map_series: model is None

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/sudipag@amgen.com/Desktop/CRBN-
> DDB1-3507636/Vseries/J1108_substracted_J1192_BPB_masked_J1186_CRBN_masked.cxs
> format session

Opened map series J1108_class_00_00140_volume.mrc as #1, 8 images, grid size
80,80,80, pixel 2.6, shown at level 0.242, step 1, values float32  
Opened map series J1192_class_00_00130_volume.mrc as #2, 10 images, grid size
80,80,80, pixel 2.6, shown at level 0.269, step 1, values float32  
Opened map series J1186_class_00_00132_volume.mrc as #3, 10 images, grid size
80,80,80, pixel 2.6, shown at level 0.228, step 1, values float32  
Log from Wed Feb 7 13:29:03 2024You can double click a model's Name or ID in
the model panel to edit those fields  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_00_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_01_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_02_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_03_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_04_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_05_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_06_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_07_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_08_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_09_00140_volume.mrc
> vseries true

Opened map series J1108_class_00_00140_volume.mrc as #1, 10 images, grid size
80,80,80, pixel 2.6, shown at level 0.201, step 1, values float32  

> movie record

> movie encode /Users/sudipag@amgen.com/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Movie encoding failed because no images were recorded.  

> close #1

> open
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_00_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_01_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_02_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_03_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_04_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_05_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_06_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_07_00140_volume.mrc

Opened J1108_class_00_00140_volume.mrc as #1.1, grid size 80,80,80, pixel 2.6,
shown at level 0.201, step 1, values float32  
Opened J1108_class_01_00140_volume.mrc as #1.2, grid size 80,80,80, pixel 2.6,
shown at level 0.213, step 1, values float32  
Opened J1108_class_02_00140_volume.mrc as #1.3, grid size 80,80,80, pixel 2.6,
shown at level 0.214, step 1, values float32  
Opened J1108_class_03_00140_volume.mrc as #1.4, grid size 80,80,80, pixel 2.6,
shown at level 0.212, step 1, values float32  
Opened J1108_class_04_00140_volume.mrc as #1.5, grid size 80,80,80, pixel 2.6,
shown at level 0.214, step 1, values float32  
Opened J1108_class_05_00140_volume.mrc as #1.6, grid size 80,80,80, pixel 2.6,
shown at level 0.22, step 1, values float32  
Opened J1108_class_06_00140_volume.mrc as #1.7, grid size 80,80,80, pixel 2.6,
shown at level 0.217, step 1, values float32  
Opened J1108_class_07_00140_volume.mrc as #1.8, grid size 80,80,80, pixel 2.6,
shown at level 0.22, step 1, values float32  

> close #1

> open
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_00_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_01_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_02_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_03_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_04_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_05_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_06_00140_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_class_07_00140_volume.mrc
> vseries true

Opened map series J1108_class_00_00140_volume.mrc as #1, 8 images, grid size
80,80,80, pixel 2.6, shown at level 0.201, step 1, values float32  

> volume #1.1 level 0.2974

> save
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1108_00140_volume_series/J1108_volume_series.cxs

> save /Users/sudipag@amgen.com/Desktop/CRBN-
> DDB1-3507636/Vseries/J1108_vseries_substracted_particles.cxs

> open
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_00_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_01_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_02_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_03_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_04_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_05_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_06_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_07_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_08_00130_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1192_00130_volume_series/J1192_class_09_00130_volume.mrc
> vseries true

Opened map series J1192_class_00_00130_volume.mrc as #2, 10 images, grid size
80,80,80, pixel 2.6, shown at level 0.269, step 1, values float32  

> hide #!1 models

> color #2.1 #00f900ff models

> color #2.1 #ff9300ff models

> color #2.1 #fffc79ff models

> color #2.1 #d4fb79ff models

> color #2.1 black models

> color #2.1 #d4fb79ff models

> color #2.1 #d4fb7987 models

> color #2.1 #d4fb7986 models

> color #2.1 #d4fb7964 models

> color #2.1 #d4fb798f models

> hide #!2 models

> open
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_00_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_01_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_02_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_03_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_04_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_05_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_06_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_07_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_08_00132_volume.mrc
> /Users/sudipag@amgen.com/Downloads/cryosparc_P39_J1186_00132_volume_series/J1186_class_09_00132_volume.mrc
> vseries true

Opened map series J1186_class_00_00132_volume.mrc as #3, 10 images, grid size
80,80,80, pixel 2.6, shown at level 0.251, step 1, values float32  

> surface dust #3.6 size 26

> volume #3.6 level 0.2277

> hide #!2.6 models

> save /Users/sudipag@amgen.com/Desktop/CRBN-
> DDB1-3507636/Vseries/J1108_substracted_J1192_BPB_masked_J1186_CRBN_masked.cxs

——— End of log from Wed Feb 7 13:29:03 2024 ———

opened ChimeraX session  

> show #!2 models

> hide #!3 models

> hide #!2 models

> show #!3 models

> surface dust #3.5 size 26

> surface dust #3.4 size 26

> surface dust #3.8 size 26

> surface dust #3.10 size 26

> hide #!3 models

> show #!3 models

> show #!3.1 models

> surface dust #3.1 size 26

> surface dust #3.5 size 26

> show #!3.2 models

> surface dust #3.1 size 26

> surface dust #3.2 size 26

> surface dust #3.5 size 26

> show #!3.3 models

> surface dust #3.1 size 26

> surface dust #3.2 size 26

> surface dust #3.3 size 26

> surface dust #3.5 size 26

> show #!3.4 models

> surface dust #3.1 size 26

> surface dust #3.2 size 26

> surface dust #3.3 size 26

> surface dust #3.4 size 26

> surface dust #3.5 size 26

> show #!3.6 models

> surface dust #3.1 size 26

> surface dust #3.2 size 26

> surface dust #3.3 size 26

> surface dust #3.4 size 26

> surface dust #3.5 size 26

> surface dust #3.6 size 26

> hide #!3 models

> show #!3 models

> surface dust #3.9 size 26

> show #!3.1 models

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> show #!3.1 models

> show #!3.2 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.3 models

> hide #!3.2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!1 models

> show #!1.1 models

> show #!1.2 models

> show #!1.3 models

> show #!1.4 models

> surface dust #1.1 size 26

> surface dust #1.2 size 26

> surface dust #1.3 size 26

> surface dust #1.4 size 26

> surface dust #1.5 size 26

> show #!1.6 models

> show #!1.7 models

> surface dust #1.1 size 26

> surface dust #1.2 size 26

> surface dust #1.3 size 26

> surface dust #1.4 size 26

> surface dust #1.5 size 26

> surface dust #1.6 size 26

> surface dust #1.7 size 26

> show #!1.8 models

> open /Users/sudipag@amgen.com/Desktop/CRBN-DDB1-3507636/8D80_IKZF-
> ligand_deleted.pdb

Chain information for 8D80_IKZF-ligand_deleted.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> hide #!1.1 models

> show #!1.1 models

> select add #4

10970 atoms, 11184 bonds, 1 pseudobond, 1513 residues, 2 models selected  

> ui mousemode right "translate selected models"

> view matrix models #4,1,0,0,-71.339,0,1,0,-87.042,0,0,1,13.363

> ui mousemode right "rotate selected models"

> view matrix models
> #4,0.8571,-0.42229,-0.29505,41.606,0.17758,0.77983,-0.60028,-1.9015,0.48358,0.4621,0.74338,-76.153

> show #!3 models

> hide #!3 models

> show #!3.1 models

> hide #!1 models

> hide #!1.1 models

> view matrix models
> #4,0.56133,-0.07893,0.82382,-112.36,0.75555,0.4551,-0.4712,-46.038,-0.33773,0.88693,0.3151,23.052

> ui mousemode right "translate selected models"

> view matrix models
> #4,0.56133,-0.07893,0.82382,-68.363,0.75555,0.4551,-0.4712,10.063,-0.33773,0.88693,0.3151,-18.861

> view matrix models
> #4,0.56133,-0.07893,0.82382,-146.99,0.75555,0.4551,-0.4712,28.179,-0.33773,0.88693,0.3151,-25.543

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.74458,-0.32122,-0.58517,228.93,-0.45936,-0.38951,0.7983,129.75,-0.48436,0.86319,0.14246,18.052

> view matrix models
> #4,-0.80209,-0.17024,-0.57242,213.94,-0.36337,-0.62153,0.69402,162.75,-0.47393,0.76467,0.43666,-7.7461

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.80209,-0.17024,-0.57242,240.25,-0.36337,-0.62153,0.69402,115.22,-0.47393,0.76467,0.43666,0.43448

> view matrix models
> #4,-0.80209,-0.17024,-0.57242,285.44,-0.36337,-0.62153,0.69402,100.55,-0.47393,0.76467,0.43666,3.4509

> view matrix models
> #4,-0.80209,-0.17024,-0.57242,288.57,-0.36337,-0.62153,0.69402,148.58,-0.47393,0.76467,0.43666,4.2457

> view matrix models
> #4,-0.80209,-0.17024,-0.57242,295.15,-0.36337,-0.62153,0.69402,139.97,-0.47393,0.76467,0.43666,0.55861

> ui mousemode right "rotate selected models"

> view matrix models
> #4,-0.98597,-0.14315,-0.085887,251.62,-0.044238,-0.27204,0.96127,18.656,-0.16097,0.95158,0.26189,-41.044

> ui mousemode right "translate selected models"

> view matrix models
> #4,-0.98597,-0.14315,-0.085887,252.13,-0.044238,-0.27204,0.96127,19.199,-0.16097,0.95158,0.26189,-37.103

> fitmap #4 inMap #3.10

Fit molecule 8D80_IKZF-ligand_deleted.pdb (#4) to map
J1186_class_09_00132_volume.mrc (#3.10) using 10970 atoms  
average map value = 0.2618, steps = 96  
shifted from previous position = 9.94  
rotated from previous position = 16.5 degrees  
atoms outside contour = 4727, contour level = 0.22773  
  
Position of 8D80_IKZF-ligand_deleted.pdb (#4) relative to
J1186_class_09_00132_volume.mrc (#3.10) coordinates:  
Matrix rotation and translation  
-0.95812442 -0.26048553 -0.11893224 277.57870397  
0.02892148 -0.50124050 0.86482455 56.99520585  
-0.28488793 0.82516982 0.48778439 -31.20689367  
Axis -0.11803351 0.49397219 0.86142880  
Axis point 133.08912154 50.89160504 0.00000000  
Rotation angle (degrees) 170.32956033  
Shift along axis -31.49205854  
  

> transparency #3.10.1 50

> select clear

> set bgColor white

> color bychain

> color zone #3.3 near #4 distance 15.6

> transparency #3.3.1 50

> ui tool show "Show Sequence Viewer"

> sequence chain /B

Alignment identifier is 4/B  

> select /B:351

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:351-360

82 atoms, 85 bonds, 10 residues, 1 model selected  

> select /B:347

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:347-362

125 atoms, 129 bonds, 16 residues, 1 model selected  

> select /B:349

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /B:349-361

108 atoms, 112 bonds, 13 residues, 1 model selected  

> select /B:352

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /B:352-362

88 atoms, 91 bonds, 11 residues, 1 model selected  

> select
> /B:78-83,96-101,119-125,133-141,143-145,155-166,178-185,320-322,346-350,356-360,368-371,385-391,400-403,423-425

643 atoms, 643 bonds, 82 residues, 1 model selected  

> select /B:347

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /B:347-360

111 atoms, 115 bonds, 14 residues, 1 model selected  

> color sel yellow

> color zone #3.3 near sel & #4 distance 15.6

[Repeated 1 time(s)]

> undo

[Repeated 1 time(s)]

> select clear

> show #!3.1 models

> show #!1.4 models

> show #!1.3 models

> show #!1.2 models

> show #!1.1 models

> hide #!1 models

> hide #!1.1 models

> hide #!1.2 models

> hide #!1.3 models

> hide #!1.4 models

> hide #!3 models

> hide #!3.1 models

> show #!3 models

> color zone #3.10 near #4 distance 15.6

> hide #!3 models

> show #!3.1 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.  

> hide #!3 models

> show #!3 models

> hide #!3 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> show #!3 models

> hide #!3 models

> show #!1.8 models

> hide #!1.8 models

> show #!1.8 models

> hide #!1.8 models

> show #!3.2 models

> hide #!3.1 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.  

[Repeated 1 time(s)]

> hide #!3 models

> hide #!3.2 models

> show #!3.2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!3.1 models

> hide #!3.1 models

> show #!3.1 models

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.  

> hide #!3 models

> show #!3.2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3.3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> show #!3.10 models

[Repeated 1 time(s)]

> hide #!3.9 models

> transparency #3.10.1 50

> hide #!3.10 models

> show #!3.9 models

> color zone #3.9 near #4 distance 15.6

> transparency #3.9.1 50

> hide #!3.9 models

> show #!3.8 models

> color zone #3.8 near #4 distance 15.6

> transparency #3.8.1 50

> hide #!3.8 models

> show #!3.7 models

> color zone #3.7 near #4 distance 15.6

> transparency #3.7.1 50

> hide #!3.7 models

> show #!3.6 models

> color zone #3.6 near #4 distance 15.6

> transparency #3.6.1 50

> show #!3.5 models

> hide #!3.6 models

> color zone #3.5 near #4 distance 15.6

> transparency #3.5.1 50

> show #!3.4 models

> hide #!3.5 models

> color zone #3.4 near #4 distance 15.6

> transparency #3.4.1 50

> hide #!3.4 models

> show #!3.3 models

> color zone #3.3 near #4 distance 15.6

> transparency #3.3.1 50

> hide #!3.3 models

> show #!3.2 models

> color zone #3.2 near #4 distance 15.6

> transparency #3.2.1 50

> hide #!3.2 models

> show #!3.1 models

> color zone #3.1 near #4 distance 15.6

> transparency #3.1.1 50

> cd /Users/sudipag@amgen.com/Desktop/CRBN-DDB1-3507636/Vseries/Vseries/J1186

Current working directory is: /Users/sudipag@amgen.com/Desktop/CRBN-
DDB1-3507636/Vseries/Vseries/J1186  

> vseries play #3 jumpto0

Expected a keyword  

> hide #!1 models

> vseries play #3 jumpto0

Expected a keyword  

> vseries play #3 jumpTo 0

> show #!3.2 models

> hide #!3.1 models

> show #!3.3 models

> hide #!3.3 models

> show #!3.4 models

> hide #!3.4 models

> show #!3.5 models

> hide #!3.5 models

> show #!3.6 models

> hide #!3.6 models

> show #!3.7 models

> hide #!3.2 models

> color zone #3.7 near #4 distance 15.6

> transparency #3.7.1 50

> hide #!3.7 models

> show #!3.8 models

> hide #!3.8 models

> show #!3.9 models

> hide #!3.9 models

> show #!3.10 models

> hide #!3.10 models

> show #!3.1 models

> hide #!3 models

> show #!3 models

> vseries play #3 jumpTo 0

> movie record

> vseries play #3 loop true

> wait 300

> movie stop

> show #3.2 models

> movie encode J1186_class_loop_withPBB_level0pt23.mp4 framerate 30

Movie saved to J1186_class_loop_withPBB_level0pt23.mp4  
  

> movie encode J1186_class_loop_withPBB_level0pt23.mp4 framerate 60

No frames have been recorded  

> movie stop

No movie being recorded.  

> hide #3.1 models

> hide #3.2 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> vseries play #3 jumpTo 0

> hide #!3 models

> show #!2 models

> hide #!2 models

> show #!3 models

> vseries play #3 jumpTo 0

> close #3.1

> movie record

> movie encode /Users/sudipag@amgen.com/Desktop/movie.mp4 framerate 25.0

Error processing trigger "new frame":  
Movie encoding failed because no images were recorded.  

> hide #!3 models

> show #!2 models

> color zone #2.9 near #4 distance 15.6

> transparency #2.3.1 0

> transparency #2.6.1 50

> vseries play #1 jumpTo 0

[Repeated 1 time(s)]

> movie record

> vseries play #2 loop true

> movie stop

> movie encode 1192_class_loop_withPBD.mp4 framerate 3

Movie saved to 1192_class_loop_withPBD.mp4  
  

> vseries play #2 jumpTo 0

> movie record

> wait 60

> movie stop

> movie encode J1192_class_wait60_withPDB.mp4

Movie saved to J1192_class_wait60_withPDB.mp4  
  

> vseries play #2 jumpTo 0

> movie record

> wait 60

> movie stop

> movie encode J1192_wait60_framerate15_withPDB.mp4 framerate 15

Movie saved to J1192_wait60_framerate15_withPDB.mp4  
  

> vseries play #2 jumpTo 0

> movie record

> vseries play #2 loop true

> wait 60

> movie stop

> movie encode J1192_wait60_framerate_5.mp4 framerate 5

Movie saved to J1192_wait60_framerate_5.mp4  
  

> vseries play #2 jumpTo 0

> movie record

> vseries play #2 loop true

> wait 60

> movie encode J1192_wait60_framerate3.mp4 framerate 3

Movie saved to J1192_wait60_framerate3.mp4  
  

> hide #2.1 models

> hide #!2 models

> show #!3 models

> vseries play #1 jumpTo 0

> movie record

> movie stop

> vseries play #3 jumpTo 0

> movie record

> vseries play #3 loop true

> wait 60

> movie stop

> hide #!4 models

> show #!4 models

> movie encode J1186_wait60_framerate3.mp4 framerate 3

Movie saved to J1186_wait60_framerate3.mp4  
  

> movie stop

No movie being recorded.  

> vseries play #3 jumpTo 0

> movie record

> volume #3 level 0.27

> hide #!3 models

> show #!3 models

> movie record

Already recording a movie  

> movie encode /Users/sudipag@amgen.com/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/sudipag@amgen.com/Desktop/movie.mp4  
  

> volume #3 level 0.27

> volume play #3 jumpto 0

Expected a density maps specifier or a keyword  

> movie record

> movie encode /Users/sudipag@amgen.com/Desktop/movie.mp4 framerate 25.0

Movie saved to /Users/sudipag@amgen.com/Desktop/movie.mp4  
  

> volume play #3 jumpto 0

Expected a density maps specifier or a keyword  

> vseries play #3 jumpTo 0

> movie record

> wait 30

> movie stop

> movie encode J1186_wait30_framerate2.mp4 framerate 2

Movie saved to J1186_wait30_framerate2.mp4  
  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show # models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> hide # models

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> show #!2 models

> hide #!2 models

> show #!3 models

> ui tool show "Side View"

> ui mousemode right zoom

> vseries play #3 jumpTo 0

> movie record

> wait 30

> movie stop

> movie encode J1186_topview_wait30_framerate2.mp4 framerate 2

Movie saved to J1186_topview_wait30_framerate2.mp4  
  

> view

> vseries play #3 jumpTo 0

> movie record

> vseries play #3 loop true

> wait 60

> movie stop

> movie encode J1186_wait60_framerate2.mp4 framerate 2

Movie saved to J1186_wait60_framerate2.mp4  
  

> hide #!3 models

> show #!2 models

> vseries play #2 jumpTo 0

> movie record

> vseries play #2 loop true

> wait 30

> movie stop

> moive encode J1192_wait30_framerate2.mp4 framerate 2

Unknown command: moive encode J1192_wait30_framerate2.mp4 framerate 2  

> movie encode J1192_wait30_framerate2.mp4 framerate 2

Movie saved to J1192_wait30_framerate2.mp4  
  

> color #2 #d4fb79d4 models

> color #2 #d4fb79ec models

> color #2 #d4fb79f4 models

> color #2 #ff2f92ff models

> color #2 #ff2f9217 models

> color #2 #ff2f9211 models

> color #2 #ff2f9219 models

> color #2 #ff2f921f models

> color #2 #ff2f9251 models

> color #2 #ff2f9219 models

> color #2 #ff2f9211 models

> color #2 #ff2f9212 models

> color #2 #9437ffff models

> color #2 #9437ff19 models

> color #2 #9437ff16 models

> color #2 #9437ff15 models

> color #2 #fffc79ff models

> color #2 #fffc7926 models

> color #2 #00fdffff models

> color #2 #00fdff15 models

> color #2 #00fdff08 models

> color #2 #d4fb79ff models

> color #2 #d4fb792d models

> color #2 #d4fb7939 models

> color #2 #d4fb793a models

> color #2 #d4fb793b models

> color #2 #ff2f92ff models

> color #2 #ff2f9213 models

> color #2 #ff2f9212 models

> color #2 #ff2f920f models

> color #2 silver models

> color #2 #c0c0c022 models

> color #2 #c0c0c023 models

> color #2 #c0c0c01f models

> color #2 #c0c0c020 models

> color #2 darkgrey models

> color #2 #a9a9a9e4 models

> color #2 #a9a9a9e8 models

> color #2 #a9a9a9e2 models

> color #2 #ebebebff models

> color #2 darkgrey models

> color #2 #011993ff models

> color #2 #531b93ff models

> color #2 #942193ff models

> color #2 #ff40ffff models

> color #2 #ff85ffff models

> color #2 #73fdffff models

> color #2 #73fa79ff models

> color #2 #d4fb79ff models

> color #2 #fffc79ff models

> color #2 #ffd479ff models

> color #2 #ff9300ff models

> color #2 #941100ff models

> color #2 black models

> color #2 #d6d6d6ff models

> lighting full

> lighting shadows false

> graphics silhouettes true

> vseries play #2 jumpTo 0

> movie record

> vseries play #2 loop true

> wait 30

> movie stop

> movie encode J1192_BPB_movement_wait30_framerate2.mp4 framerate 2

Movie saved to J1192_BPB_movement_wait30_framerate2.mp4  
  

> hide #!2 models

> show #!3 models

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows true

> lighting flat

[Repeated 1 time(s)]

> lighting full

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 253, in set_model_color  
run(ses, cmd, log=False)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 178, in color  
_set_model_colors(session, objects.models, color, opacity, undo_state)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/std_commands/color.py", line 385, in _set_model_colors  
m.model_color = c  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 255, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
AttributeError: 'NoneType' object has no attribute 'model_color'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map_series/series.py", line 94, in _set_model_color  
m.model_color = color  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 258, in log_delayed_cmd  
Command(ses).run(but.delayed_cmd_text, log_only=True)  
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'  
  
AttributeError: 'MultiColorButton' object has no attribute 'delayed_cmd_text'  
  
File
"/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/model_panel/tool.py", line 258, in log_delayed_cmd  
Command(ses).run(but.delayed_cmd_text, log_only=True)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-4.14.1
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      System Firmware Version: 2020.80.5.0.1 (iBridge: 21.16.3049.0.0,0)
      OS Loader Version: 577.140.2~22

Software:

    System Software Overview:

      System Version: macOS 13.6.4 (22G513)
      Kernel Version: Darwin 22.6.0
      Time since boot: 4 days, 22 hours, 47 minutes

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-020
      Option ROM Version: 113-D32206U1-020
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          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: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    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: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    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: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    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: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

[Tom Goddard]

User closed one volume of a series. I believe the ChimeraX volume series code was fixed to allow for deleted volumes in a series a year ago. This report is in ChimeraX 1.6.