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#16575 closed defect (fixed)

Orthoplanes: 'MRCGrid' object has no attribute 'dicom_data'

Reported by:	chimerax-bug-report@…	Owned by:	Zach Pearson
Priority:	normal	Milestone:
Component:	DICOM	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        Linux-6.8.0-49-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Volume data > Orthoplanes

Log:
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  

> open /home/lee04516/Workspace/Proj_B19/Images_PNAS/image001.cxs format
> session

Opened J431_009_volume_map_cent.mrc as #1, grid size 400,400,400, pixel 1.08,
shown at level 0.2, step 1, values float32  
Opened J496_volume_map_cent.mrc as #2, grid size 512,512,512, pixel 1.08,
shown at level 0.35, step 1, values float32  
Opened J99_volume_map_cent.mrc as #3, grid size 512,512,512, pixel 1.08, shown
at level 0.5, step 1, values float32  
Log from Tue Jan 7 13:32:28 2025 Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open B19V-HF/J431_009_volume_map_cent.mrc

Opened J431_009_volume_map_cent.mrc as #1, grid size 400,400,400, pixel 1.08,
shown at level 0.372, step 2, values float32  

> open B19V-HE/J496_volume_map_cent.mrc

Opened J496_volume_map_cent.mrc as #2, grid size 512,512,512, pixel 1.08,
shown at level 0.307, step 2, values float32  

> open B19V-VLP/J99_volume_map_cent.mrc

Opened J99_volume_map_cent.mrc as #3, grid size 512,512,512, pixel 1.08, shown
at level 0.341, step 2, values float32  

> volume step 1

> lighting soft

> set bgColor white

> volume #1 level 0.1819

> volume #1 level 0.1706

> volume #1 level 0.1321

> volume #1 level 0.13

> volume #1 level 0.12

> volume #1 level 0.1

> volume #1 level 0.125

> volume #2 level 0.125

> volume #3 level 0.125

> ui tool show "Side View"

> lighting simple

> view

> view orient

> volume #2 level 0.341

> volume #3 level 0.341

> volume #1 level 0.341

> ui tool show "Surface Color"

> color radial #1.1 palette #0000ff:#00ffff:#00ff00:#ffff00:#ff0000

> lighting soft

> volume #1 level 0.125

> volume #1 level 0.15

> color radial #1.1 palette
> 110,#0000ff:116,#00ffff:122,#00ff00:128,#ffff00:148,#ff0000

> color radial #2.1 palette
> 110,#0000ff:116,#00ffff:122,#00ff00:128,#ffff00:148,#ff0000

> color radial #3.1 palette
> 110,#0000ff:116,#00ffff:122,#00ff00:128,#ffff00:148,#ff0000

> volume #3 level 0.5427

> volume #2 level 0.341

> volume #2 level 0.3114

> volume #2 level 0.3

> volume #3 level 0.5

> tile

1 model tiled  

> tile

3 models tiled  

> tile 3

Expected a models specifier or a keyword  

> tile #1-3 3

Expected a keyword  

> tile #1-3 columns 3

3 models tiled  

> lighting soft

> camera ortho

> color radial #3.1 palette
> 100,#0000ff:116,#00ffff:122,#00ff00:128,#ffff00:148,#ff0000

> color radial #2.1 palette
> 100,#0000ff:116,#00ffff:122,#00ff00:128,#ffff00:148,#ff0000

> color radial #1.1 palette
> 100,#0000ff:116,#00ffff:122,#00ff00:128,#ffff00:148,#ff0000

> color radial #1.1 palette
> 100,#0000ff:110,#00ffff:120,#00ff00:130,#ffff00:148,#ff0000

> color radial #1.1 palette
> 100,#0000ff:110,#00ffff:120,#00ff00:130,#ffff00:140,#ff0000

> color single #2.1

> color single #3.1

> color radial #2.1 palette
> 100,#0000ff:110,#00ffff:120,#00ff00:130,#ffff00:140,#ff0000

> color radial #3.1 palette
> 100,#0000ff:110,#00ffff:120,#00ff00:130,#ffff00:140,#ff0000

> color radial #3.1 palette
> 100,#0000ff:108,#00ffff:116,#00ff00:124,#ffff00:140,#ff0000

> color radial #3.1 palette
> 100,#0000ff:108,#00ffff:116,#00ff00:124,#ffff00:132,#ff0000

> color single #2.1

> color single #1.1

> color radial #1.1 palette
> 100,#0000ff:110,#00ffff:120,#00ff00:130,#ffff00:140,#ff0000

> color single #1.1

> color radial #2.1 palette
> 100,#0000ff:108,#00ffff:116,#00ff00:124,#ffff00:132,#ff0000 center
> 754.71,0,0

[Repeated 9 time(s)]

> color radial #2.1 palette
> 100,#0000ff:108,#00ffff:116,#00ff00:124,#ffff00:132,#ff0000 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #1.1 palette
> 100,#0000ff:108,#00ffff:116,#00ff00:124,#ffff00:132,#ff0000 center
> 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 100,#0000ff:108,#00ccff:116,#00ff65:124,#66ff00:132,#ffcb00:140,#ff0000
> center 0,-2.2888e-05,-7.6294e-06

> color single #2.1

> color single #3.1

> color radial #2.1 palette
> 100,#0000ff:108,#00ccff:116,#00ff65:124,#66ff00:132,#ffcb00:140,#ff0000
> center 0,-2.2888e-05,-7.6294e-06

> color radial #2.1 palette
> 100,#0000ff:108,#00ccff:116,#00ff65:124,#66ff00:132,#ffcb00:140,#ff0000
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #3.1 palette
> 100,#0000ff:108,#00ccff:116,#00ff65:124,#66ff00:132,#ffcb00:140,#ff0000
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 100,#0000ff:108,#00aaff:116,#00ffa9:124,#00ff00:132,#aaff00:140,#ffaa00
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 102,#0000ff:108,#00aaff:116,#00ffa9:124,#00ff00:132,#aaff00:140,#ffaa00
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 110,#0000ff:116,#00aaff:122,#00ffa9:128,#00ff00:134,#aaff00:140,#ffaa00:150,#ff0000
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 104,#0000ff:110,#00aaff:116,#00ffa9:122,#00ff00:128,#aaff00:134,#ffaa00:150,#ff0000
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#0000ff:110,#00aaff:115,#00ffa9:120,#00ff00:125,#aaff00:130,#ffaa00:150,#ff0000
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#0000ff:110,#00aaff:115,#00ffa9:120,#00ff00:125,#aaff00:130,#ffaa00:135,#ff0000
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:135,#0000ff
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#ffffff:125,#deb4c9:130,#be6a93:135,#9e1f5e
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#9e1f5e:110,#be6a93:115,#deb4c9:120,#ffffff:125,#afecee:130,#5fd9de:135,#0fc6ce
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#0000ff:110,#5555ff:115,#aaaaff:120,#ffffff:125,#ffa9a9:130,#ff5555:135,#ff0000
> center 754.71,7.6294e-06,0

> color radial #3.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:135,#0000ff
> center 754.71,7.6294e-06,0

> color single #2.1

> color single #1.1

> color radial #2.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:135,#0000ff
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #1.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:135,#0000ff
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:150,#0000ff
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:160,#0000ff
> center 0,-2.2888e-05,-7.6294e-06

[Repeated 3 time(s)]

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#ffffff:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#9e1f5e:110,#be6a93:115,#deb4c9:120,#ffffff:125,#afecee:130,#5fd9de:160,#0fc6ce
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#ffffff:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color single #2.1

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#ffffff:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> set bgColor black

> set bgColor gray

> set bgColor white

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#deddda:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#f6f5f4:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> color single #1.1

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#f6f5f4:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color radial #2.1 palette
> 105,#0000ff:110,#00aaff:115,#00ffa9:120,#00ff00:125,#aaff00:130,#ffaa00:160,#ff0000
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#ff0000:110,#ffaa00:115,#aaff00:120,#00ff00:125,#00ffa9:130,#00aaff:160,#0000ff
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#0000ff:110,#00aaff:115,#00ffa9:120,#00ff00:125,#aaff00:130,#ffaa00:160,#ff0000
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#ffffff:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#9e1f5e:110,#be6a93:115,#deb4c9:120,#ffffff:125,#afecee:130,#5fd9de:160,#0fc6ce
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#0000ff:110,#5555ff:115,#aaaaff:120,#ffffff:125,#ffa9a9:130,#ff5555:160,#ff0000
> center 377.36,-1.5259e-05,1.5259e-05

> color single #2.1

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#f6f5f4:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> open
> /home/lee04516/Workspace/Proj_B19/Builds/B19V/DNAs/J127_008_volume_map_cent.mrc
> format mrc

Opened J127_008_volume_map_cent.mrc as #4, grid size 512,512,512, pixel 1.08,
shown at level 0.218, step 2, values float32  

> volume #4 step 1

> volume #4 level 0.1618

> tile #1-4 columns 3

4 models tiled  

> color radial #4.1 palette
> 105,#ff0000:110,#ff5555:115,#ffaaaa:120,#ffffff:125,#a9a9ff:130,#5555ff:135,#0000ff
> center -1.5259e-05,-377.36,0

> lighting soft

> tile #12,4,3 columns 3

2 models tiled  

> tile #12,4,3 columns 2

2 models tiled  

> lighting soft

> color radial #2.1 palette
> 105,#0000ff:110,#5555ff:115,#aaaaff:120,#ffffff:125,#ffa9a9:130,#ff5555:160,#ff0000
> center 377.36,-1.5259e-05,1.5259e-05

> color single #2.1

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#f6f5f4:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #1.1 palette
> #0fc6ce:#5fd9de:#afecee:#f9f06b:#deb4c9:#be6a93:#9e1f5e center
> 0,-2.2888e-05,-7.6294e-06

[Repeated 1 time(s)]

> color single #1.1

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#f6f5f4:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#f9f06b:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#c0bfbc:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#deddda:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 0,-2.2888e-05,-7.6294e-06

> color radial #2.1 palette
> 105,#0fc6ce:110,#5fd9de:115,#afecee:120,#deddda:125,#deb4c9:130,#be6a93:160,#9e1f5e
> center 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#99c1f1:110,#3584e4:115,#77767b:120,#ff7800:125,#ffbe6f center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#99c1f1:115,#3584e4:125,#77767b:135,#ff7800:145,#ffbe6f center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#99c1f1:101,#3584e4:107,#77767b:113,#ff7800:119,#ffbe6f center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 105,#ffbe6f:101,#ff7800:107,#77767b:113,#3584e4:119,#99c1f1 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#ffbe6f:116,#ff7800:122,#77767b:128,#3584e4:134,#99c1f1 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#99c1f1:116,#3584e4:122,#77767b:128,#ff7800:134,#ffbe6f center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#ffbe6f:116,#ff7800:122,#77767b:128,#3584e4:134,#99c1f1 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#ffbe6f:118,#ff7800:126,#77767b:134,#3584e4:142,#99c1f1 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#26a269:118,#57e389:126,#99c1f1:134,#dc8add:142,#b5835a center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#b5835a:118,#dc8add:126,#99c1f1:134,#57e389:142,#26a269 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#f66151 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #2.1 palette
> 110,#f66151:118,#ffbe6f:126,#f8e45c:134,#33d17a:142,#1c71d8 center
> 377.36,-1.5259e-05,1.5259e-05

> color single #1.1

> color radial #1.1 palette
> 110,#f66151:118,#ffbe6f:126,#f8e45c:134,#33d17a:142,#1c71d8 center
> 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#f66151 center
> 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 110,#f66151:118,#ffbe6f:126,#f8e45c:134,#33d17a:142,#1c71d8 center
> 0,-2.2888e-05,-7.6294e-06

> color single #3.1

> color radial #3.1 palette
> 110,#f66151:118,#ffbe6f:126,#f8e45c:134,#33d17a:142,#1c71d8 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #3.1 palette
> 110,#f66151:118,#ffbe6f:126,#f8e45c:134,#33d17a:142,#1c71d8 center
> 374.78,-377.36,0

> close #4

> tile #1-3 columns 3

3 models tiled  

> lighting soft

> color radial #3.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#f66151 center
> 374.78,-377.36,0

> color radial #3.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#f66151 center
> 754.71,7.6294e-06,0

> color single #2.1

> color radial #2.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#f66151 center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #1.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#f66151 center
> 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#dc8add center
> 0,-2.2888e-05,-7.6294e-06

> color radial #1.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 0,-2.2888e-05,-7.6294e-06

> color radial #2.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #3.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 754.71,7.6294e-06,0

> color single #3.1

> color radial #3.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 377.36,-1.5259e-05,1.5259e-05

> color radial #3.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 754.71,7.6294e-06,0

> tile off

> volume #1 level 0.04512

> volume #1 level 0.1324

> volume #1 level 0.2289

> volume #1 level 0.2159

> volume #2 level 0.4

> color radial #2.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 1.5259e-05,0,7.6294e-06

> volume #2 level 0.35

> volume #1 level 0.1528

> volume #1 level 0.1231

> volume #1 level 0.1138

> volume #1 level 0.2196

> volume #1 level 0.2

> surface dust #1 size 10.8

> surface dust #1 size 1

> surface dust #1 size 2

> surface dust #1 size 3

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image001.tif width 1177
> height 1176 supersample 3

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image002.tif width 1177
> height 1176 supersample 3

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image003.tif width 1177
> height 1176 supersample 3

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image001.cxs

——— End of log from Tue Jan 7 13:32:28 2025 ———

opened ChimeraX session  

> show #!2 models

> show #!1 models

> hide #!2 models

> hide #!1 models

> ui tool show "Surface Color"

> color radial #3.1 palette
> 110,#1c71d8:118,#33d17a:126,#f8e45c:134,#ffbe6f:142,#ed333b center
> 7.6294e-06,7.6294e-06,0

> show #!2 models

> hide #!3 models

> show #!1 models

> hide #!2 models

> windowsize 1176 1176

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image001.tif width 1176
> height 1176 supersample 3

> show #!2 models

> hide #!1 models

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image002.tif width 1176
> height 1176 supersample 3

> show #!3 models

> hide #!2 models

> save /home/lee04516/Workspace/Proj_B19/Images_PNAS/image003.tif width 1176
> height 1176 supersample 3

> show #!1 models

> hide #!3 models

> ui tool show Orthoplanes

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show Orthoplanes

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 1580, in
_surfaceChosen  
self._update_position_label_text()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
AttributeError: 'MRCGrid' object has no attribute 'dicom_data'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/segmentations/ui/orthoplanes.py", line 764, in
_update_position_label_text  
dicom_data = self.view.drawing.parent.data.dicom_data  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 555.42.02
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 13th Gen Intel(R) Core(TM) i7-13700K
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        26Gi        22Gi       286Mi        13Gi        35Gi
	Swap:           15Gi       3.9Gi        12Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA104GL [RTX A4000] [10de:24b0] (rev a1)	
	Subsystem: NVIDIA Corporation GA104GL [RTX A4000] [10de:14ad]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.23.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.8.dev0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    zipp: 3.19.2

Change History (2)

comment:1 by Eric Pettersen, 10 months ago

Component:	Unassigned → DICOM
Owner:	set to Zach Pearson
Platform:	→ all
Project:	→ ChimeraX
Status:	new → assigned
Summary:	ChimeraX bug report submission → Orthoplanes: 'MRCGrid' object has no attribute 'dicom_data'

comment:2 by Zach Pearson, 10 months ago

Resolution:	→ fixed
Status:	assigned → closed

Fixed in tomorrow's build.

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