color white
> projectionmode 3d maximumIntensityProjection false dimTransparentVoxels
> false btcorrection true showOutlineBox false linearinterpolation true
> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1
> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1
> alias map_sphere_15 surface unzone ##~num_residues; sel; close #10000;
> marker #10000 position cofr; sel ~sel; surface zone ##~num_residues
> nearAtoms sel distance 15; close #10000
> alias map_unsphere surface unzone ##~num_residues
> alias default_mol_display ~disp; rib; rainbow chain palette RdYlBu-5;
> lighting soft
> alias hidemaps surface unzone ##~num_residues; sel; close #10000; marker
> #10000 position cofr; sel ~sel; surface zone ##~num_residues nearAtoms sel
> distance 0; close #10000
> alias showmaps surface unzone ##~num_residues
> alias caps_off surface cap false
> alias caps_on surface cap true
> alias open_vseries "open browse vseries true"
> alias selbetween ks ri
> alias helix setattr $1 res is_helix true
> alias strand setattr $1 res is_strand true
> alias coil setattr $1 res is_strand false; setattr $1 res is_helix false
> alias rock_movie cofr showpivot false; movie record; rock y 30; wait 136;
> movie encode ~/Desktop/rock_movie.mp4; stop
> buttonpanel Shortcuts rows 3 columns 4
> buttonpanel Shortcuts add Vol_Viewer command "tool show 'Volume Viewer'"
> buttonpanel Shortcuts add Model_Panel command "tool show Models"
> buttonpanel Shortcuts add Log command "tool show Log"
> buttonpanel Shortcuts add default_disp command default_mol_display
> buttonpanel Shortcuts add map_sphere command map_sphere_15
> buttonpanel Shortcuts add map_unsphere command map_unsphere
> buttonpanel Shortcuts add cofron command cofron
> buttonpanel Shortcuts add cofroff command cofroff
> buttonpanel Shortcuts add cootmode command cootmode
> buttonpanel Shortcuts add mark_cofr command "marker #20000 position cofr"
> buttonpanel Shortcuts add hidemaps command hidemaps
> buttonpanel Shortcuts add showmaps command showmaps
> volume defaultvalues limitVoxelCount false voxelLimitForPlane
> 1000000000000000 voxelLimitForOpen 1000000000000000 saveSettings true
Saved volume settings
UCSF ChimeraX version: 1.8.dev202401040148 (2024-01-04)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> tool show Models
> tool show Log
> tool show Models
> tool show Log
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_00_00358_volume.mrc
Opened J5055_class_00_00358_volume.mrc as #1, grid size 72,72,72, pixel 5.19,
shown at level 2.31, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_01_00358_volume.mrc
Opened J5055_class_01_00358_volume.mrc as #2, grid size 72,72,72, pixel 5.19,
shown at level 2.27, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_02_00358_volume.mrc
Opened J5055_class_02_00358_volume.mrc as #3, grid size 72,72,72, pixel 5.19,
shown at level 2.26, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_03_00358_volume.mrc
Opened J5055_class_03_00358_volume.mrc as #4, grid size 72,72,72, pixel 5.19,
shown at level 2.32, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_04_00358_volume.mrc
Opened J5055_class_04_00358_volume.mrc as #5, grid size 72,72,72, pixel 5.19,
shown at level 2.16, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_05_00358_volume.mrc
Opened J5055_class_05_00358_volume.mrc as #6, grid size 72,72,72, pixel 5.19,
shown at level 2.27, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_06_00358_volume.mrc
Opened J5055_class_06_00358_volume.mrc as #7, grid size 72,72,72, pixel 5.19,
shown at level 2.22, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_07_00358_volume.mrc
Opened J5055_class_07_00358_volume.mrc as #8, grid size 72,72,72, pixel 5.19,
shown at level 2.29, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_08_00358_volume.mrc
Opened J5055_class_08_00358_volume.mrc as #9, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_09_00358_volume.mrc
Opened J5055_class_09_00358_volume.mrc as #10, grid size 72,72,72, pixel 5.19,
shown at level 2.2, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_10_00358_volume.mrc
Opened J5055_class_10_00358_volume.mrc as #11, grid size 72,72,72, pixel 5.19,
shown at level 2.18, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_11_00358_volume.mrc
Opened J5055_class_11_00358_volume.mrc as #12, grid size 72,72,72, pixel 5.19,
shown at level 2.23, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_12_00358_volume.mrc
Opened J5055_class_12_00358_volume.mrc as #13, grid size 72,72,72, pixel 5.19,
shown at level 2.16, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_13_00358_volume.mrc
Opened J5055_class_13_00358_volume.mrc as #14, grid size 72,72,72, pixel 5.19,
shown at level 2.21, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_14_00358_volume.mrc
Opened J5055_class_14_00358_volume.mrc as #15, grid size 72,72,72, pixel 5.19,
shown at level 2.18, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_15_00358_volume.mrc
Opened J5055_class_15_00358_volume.mrc as #16, grid size 72,72,72, pixel 5.19,
shown at level 2.33, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_16_00358_volume.mrc
Opened J5055_class_16_00358_volume.mrc as #17, grid size 72,72,72, pixel 5.19,
shown at level 2.37, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_17_00358_volume.mrc
Opened J5055_class_17_00358_volume.mrc as #18, grid size 72,72,72, pixel 5.19,
shown at level 2.25, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_18_00358_volume.mrc
Opened J5055_class_18_00358_volume.mrc as #19, grid size 72,72,72, pixel 5.19,
shown at level 2.18, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_19_00358_volume.mrc
Opened J5055_class_19_00358_volume.mrc as #20, grid size 72,72,72, pixel 5.19,
shown at level 2.19, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_20_00358_volume.mrc
Opened J5055_class_20_00358_volume.mrc as #21, grid size 72,72,72, pixel 5.19,
shown at level 2.22, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_21_00358_volume.mrc
Opened J5055_class_21_00358_volume.mrc as #22, grid size 72,72,72, pixel 5.19,
shown at level 2.19, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_22_00358_volume.mrc
Opened J5055_class_22_00358_volume.mrc as #23, grid size 72,72,72, pixel 5.19,
shown at level 2.2, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_23_00358_volume.mrc
Opened J5055_class_23_00358_volume.mrc as #24, grid size 72,72,72, pixel 5.19,
shown at level 2.33, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_24_00358_volume.mrc
Opened J5055_class_24_00358_volume.mrc as #25, grid size 72,72,72, pixel 5.19,
shown at level 2.28, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_25_00358_volume.mrc
Opened J5055_class_25_00358_volume.mrc as #26, grid size 72,72,72, pixel 5.19,
shown at level 2.31, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_26_00358_volume.mrc
Opened J5055_class_26_00358_volume.mrc as #27, grid size 72,72,72, pixel 5.19,
shown at level 2.19, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_27_00358_volume.mrc
Opened J5055_class_27_00358_volume.mrc as #28, grid size 72,72,72, pixel 5.19,
shown at level 2.21, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_28_00358_volume.mrc
Opened J5055_class_28_00358_volume.mrc as #29, grid size 72,72,72, pixel 5.19,
shown at level 2.25, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_29_00358_volume.mrc
Opened J5055_class_29_00358_volume.mrc as #30, grid size 72,72,72, pixel 5.19,
shown at level 2.2, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_30_00358_volume.mrc
Opened J5055_class_30_00358_volume.mrc as #31, grid size 72,72,72, pixel 5.19,
shown at level 2.34, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_31_00358_volume.mrc
Opened J5055_class_31_00358_volume.mrc as #32, grid size 72,72,72, pixel 5.19,
shown at level 2.32, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_32_00358_volume.mrc
Opened J5055_class_32_00358_volume.mrc as #33, grid size 72,72,72, pixel 5.19,
shown at level 2.35, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_33_00358_volume.mrc
Opened J5055_class_33_00358_volume.mrc as #34, grid size 72,72,72, pixel 5.19,
shown at level 2.25, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_34_00358_volume.mrc
Opened J5055_class_34_00358_volume.mrc as #35, grid size 72,72,72, pixel 5.19,
shown at level 2.24, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_35_00358_volume.mrc
Opened J5055_class_35_00358_volume.mrc as #36, grid size 72,72,72, pixel 5.19,
shown at level 2.28, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_36_00358_volume.mrc
Opened J5055_class_36_00358_volume.mrc as #37, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_37_00358_volume.mrc
Opened J5055_class_37_00358_volume.mrc as #38, grid size 72,72,72, pixel 5.19,
shown at level 2.17, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_38_00358_volume.mrc
Opened J5055_class_38_00358_volume.mrc as #39, grid size 72,72,72, pixel 5.19,
shown at level 2.35, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_39_00358_volume.mrc
Opened J5055_class_39_00358_volume.mrc as #40, grid size 72,72,72, pixel 5.19,
shown at level 2.29, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_40_00358_volume.mrc
Opened J5055_class_40_00358_volume.mrc as #41, grid size 72,72,72, pixel 5.19,
shown at level 2.37, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_41_00358_volume.mrc
Opened J5055_class_41_00358_volume.mrc as #42, grid size 72,72,72, pixel 5.19,
shown at level 2.16, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_42_00358_volume.mrc
Opened J5055_class_42_00358_volume.mrc as #43, grid size 72,72,72, pixel 5.19,
shown at level 2.29, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_43_00358_volume.mrc
Opened J5055_class_43_00358_volume.mrc as #44, grid size 72,72,72, pixel 5.19,
shown at level 2.19, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_44_00358_volume.mrc
Opened J5055_class_44_00358_volume.mrc as #45, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_45_00358_volume.mrc
Opened J5055_class_45_00358_volume.mrc as #46, grid size 72,72,72, pixel 5.19,
shown at level 2.38, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_46_00358_volume.mrc
Opened J5055_class_46_00358_volume.mrc as #47, grid size 72,72,72, pixel 5.19,
shown at level 2.29, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_47_00358_volume.mrc
Opened J5055_class_47_00358_volume.mrc as #48, grid size 72,72,72, pixel 5.19,
shown at level 2.37, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_48_00358_volume.mrc
Opened J5055_class_48_00358_volume.mrc as #49, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_49_00358_volume.mrc
Opened J5055_class_49_00358_volume.mrc as #50, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_50_00358_volume.mrc
Opened J5055_class_50_00358_volume.mrc as #51, grid size 72,72,72, pixel 5.19,
shown at level 2.3, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_51_00358_volume.mrc
Opened J5055_class_51_00358_volume.mrc as #52, grid size 72,72,72, pixel 5.19,
shown at level 2.42, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_52_00358_volume.mrc
Opened J5055_class_52_00358_volume.mrc as #53, grid size 72,72,72, pixel 5.19,
shown at level 2.47, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_53_00358_volume.mrc
Opened J5055_class_53_00358_volume.mrc as #54, grid size 72,72,72, pixel 5.19,
shown at level 2.4, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_54_00358_volume.mrc
Opened J5055_class_54_00358_volume.mrc as #55, grid size 72,72,72, pixel 5.19,
shown at level 2.4, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_55_00358_volume.mrc
Opened J5055_class_55_00358_volume.mrc as #56, grid size 72,72,72, pixel 5.19,
shown at level 2.24, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_56_00358_volume.mrc
Opened J5055_class_56_00358_volume.mrc as #57, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_57_00358_volume.mrc
Opened J5055_class_57_00358_volume.mrc as #58, grid size 72,72,72, pixel 5.19,
shown at level 2.42, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_58_00358_volume.mrc
Opened J5055_class_58_00358_volume.mrc as #59, grid size 72,72,72, pixel 5.19,
shown at level 2.38, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_59_00358_volume.mrc
Opened J5055_class_59_00358_volume.mrc as #60, grid size 72,72,72, pixel 5.19,
shown at level 2.28, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_60_00358_volume.mrc
Opened J5055_class_60_00358_volume.mrc as #61, grid size 72,72,72, pixel 5.19,
shown at level 2.42, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_61_00358_volume.mrc
Opened J5055_class_61_00358_volume.mrc as #62, grid size 72,72,72, pixel 5.19,
shown at level 2.43, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_62_00358_volume.mrc
Opened J5055_class_62_00358_volume.mrc as #63, grid size 72,72,72, pixel 5.19,
shown at level 2.34, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_63_00358_volume.mrc
Opened J5055_class_63_00358_volume.mrc as #64, grid size 72,72,72, pixel 5.19,
shown at level 2.42, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_64_00358_volume.mrc
Opened J5055_class_64_00358_volume.mrc as #65, grid size 72,72,72, pixel 5.19,
shown at level 2.37, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_65_00358_volume.mrc
Opened J5055_class_65_00358_volume.mrc as #66, grid size 72,72,72, pixel 5.19,
shown at level 2.35, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_66_00358_volume.mrc
Opened J5055_class_66_00358_volume.mrc as #67, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_67_00358_volume.mrc
Opened J5055_class_67_00358_volume.mrc as #68, grid size 72,72,72, pixel 5.19,
shown at level 2.23, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_68_00358_volume.mrc
Opened J5055_class_68_00358_volume.mrc as #69, grid size 72,72,72, pixel 5.19,
shown at level 2.36, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_69_00358_volume.mrc
Opened J5055_class_69_00358_volume.mrc as #70, grid size 72,72,72, pixel 5.19,
shown at level 2.45, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_70_00358_volume.mrc
Opened J5055_class_70_00358_volume.mrc as #71, grid size 72,72,72, pixel 5.19,
shown at level 2.4, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_71_00358_volume.mrc
Opened J5055_class_71_00358_volume.mrc as #72, grid size 72,72,72, pixel 5.19,
shown at level 1.81, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_72_00358_volume.mrc
Opened J5055_class_72_00358_volume.mrc as #73, grid size 72,72,72, pixel 5.19,
shown at level 2.41, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_73_00358_volume.mrc
Opened J5055_class_73_00358_volume.mrc as #74, grid size 72,72,72, pixel 5.19,
shown at level 2.25, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_74_00358_volume.mrc
Opened J5055_class_74_00358_volume.mrc as #75, grid size 72,72,72, pixel 5.19,
shown at level 2.4, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_75_00358_volume.mrc
Opened J5055_class_75_00358_volume.mrc as #76, grid size 72,72,72, pixel 5.19,
shown at level 2.24, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_76_00358_volume.mrc
Opened J5055_class_76_00358_volume.mrc as #77, grid size 72,72,72, pixel 5.19,
shown at level 2.37, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_77_00358_volume.mrc
Opened J5055_class_77_00358_volume.mrc as #78, grid size 72,72,72, pixel 5.19,
shown at level 2.25, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_78_00358_volume.mrc
Opened J5055_class_78_00358_volume.mrc as #79, grid size 72,72,72, pixel 5.19,
shown at level 2.27, step 1, values float32
> open
> /Users/oc2188/Downloads/cryosparc_P1_J5055_00358_volume_series/J5055_class_79_00358_volume.mrc
Opened J5055_class_79_00358_volume.mrc as #80, grid size 72,72,72, pixel 5.19,
shown at level 2.22, step 1, values float32
> volume #* level 1.3
> tool show Models
> hide #!2-80 target m
> symclip 10
> select clear
> show #!2 target m
> hide #!1 target m
> show #!3 target m
> hide #!2 target m
> show #!4 target m
> hide #!3 target m
> show #!5 target m
> hide #!4 target m
> show #!6 target m
> hide #!5 target m
> show #!5 target m
> hide #!6 target m
> show #!4 target m
> hide #!5 target m
> show #!3 target m
> hide #!4 target m
> show #!2 target m
> hide #!3 target m
> show #!1 target m
> hide #!2 target m
> show #!80 target m
> hide #!1 target m
> show #!79 target m
> hide #!80 target m
> show #!80 target m
> hide #!79 target m
> show #!1 target m
> hide #!80 target m
> volume #* level 1.1
> show #!2 target m
> hide #!1 target m
> show #!3 target m
> hide #!2 target m
> show #!4 target m
> hide #!3 target m
> show #!5 target m
> hide #!4 target m
> show #!6 target m
> hide #!5 target m
> show #!7 target m
> hide #!6 target m
> show #!8 target m
> hide #!7 target m
> show #!9 target m
> hide #!8 target m
> show #!10 target m
> hide #!9 target m
> show #!11 target m
> hide #!10 target m
> show #!12 target m
> hide #!11 target m
> show #!13 target m
> hide #!12 target m
> show #!14 target m
> hide #!13 target m
> show #!15 target m
> hide #!14 target m
> show #!16 target m
> hide #!15 target m
> volume #* level 10.5
> volume #* level 0.5
> show #!17 target m
> hide #!16 target m
> show #!18 target m
> hide #!17 target m
> show #!19 target m
> hide #!18 target m
> show #!20 target m
> hide #!19 target m
> show #!21 target m
> hide #!20 target m
> show #!22 target m
> hide #!21 target m
> show #!23 target m
> hide #!22 target m
> show #!24 target m
> hide #!23 target m
> show #!25 target m
> hide #!24 target m
> show #!26 target m
> hide #!25 target m
> show #!27 target m
> hide #!26 target m
> show #!28 target m
> hide #!27 target m
> show #!29 target m
> hide #!28 target m
> show #!30 target m
> hide #!29 target m
> show #!31 target m
> hide #!30 target m
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 420, in _seq_key_press
self._next_model()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 399, in _next_model
self._show_next_model(1)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 425, in _show_next_model
cur_shown = [m for m in self.models
^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/model_panel/tool.py", line 426, in <listcomp>
if m.display and m in self.skip_models and not self.skip_models[m]]
^^^^^^^^^
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
TypeError: object of type 'NoneType' has no len()
TypeError: object of type 'NoneType' has no len()
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/graphics/drawing.py", line 389, in get_display
return self._any_displayed_positions and len(self._positions) > 0
^^^^^^^^^^^^^^^^^^^^
See log for complete Python traceback.
OpenGL version: 4.1 Metal - 88
OpenGL renderer: Apple M2 Max
OpenGL vendor: Apple
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,5
Model Number: Z17J00171LL/A
Chip: Apple M2 Max
Total Number of Cores: 12 (8 performance and 4 efficiency)
Memory: 64 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 8 hours, 12 minutes
Graphics/Displays:
Apple M2 Max:
Chipset Model: Apple M2 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 30
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.14
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.52
ChimeraX-AtomicLibrary: 12.1.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.11
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.8.dev202401040148
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.3
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.9
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.15
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.2.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11.1
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.14.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.5
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.0
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (7)
comment:1 by , 22 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → self._positions is None |
comment:2 by , 22 months ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
This code is calling "m.display" to see if a model is displayed on a model that has been closed (ie. deleted). I'd guess that is a bug in the Model Panel _show_next_model code although I have not studied that code. Maybe that code needs to check if the model is deleted (m.deleted) before asking if it is displayed if there is a possibility that the models in the list it is scanning have been closed.
Reassigning to Eric since he wrote the _show_next_model code.
comment:3 by , 22 months ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
Using the arrow keys does not close any models -- it only hides and shows models. Using the maps that Oliver supplied (https://www.dropbox.com/s/9pksw6kef16xc2b/cryosparc_P1_J5055_00358_volume_series.zip?dl=0 -- but probably happens with any maps) you do not get the error using the up/down arrow keys rapidly unless there is a clip cap being shown. I'm guessing this error is because of a destroyed clip-cap model.
comment:4 by , 22 months ago
| Cc: | added; removed |
|---|---|
| Owner: | changed from to |
comment:6 by , 22 months ago
Yes clip caps will dynamically be created and deleted as models are shown and hidden so that is probably the issue. If your code makes a list of models and then changes display, you cannot rely on those clip cap models in your list still being open.
I would think this show/hide models would only apply to top level models, so it would never be looking at clip cap models.
comment:7 by , 22 months ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
Indeed my code keeps a list of models and also a list of top-level and near-top-level (grouped) models that participate in the arrow display sequence. I fixed the problem two ways. One was that the code knows when the main model list needs updating (which happens when the table redraws), so if that's the case then it ignores that arrow event. The other is along the lines of what you said. The code figured out currently displayed models in the display sequence with "m.display and m-in-display-sequence" and I swapped the order of those tests.
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This _seems_ like it would have to be a bug in the drawing code...