cannot select an axis to squeeze out which has size not equal to one

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-150-generic-x86_64-with-glibc2.27
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /home/junhe/Desktop/sperm-tem-segmentation/m1.cxs

Opened sperm-3drendring-rtx.mrc as #15.1, grid size 484,824,463, pixel 100,
shown at step 1, values float32  
Opened fib-2.mrc as #15.2, grid size 484,463,5, pixel 100, shown at level
-0.0365, step 1, values float32  
Opened fib-1.mrc as #15.3, grid size 484,463,5, pixel 100, shown at level
-0.0431, step 1, values float32  
Log from Mon Jun 3 04:37:06 2024UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open all.cxs

Log from Wed Jan 10 22:16:40 2024UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /media/junhe/Win10/sperm-paper/fs1/2th/a1.cxs

Log from Sat Jul 15 11:08:47 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open all.cxs

Log from Sat Jul 15 09:58:40 2023UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open C:\\\sperm-paper\\\fs1\\\2th\\\all.cxs

Log from Fri Jul 14 20:22:17 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open all.cxs

Log from Fri Jul 14 18:53:59 2023UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open pm.mod

Read IMOD model pm.mod, pixel size 10, 2 surfaces  

> open acrosome.mod

Read IMOD model acrosome.mod, pixel size 10, 2 surfaces  

> hide #1.2 models

> show #1.2 models

> hide #1.1 models

> set bgColor white

> close #1.1

> hide #2.1 models

> hide #2.2 models

> show #2.1 models

> hide #2.1 models

> hide #1.2 models

> hide #!2 models

> show #2.1 models

> close #2.1

> color #2.2 #729fcf transparency 0

> show #2.2 models

> show #1.2 models

> color #1.2 #8ae234 transparency 0

> select #1.2

1 model selected  

> transparency sel 50

> transparency #1 80

> transparency #1 90

> ~select #1.2

Nothing selected  

> open /home/junhe/Downloads/nucleus.mod

Read IMOD model /home/junhe/Downloads/nucleus.mod, pixel size 10, 2 surfaces  

> hide #3.1 models

> hide #3.2 models

> show #3.1 models

> show #3.2 models

> hide #3.1 models

> close #3.1

> color #3 #8640bf models transparency 0

> color #3 #9140bf models transparency 0

> color #3 #b689cf models transparency 0

> color #3 #b387cc models transparency 0

> color #3 #9b80aa models transparency 0

> color #3 #c18fdd models transparency 0

> color #3 #ce8fdd models transparency 0

> color #3 #c68fdd models transparency 0

> color #3 #cd8fdd models transparency 0

> color #3 #d28fdd models transparency 0

> color #3 #d58fdd models transparency 0

> color #3 #c68fdd models transparency 0

> color #3 #bc85d3 models transparency 0

> color #3 #bd93ce models transparency 0

> color #3 #bb92cc models transparency 0

[Repeated 1 time(s)]

> color #1 rgb(1,1,1)

> color #3 rgb(220,221,254)

> hide #!3 models

> show #!3 models

> hide #3.2 models

> show #3.2 models

> hide #2.2 models

> show #2.2 models

> hide #!1 models

> color #3 rgb(168,240,237)

> color #3.2 #bb92cc transparency 0

> open /home/junhe/Downloads/calyx.mod

Read IMOD model /home/junhe/Downloads/calyx.mod, pixel size 10, 3 surfaces  

> hide #4.1 models

> color #4.1 #3465a4 transparency 0

> color #4.1 #204a87 transparency 0

> color #4.2 #3465a4 transparency 0

> show #4.1 models

> hide #4.1 models

> color #4.3 #3465a4 transparency 0

> hide #4.2 models

> show #4.2 models

> show #4.1 models

> hide #4.2 models

> color #4.1 #3465a4 transparency 0

> hide #4.1 models

> show #4.2 models

> close #4.1

> open /home/junhe/Downloads/nm.mod

Read IMOD model /home/junhe/Downloads/nm.mod, pixel size 10, 2 surfaces  

> hide #5.1 models

> close #5.1

> color #5.2 #edd400 transparency 0

> open /home/junhe/Downloads/sc.mod

Read IMOD model /home/junhe/Downloads/sc.mod, pixel size 10, 1 surfaces  

> color #6 #75507b transparency 0

> open /home/junhe/Downloads/mt.mod

Read IMOD model /home/junhe/Downloads/mt.mod, pixel size 10, 1 surfaces  

> color #7 #204a87 transparency 0

> open /home/junhe/Downloads/mito.mod

Read IMOD model /home/junhe/Downloads/mito.mod, pixel size 10, 5 surfaces  

> color #8 #f57900 models transparency 0

> open /home/junhe/Downloads/vacuole.mod

Read IMOD model /home/junhe/Downloads/vacuole.mod, pixel size 10, 3 surfaces  

> hide #5.2 models

> hide #!3 models

> color #9 #4e9a06 models transparency 0

> color #9 #d3d7cf models transparency 0

> color #9 #73d216 models transparency 0

> show #5.2 models

> hide #5.2 models

> open /home/junhe/Downloads/nuclear-lipid.mod

Read IMOD model /home/junhe/Downloads/nuclear-lipid.mod, pixel size 10, 4
surfaces  

> hide #10.3 models

> show #10.3 models

> hide #10.3 models

> close #10.3

> close #10.1

> color #10 #4e9a06 models transparency 0

> color #9 #babdb6 models transparency 0

[Repeated 1 time(s)]

> open /home/junhe/Downloads/vesicle.mod

Read IMOD model /home/junhe/Downloads/vesicle.mod, pixel size 10, 8 surfaces  

> color #11 #bf40ae models transparency 0

> color #11 #bf40a3 models transparency 0

> color #11 #d579c1 models transparency 0

> color #11 #da9bcc models transparency 0

[Repeated 1 time(s)]

> show #5.2 models

> hide #5.2 models

> show #5.2 models

> show #!3 models

> hide #!3 models

> show #!3 models

> open /home/junhe/Downloads/pm.mod

Read IMOD model /home/junhe/Downloads/pm.mod, pixel size 10, 2 surfaces  

> hide #12.1 models

> close #12.1

> color #12.2 #4e9a06 transparency 0

> color #12.2 #8ae234 transparency 0

> transparency #12 90

> save /home/junhe/Downloads/all.cxs includeMaps true

——— End of log from Fri Jul 14 18:53:59 2023 ———

opened ChimeraX session  

> open /media/junhe/Win10/sperm-paper/fs1/2th/pr.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/pr.mod, pixel size 10,
2 surfaces  

> hide #13.2 models

> hide #13.1 models

> show #13.2 models

> show #13.1 models

> color #13 #ef2929 models transparency 0

> close #13

> open /media/junhe/Win10/sperm-paper/fs1/2th/pr.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/pr.mod, pixel size 10,
2 surfaces  

> hide #13.1 models

> color #13.1 #ef2929 transparency 0

> color #13.2 #ef2929 transparency 0

> save /media/junhe/Win10/sperm-paper/fs1/2th/all.cxs includeMaps true

——— End of log from Fri Jul 14 20:22:17 2023 ———

opened ChimeraX session  

> lighting soft

> save C:/sperm-paper/fs1/2th/all.cxs

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> color #2 #e5f3ffff models

> color #2 #729fcfff models

> color #3 #e5f3ffff models

> color #3 #cbcbfdff models

> color #4 royalblue models

> color #5 #edd400ff models

> color #6 #5c3566ff models

> color #7 #1c4175ff models

> color #7 #1d447aff models

> color #8 darkorange models

> color #10 lawngreen models

> color #10 white models

[Repeated 1 time(s)]

> color #10 #050708ff models

> color #11 darkorange models

> color #13 #ef2929ff models

> color #10 #fcb9feff models

> save C:/sperm-paper/fs1/2th/all.cxs

——— End of log from Sat Jul 15 09:58:40 2023 ———

opened ChimeraX session  

> color #11 #ffb2ff models transparency 0

> transparency #5 90

[Repeated 1 time(s)]

> color #3.2 #bf404062 models

> color #3.2 #bf4040 models transparency 0

> color #12.2 #bf4040cd models

> color #12.2 #8ae234 models transparency 0

> color #12.2 #bf404052 models

> color #12.2 #47bf4052 models

> color #12.2 #68bf4052 models

> color #12.2 #68bf4005 models

> color #12.2 #68bf4006 models

[Repeated 1 time(s)]

> save /home/junhe/Desktop/sem-1.png pixelSize 13 transparentBackground true

> save /media/junhe/Win10/sperm-paper/fs1/2th/a1.cxs

——— End of log from Sat Jul 15 11:08:47 2023 ———

opened ChimeraX session  

> open /media/junhe/Win10/sperm-paper/fs1/2th/calyx-1.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/calyx-1.mod, pixel size
10, 4 surfaces  

> close #14

> open /media/junhe/Win10/sperm-paper/fs1/2th/calyx-1.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/calyx-1.mod, pixel size
10, 4 surfaces  

> close #14

> open /media/junhe/Win10/sperm-paper/fs1/2th/calyx-2.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/calyx-2.mod, pixel size
10, 4 surfaces  

> close #14

> open /media/junhe/Win10/sperm-paper/fs1/2th/calyx-3.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/calyx-3.mod, pixel size
10, 4 surfaces  

> close #14

> open /media/junhe/Win10/sperm-paper/fs1/2th/calyx-4.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/calyx-4.mod, pixel size
10, 4 surfaces  

> hide #!14 models

> color #4.2 #ffffb2 models transparency 0

> color #4.2 royalblue models transparency 0

> color #14 royalblue models transparency 0

> show #!14 models

> graphics silhouettes true

> save /home/junhe/Desktop/image1.png supersample 3

> close #14

> open /media/junhe/Win10/sperm-paper/fs1/2th/calyx-5.mod

Read IMOD model /media/junhe/Win10/sperm-paper/fs1/2th/calyx-5.mod, pixel size
10, 4 surfaces  

> color #14 royalblue models transparency 0

> save /media/junhe/Win10/sperm-paper/fs1/2th/all.cxs

——— End of log from Wed Jan 10 22:16:40 2024 ———

opened ChimeraX session  

> open /home/junhe/Desktop/sperm-tem-segmentation/sperm-3drendring-rtx.mrc
> /home/junhe/Desktop/sperm-tem-segmentation/fib-2.mrc
> /home/junhe/Desktop/sperm-tem-segmentation/fib-1.mrc

Opened sperm-3drendring-rtx.mrc as #15.1, grid size 484,824,463, pixel 100,
shown at level 211, step 4, values float32  
Opened fib-2.mrc as #15.2, grid size 484,463,5, pixel 100, shown at level
0.0002, step 1, values float32  
Opened fib-1.mrc as #15.3, grid size 484,463,5, pixel 100, shown at level
0.0002, step 1, values float32  

> volume #15.2 level -0.03647

> volume #15.3 level -0.04313

> volume #15.1 level 208.6

> volume #15.1 style image region 0,0,228,483,823,228 step 1 showOutlineBox
> true

> volume #15.1 level 73.9,0 level 208.9,0.8 level 254.8,1

> volume #15.1 level 73.9,0 level 173.7,0.9406 level 254.8,1

> volume #15.1 level 98.86,0.2031 level 173.7,0.9406 level 254.8,1

> volume #15.1 level 98.86,0.2031 level 173.7,0.9406 level 236.6,0.7812

> volume #15.1 level 98.86,0.2031 level 38.66,0.2812 level 236.6,0.7812

> volume #15.1 level 105.6,0.8281 level 38.66,0.2812 level 236.6,0.7812

> volume #15.1 level 105.6,0.8281 level 35.57,0.2969 level 236.6,0.7812

> volume #15.1 level 105.6,0.8281 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 150.2,1 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 180,1 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 113.5,0.875 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 156.4,0.9688 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 150,0.9688 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 80,0.9688 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 200,0.9688 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 160,0.9688 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 120,0.9688 level 18.07,0.125 level 236.6,0.7812

> volume #15.1 level 120,0.9688 level -7.194,0 level 236.6,0.7812

> volume #15.1 level 120,0.9688 level 24.74,0.125 level 236.6,0.7812

> volume #15.1 level 143.4,0.9688 level 24.74,0.125 level 236.6,0.7812

> volume #15.1 level 143.4,0.9688 level 24.74,0.125 level 237.8,1

> select #15.1

3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15.1,0.99946,0.010478,0.031236,847.48,0.03081,0.038563,-0.99878,-61242,-0.01167,0.9992,0.03822,45954

> ui mousemode right "translate selected models"

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-6533.3,0.03081,0.038563,-0.99878,-58114,-0.01167,0.9992,0.03822,81163

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-7236.7,0.03081,0.038563,-0.99878,9968.1,-0.01167,0.9992,0.03822,94719

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-3942.9,0.03081,0.038563,-0.99878,8524.3,-0.01167,0.9992,0.03822,87049

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-5463.1,0.03081,0.038563,-0.99878,8741.5,-0.01167,0.9992,0.03822,99491

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-4940.9,0.03081,0.038563,-0.99878,14808,-0.01167,0.9992,0.03822,97831

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-3649.7,0.03081,0.038563,-0.99878,14980,-0.01167,0.9992,0.03822,95545

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-10438,0.03081,0.038563,-0.99878,14933,-0.01167,0.9992,0.03822,96579

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-22851,0.03081,0.038563,-0.99878,12030,-0.01167,0.9992,0.03822,1.4994e+05

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-6304.6,0.03081,0.038563,-0.99878,13679,-0.01167,0.9992,0.03822,99992

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-7275,0.03081,0.038563,-0.99878,14241,-0.01167,0.9992,0.03822,96391

> view matrix models
> #15.1,0.99946,0.010478,0.031236,-7087.2,0.03081,0.038563,-0.99878,14251,-0.01167,0.9992,0.03822,96389

> ~select #15.1

Nothing selected  

> select #15.2

2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #15.2,0.97916,0.01889,-0.2022,27078,-0.021127,0.99974,-0.0089118,1548,0.20198,0.012998,0.9793,-809.73

> ui mousemode right "rotate selected models"

[Repeated 1 time(s)]

> view matrix models
> #15.2,0.80773,-0.068399,0.58557,-73987,0.047756,0.99757,0.05065,-7529.3,-0.58762,-0.012947,0.80904,35539

> view matrix models
> #15.2,0.99985,-0.0017242,0.017331,-2287,0.0017079,1,0.00095442,-156.05,-0.017333,-0.00092467,0.99985,324.03

> view matrix models
> #15.2,0.98549,-0.05078,0.16197,-19792,0.16554,0.076574,-0.98323,1.6796e+05,0.037525,0.99577,0.083869,84443

> view matrix models
> #15.2,0.99302,-0.074211,0.091721,-9418.5,0.097959,0.085316,-0.99153,1.6978e+05,0.065757,0.99359,0.09199,82991

> ui mousemode right "translate selected models"

> view matrix models
> #15.2,0.99302,-0.074211,0.091721,-8298.7,0.097959,0.085316,-0.99153,1.5093e+05,0.065757,0.99359,0.09199,76907

> view matrix models
> #15.2,0.99302,-0.074211,0.091721,71980,0.097959,0.085316,-0.99153,1.6063e+05,0.065757,0.99359,0.09199,33027

> select #15.3

2 models selected  

> ~select #15.2

2 models selected  

> view matrix models #15.3,1,0,0,85378,0,1,0,15601,0,0,1,-94326

> ui mousemode right "rotate selected models"

> view matrix models
> #15.3,0.99596,0.041452,0.079705,72947,0.085231,-0.15543,-0.98416,1.9416e+05,-0.028407,0.98698,-0.15834,24434

> view matrix models
> #15.3,0.99681,-0.03541,0.071497,77109,0.071509,-0.0009286,-0.99744,1.9003e+05,0.035386,0.99937,0.0016065,1198.4

> ui mousemode right "translate selected models"

> view matrix models
> #15.3,0.99681,-0.03541,0.071497,74705,0.071509,-0.0009286,-0.99744,1.6187e+05,0.035386,0.99937,0.0016065,2305.3

> view matrix models
> #15.3,0.99681,-0.03541,0.071497,73211,0.071509,-0.0009286,-0.99744,1.6272e+05,0.035386,0.99937,0.0016065,-19273

> ~select #15.3

Nothing selected  

> select #15.2

2 models selected  

> view matrix models
> #15.2,0.99302,-0.074211,0.091721,71019,0.097959,0.085316,-0.99153,1.6159e+05,0.065757,0.99359,0.09199,10942

> ui mousemode right "rotate selected models"

> view matrix models
> #15.2,0.99538,-0.084302,0.045984,77606,0.04243,-0.043483,-0.99815,1.6847e+05,0.086146,0.99549,-0.039706,28470

> view matrix models
> #15.2,0.99474,-0.042474,0.093237,69523,0.093328,0.0001581,-0.99564,1.6561e+05,0.042274,0.9991,0.0041213,23039

> ui mousemode right "translate selected models"

> view matrix models
> #15.2,0.99474,-0.042474,0.093237,69731,0.093328,0.0001581,-0.99564,1.6194e+05,0.042274,0.9991,0.0041213,23002

> volume #15.2 color #888a85

> volume #15.3 color #888a85

> save /home/junhe/Desktop/sperm-tem-segmentation/m1.cxs includeMaps true

——— End of log from Mon Jun 3 04:37:06 2024 ———

opened ChimeraX session  

> hide #1.2 models

> show #1.2 models

> hide #1.2 models

> close #1.2

> close #13.1

> save /home/junhe/Desktop/sperm-tem-segmentation/m2.cxs includeMaps true

> hide #1-14

> volume #15.1 level 157.1,0.9531 level 24.74,0.125 level 237.8,1

> volume #15.1 level 157.1,0.9531 level 3.64,0.0625 level 237.8,1

> volume #15.1 level 157.1,0.9531 level 3.64,0.0625 level 246.3,0.9062

> volume #15.1 level 157.5,0.9844 level 3.64,0.0625 level 246.3,0.9062

> volume #15.1 orthoplanes xyz positionPlanes 242,410,231

> turn y 1 360 models #15.1 center #14

> turn y 3 120 models #15.1 center #14

> wait 120

> turn y 3 120 models #15.1 center #14

> wait 120

> turn y 3 120 models #15.1 center #14

> wait 120

> volume #15.1 orthoplanes xyz positionPlanes 242,410,231

> wait 10

> turn y 3 120 models #15.1 center #14

> wait 120

> volume #15.1 orthoplanes xyz positionPlanes 242,410,231

> wait 10

> turn y 3 120 models #15.1 center #14

> wait 120

> volume #15.1 orthoplanes xyz positionPlanes 242,410,231

> wait 10

> turn y 3 120 models #15.1 center #14

> wait 120

> volume #15.1 planes z,0,463

> wait 460

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
cannot select an axis to squeeze out which has size not equal to one  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 203, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 597, in _compute_shadowmaps  
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1584, in use_multishadow_map  
draw_depth(r, sdrawings, opaque_only = not mat.transparent_cast_shadows)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1523, in draw_depth  
draw_opaque(r, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1499, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1512, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 783, in draw  
pd.update_region()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 985, in update_region  
self._update_textures(planes)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1053, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1053, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1060, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1079, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 231, in _color_plane  
m = self._matrix_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 208, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
File "<__array_function__ internals>", line 5, in squeeze  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/core/fromnumeric.py", line 1508, in squeeze  
return squeeze(axis=axis)  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  

> graphics restart

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
cannot select an axis to squeeze out which has size not equal to one  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 203, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 597, in _compute_shadowmaps  
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1584, in use_multishadow_map  
draw_depth(r, sdrawings, opaque_only = not mat.transparent_cast_shadows)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1523, in draw_depth  
draw_opaque(r, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1499, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1512, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 783, in draw  
pd.update_region()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 985, in update_region  
self._update_textures(planes)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1053, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1053, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1060, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1079, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 231, in _color_plane  
m = self._matrix_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 208, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
File "<__array_function__ internals>", line 5, in squeeze  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/core/fromnumeric.py", line 1508, in squeeze  
return squeeze(axis=axis)  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  

> graphics restart

An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
cannot select an axis to squeeze out which has size not equal to one  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/updateloop.py", line 73, in draw_new_frame  
view.draw(check_for_changes = False)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 165, in draw  
self._draw_scene(camera, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 203, in _draw_scene  
shadow, multishadow = self._compute_shadowmaps(opaque_drawings,
transparent_drawings, camera)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/view.py", line 597, in _compute_shadowmaps  
multishadow_enabled = r.multishadow.use_multishadow_map(shadow_drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/opengl.py", line 1584, in use_multishadow_map  
draw_depth(r, sdrawings, opaque_only = not mat.transparent_cast_shadows)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1523, in draw_depth  
draw_opaque(r, drawings)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1499, in draw_opaque  
_draw_multiple(drawings, renderer, Drawing.OPAQUE_DRAW_PASS)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1512, in _draw_multiple  
d.draw(renderer, draw_pass)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 783, in draw  
pd.update_region()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 985, in update_region  
self._update_textures(planes)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1053, in _update_textures  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1053, in <listcomp>  
textures = [self._plane_texture(k, axis) for k,axis in planes]  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1060, in _plane_texture  
self._fill_plane_texture(k, axis, t)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 1079, in _fill_plane_texture  
data = ir._color_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 231, in _color_plane  
m = self._matrix_plane(plane, axis)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/map/image3d.py", line 208, in _matrix_plane  
p = squeeze(m, 2-axis) # Reduce from 3d array to 2d.  
File "<__array_function__ internals>", line 5, in squeeze  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/numpy/core/fromnumeric.py", line 1508, in squeeze  
return squeeze(axis=axis)  
ValueError: cannot select an axis to squeeze out which has size not equal to
one  
  




OpenGL version: 3.3.0 NVIDIA 530.41.03
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Supermicro
Model: C9X299-RPGF-L
OS: Ubuntu 18.04 bionic
Architecture: 64bit ELF
Virutal Machine: none
CPU: 36 Intel(R) Core(TM) i9-10980XE CPU @ 3.00GHz
Cache Size: 25344 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           125G        4.7G         14G        275M        106G        119G
	Swap:          2.0G        512K        2.0G

Graphics:
	07:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 41)	
	Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:097b]	
	Kernel driver in use: ast
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

[Eric Pettersen]

1.3

[Tom Goddard]

Not worth trying to debug on such an old ChimeraX version. I believe some improvements have been made which may have fixed this bug.