![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 13 months ago
Closed 13 months ago
#16024 closed defect (duplicate)
Bad interaction of colors with "Background" target
| Reported by: | 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.
> 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.
> select clear
Drag select of 623 atoms, 1708 residues, 605 bonds, 1 pseudobonds
> ui tool show "Color Actions"
> color sel white target c
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #6/D
Alignment identifier is 6/D
> sequence chain #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
> select #6/C:59
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/C:59-72
116 atoms, 118 bonds, 14 residues, 1 model selected
> color sel red
> select #6/B:58-59
16 atoms, 15 bonds, 2 residues, 1 model selected
> select #6/B:59-72
116 atoms, 118 bonds, 14 residues, 1 model selected
> color sel red
> 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
> select #6/D:58
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/D:57-58
17 atoms, 16 bonds, 2 residues, 1 model selected
> select #6/D:59
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/D:59-72
116 atoms, 118 bonds, 14 residues, 1 model selected
> color sel red
> select clear
> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs
> select clear
> select add #5
14260 atoms, 14644 bonds, 1840 residues, 1 model selected
> view matrix models
> #5,-0.961,0.27385,0.038613,-32.733,0.26683,0.95481,-0.1309,-102.39,-0.072715,-0.11549,-0.99064,-20.438
> view matrix models
> #5,-0.961,0.27385,0.038613,-32.343,0.26683,0.95481,-0.1309,-102.57,-0.072715,-0.11549,-0.99064,-21.341
> select subtract #5
Nothing selected
> select add #9
14888 atoms, 15300 bonds, 1904 residues, 1 model selected
> view matrix models
> #9,0.016581,0.98326,0.18146,46.051,0.089293,0.1793,-0.97973,112.01,-0.99587,0.032449,-0.084825,4.7434
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.017751,0.98301,0.1827,46.019,0.090782,0.18039,-0.9794,111.96,-0.99571,0.033971,-0.086037,4.7356
> view matrix models
> #9,0.024414,0.98217,0.18642,45.828,0.09409,0.1834,-0.97853,111.86,-0.99526,0.04143,-0.087934,4.7158
> view matrix models
> #9,0.034998,0.9882,0.14911,45.42,0.11759,0.1441,-0.98255,111.15,-0.99245,0.051921,-0.11116,4.5743
> select clear
> select add #9
14888 atoms, 15300 bonds, 1904 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #9,0.034998,0.9882,0.14911,43.346,0.11759,0.1441,-0.98255,105.27,-0.99245,0.051921,-0.11116,4.2383
> select clear
> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs
> select add #5
14260 atoms, 14644 bonds, 1840 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96659,0.24873,0.062014,-33.065,0.2427,0.96583,-0.090974,-103.71,-0.082523,-0.072884,-0.99392,-21.178
> select clear
> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs
> ui tool show "Show Sequence Viewer"
> sequence chain #6/A
Alignment identifier is 6/A
> select #6/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A
3624 atoms, 3720 bonds, 469 residues, 1 model selected
> select #6/A:469
10 atoms, 9 bonds, 1 residue, 1 model selected
> select #6/A
3624 atoms, 3720 bonds, 469 residues, 1 model selected
> select #6/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:1-149
1146 atoms, 1168 bonds, 149 residues, 1 model selected
> select #6/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:1-82
638 atoms, 649 bonds, 82 residues, 1 model selected
> select #6/A:82
6 atoms, 5 bonds, 1 residue, 1 model selected
> select #6/A:1-82
638 atoms, 649 bonds, 82 residues, 1 model selected
> select #6/A:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:7-23
118 atoms, 117 bonds, 17 residues, 1 model selected
> select #6/A:24
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:7-24
126 atoms, 125 bonds, 18 residues, 1 model selected
> select clear
Drag select of 17 atoms, 476 residues, 16 bonds
> color sel white
> select #6/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:7-24
126 atoms, 125 bonds, 18 residues, 1 model selected
> color sel orange
> select clear
Drag select of 121 residues
> color sel white
> select #6/A:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/A:7-30
171 atoms, 170 bonds, 24 residues, 1 model selected
> select #6/A:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs
> select clear
> select #6/A:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> view matrix models
> #6,0.97103,0.054144,0.23274,7.9024,-0.092291,0.98339,0.15628,5.6411,-0.22041,-0.17323,0.9599,0.14541
> undo
> select #6/C:467
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/C:173
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel target ab
> select #6/C:173@CB
1 atom, 1 residue, 1 model selected
> select #6/A:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> select #6/A:27
4 atoms, 3 bonds, 1 residue, 1 model selected
> show sel target ab
> select #6/A:26
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
[Repeated 2 time(s)]
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
> view matrix models
> #6,0.69023,-0.26047,-0.67508,-19.736,-0.54248,0.43113,-0.721,-19.513,0.47885,0.86388,0.15628,-31.077
> undo
> ui mousemode right zoom
> select #6/C:173@CB
1 atom, 1 residue, 1 model selected
> ui tool show Distances
Exactly two atoms must be selected!
> select clear
> select #6/C:173@CG
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 3 time(s)]
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
> select #6/C:173@CB
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
[Repeated 1 time(s)]
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #6/C:173@CD
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> ~distance #6/B:36@NE2 #6/D:466@CG2
Exactly two atoms must be selected!
> select clear
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #6/C:173@NE
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select clear
> select #6/C:173@NH1
1 atom, 1 residue, 1 model selected
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
[Repeated 1 time(s)]
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
> select clear
[Repeated 1 time(s)]
> select #6/A:26@CG2
1 atom, 1 residue, 1 model selected
> select #6/C:173@NE
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> show sel target ab
> select #6/C:173@NH1
1 atom, 1 residue, 1 model selected
Exactly two atoms must be selected!
> select #6/C:173@CD
1 atom, 1 residue, 1 model selected
> select add #6/A:26@CG2
2 atoms, 1 bond, 2 residues, 1 model selected
> distance #6/C:173@CD #6/A:26@CG2
Distance between fold_ch23_fl_plusgly_model_4.cif #6/C ARG 173 CD and /A ILE
26 CG2: 90.397Å
> select clear
> select #6/A:23
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel target ab
> select clear
[Repeated 2 time(s)]
> select #6/A:23@CG
1 atom, 1 residue, 1 model selected
> select add #6/C:173@CB
2 atoms, 2 residues, 1 model selected
> distance #6/A:23@CG #6/C:173@CB
Distance between fold_ch23_fl_plusgly_model_4.cif #6/A MET 23 CG and /C ARG
173 CB: 98.806Å
> ~distance #6/C:173@CD #6/A:26@CG2
> ~distance #6/A:23@CG #6/C:173@CB
Drag select of 10 atoms, 40 residues, 8 bonds
> hide sel target a
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #6/D
Destroying pre-existing alignment with identifier 6/D
Alignment identifier is 6/D
> sequence chain #5/D
Alignment identifier is 5/D
> 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
> select #6/B:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #6/B:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #6/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/A:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #6/C:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/C:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #5/D:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/D:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #6/D:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #6/D:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select clear
> ui tool show "Show Sequence Viewer"
> sequence chain #5/A
Alignment identifier is 5/A
> 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:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/D:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> select #5/C:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/C:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #5/B:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #5/B:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #5/A:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #5/A:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select clear
> select add #6
14888 atoms, 15300 bonds, 1904 residues, 1 model selected
> select add #5
29148 atoms, 29944 bonds, 3744 residues, 2 models selected
> select subtract #6
14260 atoms, 14644 bonds, 1840 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #5,-0.96556,0.25356,0.058379,-32.951,0.24702,0.96379,-0.10042,-103.44,-0.081728,-0.082541,-0.99323,-21.213
> select subtract #5
Nothing selected
> select add #9
14888 atoms, 15300 bonds, 1904 residues, 1 model selected
> view matrix models
> #9,0.04315,0.98488,0.16777,43.139,0.14892,0.15971,-0.97587,104.31,-0.98791,0.067093,-0.13978,4.0302
> ui mousemode right "translate selected models"
> select clear
[Repeated 1 time(s)]
> ui tool show "Modeller Comparative"
> ui tool show "Show Sequence Viewer"
> sequence chain #9/D
Alignment identifier is 9/D
> 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
> select #9/C:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/C:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #9/B:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/B:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #9/A:7-8
15 atoms, 14 bonds, 2 residues, 1 model selected
> select #9/A:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select #9/D:7
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #9/D:7-26
143 atoms, 142 bonds, 20 residues, 1 model selected
> color sel orange
> select clear
> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs
> select add #5
14260 atoms, 14644 bonds, 1840 residues, 1 model selected
> select subtract #5
Nothing selected
> select add #6
14888 atoms, 15300 bonds, 1904 residues, 1 model selected
> select subtract #6
Nothing selected
> select add #9
14888 atoms, 15300 bonds, 1904 residues, 1 model selected
> ui mousemode right "rotate selected models"
> view matrix models
> #9,0.036603,0.98775,0.15169,43.303,0.13034,0.14578,-0.98069,104.88,-0.99079,0.055667,-0.1234,4.1589
> select clear
> save
> /Users/kellykeisen/Documents/Proposals/Influenza_NA_R21/AF_CH23_FL_v_Del.cxs
> 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: 7 days, 2 hours, 50 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 , 13 months ago
| Component: | Unassigned → Depiction |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Bad interaction of colors with "Background" target |
comment:2 by , 13 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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