Context Navigation

← Previous Ticket
Next Ticket →

#16022 closed defect (duplicate)

Bad interaction of colors with "Background" target

Reported by:	kklee@…	Owned by:	pett
Priority:	normal	Milestone:
Component:	Depiction	Version:
Keywords:		Cc:
Blocked By:		Blocking:
Notify when closed:		Platform:	all
Project:	ChimeraX

Description

The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9.dev202405092350 (2024-05-09 23:50:32 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.9.dev202405092350 (2024-05-09)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/kellykeisen/Downloads/fold_ch23_stalk_deletion_model_1.cif

Chain information for fold_ch23_stalk_deletion_model_1.cif #1  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_stalk_deletion_model_4.cif

Chain information for fold_ch23_stalk_deletion_model_4.cif #2  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_stalk_deletion_model_2.cif

Chain information for fold_ch23_stalk_deletion_model_2.cif #3  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_stalk_deletion_model_0.cif

Chain information for fold_ch23_stalk_deletion_model_0.cif #4  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_stalk_deletion_model_3.cif

Chain information for fold_ch23_stalk_deletion_model_3.cif #5  
---  
Chain | Description  
A B C D | .  
  

> hide #1 models

> hide #2 models

> hide #!3 models

> hide #4 models

> hide #5 models

> show #4 models

> hide #4 models

> show #!3 models

> hide #!3 models

> show #2 models

> hide #2 models

> show #1 models

> open /Users/kellykeisen/Downloads/fold_ch23_fl_plusgly_model_4.cif

Chain information for fold_ch23_fl_plusgly_model_4.cif #6  
---  
Chain | Description  
A B C D | .  
  

> hide #1 models

> hide #6 models

> open /Users/kellykeisen/Downloads/fold_ch23_fl_plusgly_model_0.cif

Chain information for fold_ch23_fl_plusgly_model_0.cif #7  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_fl_plusgly_model_2.cif

Chain information for fold_ch23_fl_plusgly_model_2.cif #8  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_fl_plusgly_model_3.cif

Chain information for fold_ch23_fl_plusgly_model_3.cif #9  
---  
Chain | Description  
A B C D | .  
  

> open /Users/kellykeisen/Downloads/fold_ch23_fl_plusgly_model_1.cif

Chain information for fold_ch23_fl_plusgly_model_1.cif #10  
---  
Chain | Description  
A B C D | .  
  

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> show #9 models

> hide #9 models

> show #8 models

> hide #8 models

> show #7 models

> hide #7 models

> show #6 models

> hide #6 models

> show #5 models

> hide #5 models

> show #6 models

> ui tool show "Show Sequence Viewer"

> sequence chain #6/A

Alignment identifier is 6/A  

> select #6/A:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #6/A:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #6/A:59

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

> select #6/A:57-59

25 atoms, 24 bonds, 3 residues, 1 model selected  

> select #6/A:59

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

> select #6/A:59-72

116 atoms, 118 bonds, 14 residues, 1 model selected  

> color sel red

> color sel cornflower blue

> select clear

> hide #6 models

> show #7 models

> hide #7 models

> show #8 models

> hide #8 models

> show #9 models

> ui tool show "Show Sequence Viewer"

> sequence chain #9/A

Alignment identifier is 9/A  

> select #9/A:59-60

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #9/A:59-72

116 atoms, 118 bonds, 14 residues, 1 model selected  

> color sel red

> select #9/A:45-93

376 atoms, 383 bonds, 49 residues, 1 model selected  

> select #9/A:24-45

176 atoms, 179 bonds, 22 residues, 1 model selected  

> select #9/A:45-75

256 atoms, 262 bonds, 31 residues, 1 model selected  

> select #9/A:45-75

256 atoms, 262 bonds, 31 residues, 1 model selected  

> select #9/A:73

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

> select #9/A:73-95

161 atoms, 162 bonds, 23 residues, 1 model selected  

> color sel yellow

> select #9/A:49

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

> select #9/A:45-49

38 atoms, 39 bonds, 5 residues, 1 model selected  

> select #9/A:55

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:44-45

21 atoms, 21 bonds, 2 residues, 1 model selected  

> select #9/A:45-58

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

> color sel white

> select clear

> hide #9 models

> show #6 models

> select #6/A:42-43

17 atoms, 16 bonds, 2 residues, 1 model selected  

> select #6/A:43-58

134 atoms, 137 bonds, 16 residues, 1 model selected  

> color sel orange red

> select #6/A:73-74

19 atoms, 19 bonds, 2 residues, 1 model selected  

> select #6/A:73-95

161 atoms, 162 bonds, 23 residues, 1 model selected  

> color sel yellow

> select clear

> hide #6 models

> show #9 models

> show #6 models

> select add #9

14888 atoms, 15300 bonds, 1904 residues, 1 model selected  

> select clear

> select add #9

14888 atoms, 15300 bonds, 1904 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #9,-0.38588,0.91597,-0.10996,42.717,-0.030296,-0.13171,-0.99083,-0.97155,-0.92205,-0.37901,0.078573,27.169

> view matrix models
> #9,-0.026505,0.98302,0.18158,32.156,0.20644,0.18311,-0.96117,-8.3479,-0.9781,0.012009,-0.20779,28.194

> view matrix models
> #9,0.14258,0.97882,0.14688,26.877,0.037429,0.14296,-0.98902,-3.1993,-0.98908,0.14651,-0.016254,28.93

> view matrix models
> #9,0.12183,0.97396,0.19121,27.595,0.040377,0.18762,-0.98141,-3.2728,-0.99173,0.12729,-0.016467,29.016

> ui mousemode right "translate selected models"

> view matrix models
> #9,0.12183,0.97396,0.19121,85.986,0.040377,0.18762,-0.98141,47.879,-0.99173,0.12729,-0.016467,40.187

> view matrix models
> #9,0.12183,0.97396,0.19121,84.053,0.040377,0.18762,-0.98141,47.654,-0.99173,0.12729,-0.016467,42.742

> select clear

> show #1 models

> select add #1

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.82583,0.071295,0.5594,4.7198,0.55979,0.016158,-0.82847,-39.447,-0.068105,0.99732,-0.026567,33.031

> view matrix models
> #1,-0.76955,-0.58163,-0.26362,-22.034,-0.4254,0.15903,0.89093,-27.655,-0.47626,0.79776,-0.36981,24.5

> view matrix models
> #1,-0.82952,-0.53855,-0.14787,-20.008,-0.29611,0.19962,0.93406,-26.028,-0.47352,0.81861,-0.32506,25.432

> ui mousemode right "translate selected models"

> view matrix models
> #1,-0.82952,-0.53855,-0.14787,-59.46,-0.29611,0.19962,0.93406,-54.615,-0.47352,0.81861,-0.32506,-24.346

> view matrix models
> #1,-0.82952,-0.53855,-0.14787,-68.118,-0.29611,0.19962,0.93406,-60.398,-0.47352,0.81861,-0.32506,-32.831

> view matrix models
> #1,-0.82952,-0.53855,-0.14787,-83.298,-0.29611,0.19962,0.93406,-70.906,-0.47352,0.81861,-0.32506,-40.747

> view matrix models
> #1,-0.82952,-0.53855,-0.14787,-78.186,-0.29611,0.19962,0.93406,-67.586,-0.47352,0.81861,-0.32506,-38.895

> select clear

> show #2 models

> hide #1 models

> hide #2 models

> show #!3 models

> hide #!3 models

> show #4 models

> hide #4 models

> show #5 models

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #5,0.015219,0.57372,0.81891,-22.875,0.88593,0.37197,-0.27706,6.9823,-0.46357,0.72972,-0.50261,45.112

> view matrix models
> #5,-0.42089,0.86877,0.26094,-6.0463,0.90414,0.42504,0.043237,-2.3007,-0.073345,0.25412,-0.96439,57.818

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.42089,0.86877,0.26094,-65.279,0.90414,0.42504,0.043237,-51.616,-0.073345,0.25412,-0.96439,-18.77

> view matrix models
> #5,-0.42089,0.86877,0.26094,-84.636,0.90414,0.42504,0.043237,-67.077,-0.073345,0.25412,-0.96439,-36.841

> ui mousemode right "rotate selected models"

> select clear

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:9-10

15 atoms, 14 bonds, 2 residues, 1 model selected  

> select #5/A:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select clear

> ui mousemode right "translate selected models"

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.42089,0.86877,0.26094,-30.395,0.90414,0.42504,0.043237,-37.987,-0.073345,0.25412,-0.96439,-19.825

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.91811,0.3883,0.079384,-25.753,0.37637,0.91697,-0.13233,-32.019,-0.12418,-0.091619,-0.98802,-19.659

> select clear

> select add #4

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> select subtract #4

Nothing selected  

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.90431,0.42301,0.057306,-25.041,0.42061,0.90589,-0.049441,-34.454,-0.072827,-0.020607,-0.99713,-19.291

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.90431,0.42301,0.057306,-10.687,0.42061,0.90589,-0.049441,-12.374,-0.072827,-0.020607,-0.99713,-16.151

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.90431,0.42301,0.057306,-23.718,0.42061,0.90589,-0.049441,-33.888,-0.072827,-0.020607,-0.99713,-20.617

> select clear

> hide #9 models

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.90431,0.42301,0.057306,-23.358,0.42061,0.90589,-0.049441,-33.426,-0.072827,-0.020607,-0.99713,-20.574

Drag select of 1 residues  

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.90431,0.42301,0.057306,-47.915,0.42061,0.90589,-0.049441,-68.021,-0.072827,-0.020607,-0.99713,-23.808

> view matrix models
> #5,-0.90431,0.42301,0.057306,-63.228,0.42061,0.90589,-0.049441,-87.715,-0.072827,-0.020607,-0.99713,-23.297

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.90431,0.42301,0.057306,-47.05,0.42061,0.90589,-0.049441,-101.3,-0.072827,-0.020607,-0.99713,-17.255

> ui mousemode right "rotate selected models"

> view matrix models
> #5,-0.90025,0.43374,0.037741,-46.462,0.42977,0.89918,-0.082302,-100.36,-0.069634,-0.057872,-0.99589,-17.349

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.961,0.27385,0.038613,-46.724,0.26683,0.95481,-0.1309,-98.825,-0.072715,-0.11549,-0.99064,-17.59

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.961,0.27385,0.038613,-36.348,0.26683,0.95481,-0.1309,-103.17,-0.072715,-0.11549,-0.99064,-14.573

> ui mousemode right "translate selected models"

> view matrix models
> #5,-0.961,0.27385,0.038613,-19.123,0.26683,0.95481,-0.1309,-56.474,-0.072715,-0.11549,-0.99064,-14.81

> view matrix models
> #5,-0.961,0.27385,0.038613,-35.723,0.26683,0.95481,-0.1309,-101.24,-0.072715,-0.11549,-0.99064,-13.611

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.961,0.27385,0.038613,-32.287,0.26683,0.95481,-0.1309,-102.17,-0.072715,-0.11549,-0.99064,-21.374

> select clear

> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs

> open /Users/kellykeisen/Documents/CH505_new.gro

Chain information for GROup of MAchos and Cynical Suckers #11  
---  
Chain | Description  
? | No description available  
  

> select clear

> hide #5 models

> hide #6 models

> select clear

> hide #11 models

> show #11 models

> hide #11 models

> show #2 models

> hide #2 models

> show #1 models

> hide #1 models

> show #5 models

> show #6 models

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> view matrix models
> #5,-0.961,0.27385,0.038613,-33.57,0.26683,0.95481,-0.1309,-102.24,-0.072715,-0.11549,-0.99064,-18.921

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> color sel byelement

[Repeated 1 time(s)]

> select clear

> select add #5

14260 atoms, 14644 bonds, 1840 residues, 1 model selected  

> color sel white

> color sel byelement

> select clear

> ui tool show "Show Sequence Viewer"

>

Incomplete command: devel  

> sequence chain #5/B

Alignment identifier is 5/B  

> sequence chain #5/C

Alignment identifier is 5/C  

> sequence chain #5/D

Alignment identifier is 5/D  

> select #5/D:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/D:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel yellow

> color sel orange

> select #5/C:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/C:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #5/B:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/B:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> ui tool show "Show Sequence Viewer"

> sequence chain #5/D

Destroying pre-existing alignment with identifier 5/D  
Alignment identifier is 5/D  

> select #5/D:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/D:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #5/A

Alignment identifier is 5/A  

> select #5/A:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #5/A:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select clear

> ui tool show "Show Sequence Viewer"

>

Incomplete command: devel  

> sequence chain #6/A

Destroying pre-existing alignment with identifier 6/A  
Alignment identifier is 6/A  

> sequence chain #6/B

Alignment identifier is 6/B  

> sequence chain #6/C

Alignment identifier is 6/C  

> sequence chain #6/D

Alignment identifier is 6/D  

> select #6/D:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #6/D:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #6/C:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #6/C:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #6/B:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #6/B:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select clear

> show #1 models

> hide #1 models

> show #7 models

> hide #7 models

> show #9 models

> hide #9 models

> show #9 models

> select add #9

14888 atoms, 15300 bonds, 1904 residues, 1 model selected  

> view matrix models
> #9,0.12183,0.97396,0.19121,54.817,0.040377,0.18762,-0.98141,105.08,-0.99173,0.12729,-0.016467,-4.7335

> view matrix models
> #9,0.12183,0.97396,0.19121,36.049,0.040377,0.18762,-0.98141,110.84,-0.99173,0.12729,-0.016467,17.796

> view matrix models
> #9,0.12183,0.97396,0.19121,36.074,0.040377,0.18762,-0.98141,115.93,-0.99173,0.12729,-0.016467,17.749

> view matrix models
> #9,0.12183,0.97396,0.19121,44.214,0.040377,0.18762,-0.98141,113.14,-0.99173,0.12729,-0.016467,5.6863

> view matrix models
> #9,0.12183,0.97396,0.19121,44.198,0.040377,0.18762,-0.98141,113.14,-0.99173,0.12729,-0.016467,5.7085

> ui mousemode right "rotate selected models"

> view matrix models
> #9,0.11931,0.97425,0.19134,44.275,0.04128,0.18768,-0.98136,113.11,-0.992,0.12499,-0.017824,5.7146

> view matrix models
> #9,0.12166,0.974,0.19111,44.207,0.040298,0.18753,-0.98143,113.14,-0.99175,0.1271,-0.016435,5.7101

> view matrix models
> #9,0.016581,0.98326,0.18146,47.35,0.089293,0.1793,-0.97973,111.67,-0.99587,0.032449,-0.084825,5.7084

> color sel white

> color sel byelement

> select clear

> ui tool show "Selection Inspector"

> ui tool show Distances

> select clear

Exactly two atoms must be selected!  

> select #6/B:36

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> view matrix models
> #6,0.93012,0.047966,-0.36411,-11.438,-0.036989,0.99863,0.037066,1.4494,0.36539,-0.021008,0.93062,-4.4422

> undo

> view matrix models
> #6,0.9975,0.01528,0.069016,2.1425,-0.016511,0.99971,0.017302,0.63836,-0.068732,-0.018398,0.99747,0.34613

> undo

> ui mousemode right "translate selected models"

> select clear

[Repeated 4 time(s)]Exactly two atoms must be selected!  

> select clear

[Repeated 1 time(s)]

> select #6/B:36@NE2

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select #6/D:466

7 atoms, 6 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

[Repeated 1 time(s)]

> select #6/D:466@OG1

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select add #6/B:36@NE2

1 atom, 1 bond, 1 residue, 1 model selected  
Exactly two atoms must be selected!  

> select add #6/D:466@CG2

2 atoms, 1 bond, 2 residues, 1 model selected  

> distance #6/B:36@NE2 #6/D:466@CG2

Distance between fold_ch23_fl_plusgly_model_4.cif #6/B HIS 36 NE2 and /D THR
466 CG2: 106.762Å  

> select #5/C:37

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

> show sel target ab

> select clear

> select #5/C:36

10 atoms, 10 bonds, 1 residue, 1 model selected  

> show sel target ab

> select clear

> select #5/A:452

7 atoms, 6 bonds, 1 residue, 1 model selected  

> view matrix models
> #5,-0.961,0.27385,0.038613,-33.579,0.26683,0.95481,-0.1309,-101.78,-0.072715,-0.11549,-0.99064,-17.31

> undo

> ui tool show "Show Sequence Viewer"

> select add #9

14895 atoms, 15306 bonds, 1905 residues, 2 models selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #9/A

Alignment identifier is 9/A  

> sequence chain #9/B

Alignment identifier is 9/B  

> sequence chain #9/C

Alignment identifier is 9/C  

> sequence chain #9/D

Alignment identifier is 9/D  

> select #9/A:8-9

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #9/A:8-14

46 atoms, 45 bonds, 7 residues, 1 model selected  

> select #9/A:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/A:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #9/B:3-44,105-110,143-145,410-413,466-468

438 atoms, 440 bonds, 58 residues, 1 model selected  

> select #9/B:8

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/B:8-9

14 atoms, 13 bonds, 2 residues, 1 model selected  

> select #9/B:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/B:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #9/C:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/C:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select #9/D:9

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select #9/D:9-34

191 atoms, 192 bonds, 26 residues, 1 model selected  

> color sel orange

> select clear

> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs

> select #9/A:59

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

> select #9/A:59-72

116 atoms, 118 bonds, 14 residues, 1 model selected  

> color sel red

> select #9/B:59

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

> select #9/B:59-72

116 atoms, 118 bonds, 14 residues, 1 model selected  

> color sel red

> select #9/C:59

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

> select #9/C:59-72

116 atoms, 118 bonds, 14 residues, 1 model selected  

> color sel red

> select #9/D:58-59

16 atoms, 15 bonds, 2 residues, 1 model selected  

> select #9/D:59-72

116 atoms, 118 bonds, 14 residues, 1 model selected  

> color sel red

> select clear

> ui tool show "Color Actions"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 64, in <lambda>  
button.released.connect(lambda *, clr=spaced_name: self._color(clr))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
TypeError: can only concatenate str (not "NoneType") to str  
  
TypeError: can only concatenate str (not "NoneType") to str  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Color Actions"

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 64, in <lambda>  
button.released.connect(lambda *, clr=spaced_name: self._color(clr))  
^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
TypeError: can only concatenate str (not "NoneType") to str  
  
TypeError: can only concatenate str (not "NoneType") to str  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/color_actions/tool.py", line 226, in _color  
commands.append("color "  
^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac14,2
      Model Number: Z1610005LLL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 6 days, 20 hours, 40 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    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: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    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.dev202405092350
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DiffPlot: 1.0
    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: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 1.3.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.4
    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: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.1
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (2)

comment:1 by pett, 13 months ago

Component:	Unassigned → Depiction
Owner:	set to pett
Platform:	→ all
Project:	→ ChimeraX
Status:	new → accepted
Summary:	ChimeraX bug report submission → Bad interaction of colors with "Background" target

comment:2 by pett, 13 months ago

Resolution:	→ duplicate
Status:	accepted → closed

Hi Kelly,

Thanks for reporting this problem. It was fixed about two weeks after the build you have, so if you get a current daily build then it won't happen again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.

Download in other formats: