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Opened 4 years ago
Closed 4 years ago
#5699 closed defect (fixed)
combine: 'was_deleted' attribute missing
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Structure Editing | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3rc202111250017 (2021-11-25 00:17:48 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.3rc202111250017 (2021-11-25)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__2.cxs
> format session
Opened atp_cytrate_lyase_flipped.mrc as #1, grid size 256,256,256, pixel 0.96,
shown at level 0.313, step 1, values float32
Opened fliped_resol.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32
Log from Mon Nov 29 17:38:52 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__1.cxs
Opened atp_cytrate_lyase_flipped.mrc as #1, grid size 256,256,256, pixel 0.96,
shown at level 0.313, step 1, values float32
Opened fliped_resol.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32
Log from Mon Nov 1 10:59:51 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B.cxs
Opened atp_cytrate_lyase_flipped.mrc as #1, grid size 256,256,256, pixel 0.96,
shown at level 0.313, step 1, values float32
Opened fliped_resol.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32
Log from Mon Nov 1 09:57:04 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)
© 2016-2021 Regents of the University of California. All rights reserved.
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B.cxs
Opened atp_cytrate_lyase_flipped.mrc as #1, grid size 256,256,256, pixel 0.96,
shown at level 0.313, step 1, values float32
Opened fliped_resol.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32
Log from Mon Nov 1 09:52:11 2021UCSF ChimeraX version: 1.3.dev202110020016
(2021-10-02)
© 2016-2021 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/atp_cytrate_lyase_flipped.mrc
Opened atp_cytrate_lyase_flipped.mrc as #1, grid size 256,256,256, pixel 0.96,
shown at level 0.42, step 1, values float32
> volume #1 level 0.3201
> surface dust #1 size 9.6
> volume #1 level 0.2566
> pub preset
Unknown command: pub preset
> preset pub
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> ui tool show "Surface Color"
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/fliped_resol.mrc
Opened fliped_resol.mrc as #2, grid size 256,256,256, pixel 0.96, shown at
level 10.2, step 1, values float32
> color sample #2.1 map #1 palette
> #ff0000:#ff9100:#daff00:#48ff00:#00ff48:#00ffda:#0091ff:#0000ff
Map values for surface "surface": minimum -0.5656, mean 0.006037, maximum
0.4944
> color sample #2.1 map #1 palette
> 5,#ff0000:6,#ff9100:7,#daff00:8,#48ff00:9,#00ff48:10,#00ffda:11,#0091ff:12,#0000ff
Map values for surface "surface": minimum -0.5656, mean 0.006037, maximum
0.4944
> color sample #2.1 map #1 palette
> 5,#ff0000:6,#ff9100:7,#daff00:8,#48ff00:9,#00ff48:10,#00ffda:11,#0091ff:12,#0000ff
Map values for surface "surface": minimum -0.5656, mean 0.006037, maximum
0.4944
> color sample #1.1 map #2 palette
> 5,#ff0000:6,#ff9100:7,#daff00:8,#48ff00:9,#00ff48:10,#00ffda:11,#0091ff:12,#0000ff
Map values for surface "surface": minimum 0, mean 7.576, maximum 13.94
> ui tool show "Side View"
> view
> scalebar
> key red:5 #ff9100:6 #daff00:7 #48ff00:8 #00ff48:9 #00ffda:10 #0091ff:11
> blue:12 showTool true
> ui mousemode right "color key"
> key pos 0.308703,0.0184406 size 0.502814,0.0249364
> key pos 0.237454,0.0380889
> volume #1 level 0.3126
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/5B__atp_citrate_lyase.cxs
> includeMaps true
> ui mousemode right translate
> color sample #1.1 map #2 palette
> 6,#ff0000:7,#ff9100:8,#daff00:9,#48ff00:10,#00ff48:11,#00ffda:12,#0091ff:13,#0000ff
Map values for surface "surface": minimum 0, mean 7.74, maximum 12.98
> key red:6 #ff9100:7 #daff00:8 #48ff00:9 #00ff48:10 #00ffda:11 #0091ff:12
> blue:13 showTool true
> ui mousemode right "color key"
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/5B__atp_citrate_lyase.cxs
> includeMaps true
> view
[Repeated 1 time(s)]
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/5B__atp_citrate_lyase.cxs
> includeMaps true
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/top__atp_citrate_lyase__top.jpg
> width 3000 height 1618 supersample 4
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/side__atp_citrate_lyase__top.jpg
> width 3000 height 1618 supersample 4
> turn y 90
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/side__atp_citrate_lyase.jpg
> width 3000 height 1618 supersample 4
> turn y -90
> color single #1.1
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/top_grey.jpg
> width 3000 height 1618 supersample 4
> turn y 90
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/map/local_resolution/side_atp_citrate_lyase.jpg
> width 3000 height 1618 supersample 3
> turn y -90
> open
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/model/6uuz.pdb
6uuz.pdb title:
Structure of ACLY In the presence of citrate and coa [more info...]
Chain information for 6uuz.pdb #5
---
Chain | Description
A B C D | No description available
Non-standard residues in 6uuz.pdb #5
---
COA — coenzyme A
> hide #4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> hide #!1 models
> show #!1 models
> show #!2 models
> hide #!2 models
> select #5
31786 atoms, 32476 bonds, 8 pseudobonds, 4090 residues, 2 models selected
> key pos 0.349055,0.188552 size 0.113932,0.00362391
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #5,0.30703,-0.2184,0.9263,0.00025349,0.071952,0.97585,0.20624,0.00038236,-0.94898,0.0033274,0.31533,-0.0022956
> view matrix models
> #5,-0.14983,-0.187,0.97087,-0.00039246,0.011013,0.98157,0.19076,0.00026809,-0.98865,0.039274,-0.14501,-0.0029594
> ui mousemode right "translate selected models"
> view matrix models
> #5,-0.14983,-0.187,0.97087,109.87,0.011013,0.98157,0.19076,117.52,-0.98865,0.039274,-0.14501,-6.2943
> view matrix models
> #5,-0.14983,-0.187,0.97087,122.21,0.011013,0.98157,0.19076,119.37,-0.98865,0.039274,-0.14501,-6.7891
> move model #5 z10
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> move z 50l #5
Expected a number or a keyword
> move z 50 #5
Expected an integer >= 1 or a keyword
> move z50 #5
Missing or invalid "axis" argument: Expected 3 floats or "x", or "y", or "z"
or two atoms
> ui mousemode right select
> select clear
> select /C:669
9 atoms, 8 bonds, 1 residue, 1 model selected
> select clear
> ui mousemode right select
[Repeated 1 time(s)]
> select #5
31786 atoms, 32476 bonds, 8 pseudobonds, 4090 residues, 2 models selected
> select clear
> ui mousemode right "translate selected models"
> select #5
31786 atoms, 32476 bonds, 8 pseudobonds, 4090 residues, 2 models selected
> view matrix models
> #5,-0.14983,-0.187,0.97087,136.81,0.011013,0.98157,0.19076,119.89,-0.98865,0.039274,-0.14501,121.18
> surface dust #1 size 9.6
> fitmap #5 inMap #1
Fit molecule 6uuz.pdb (#5) to map atp_cytrate_lyase_flipped.mrc (#1) using
31786 atoms
average map value = 0.2003, steps = 188
shifted from previous position = 14.3
rotated from previous position = 13.9 degrees
atoms outside contour = 22492, contour level = 0.3126
Position of 6uuz.pdb (#5) relative to atp_cytrate_lyase_flipped.mrc (#1)
coordinates:
Matrix rotation and translation
-0.00007577 0.00014206 0.99999999 122.88295233
0.00092225 0.99999957 -0.00014199 122.88359124
-0.99999957 0.00092224 -0.00007590 121.92678236
Axis 0.00053212 0.99999978 0.00039010
Axis point 122.34356185 0.00000000 -0.46467262
Rotation angle (degrees) 90.00435733
Shift along axis 122.99651586
Window position QRect(1790,1686 100x30) outside any known screen, using
primary screen
> color #5 #ffd479
> color #5 #ff9300
> ui mousemode right select
> select clear
> select ::name="COA"
192 atoms, 200 bonds, 4 residues, 1 model selected
> color sel red
> color #1 #b2b2b254 models
> color #1 #b2b2b256 models
> color #5 #ff9300
> color #5 #ffd479
> color #5 #fffc79
> color #5 #d4fb79
> color #5 #fffc79
> color #5 #ffd479
> color #5 #fffc79
> color #5 #fffb00
> color #5 #fffc79
> select clear
> select ::name="COA"
192 atoms, 200 bonds, 4 residues, 1 model selected
> color #5 #ff2600
> color #5 #fffb00
> color #5 #fffc79
> color sel red
> select clear
> select /A
7947 atoms, 8119 bonds, 2 pseudobonds, 1023 residues, 2 models selected
> select clear
> ui tool show "Segment Map"
Segmenting atp_cytrate_lyase_flipped.mrc, density threshold 0.312598
Only showing 60 of 402 regions.
Showing 60 of 402 region surfaces
1698 watershed regions, grouped to 402 regions
Showing atp_cytrate_lyase_flipped.seg - 402 regions, 60 surfaces
Segmenting fliped_resol.mrc, density threshold 10.196438
Showing 58 region surfaces
626 watershed regions, grouped to 58 regions
Showing fliped_resol.seg - 58 regions, 58 surfaces
Segmenting atp_cytrate_lyase_flipped.mrc, density threshold 0.312598
Only showing 60 of 402 regions.
Showing 60 of 402 region surfaces
1698 watershed regions, grouped to 402 regions
Showing atp_cytrate_lyase_flipped.seg - 402 regions, 60 surfaces
> hide #!1 models
> hide #!5 models
> hide #!6 models
> show #!1 models
> show #!2 models
> hide #!2 models
> show #4 models
> hide #4 models
> show #!5 models
> select /A:891
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add /C:172
19 atoms, 18 bonds, 2 residues, 1 model selected
> ui tool show Distances
> ui mousemode right "tape measure"
> marker segment #7 position 195.9,164.7,149.6 toPosition 129,124.2,167 color
> yellow radius 0.1 label 80.13 labelHeight 8.013 labelColor yellow
> marker segment #7 position 128,124.4,166.1 toPosition 73.76,185.1,126.6
> color yellow radius 0.24 label 90.39 labelHeight 9.039 labelColor yellow
> marker delete #7
> ui tool show "Side View"
> view
> ui mousemode right select
> select clear
> ui mousemode right "tape measure"
> marker segment #7 position 128.5,121.3,182.6 toPosition 190.9,172.6,122.9
> color yellow radius 0.24 label 100.5 labelHeight 10.05 labelColor yellow
> marker segment #7 position 126.4,121.5,163.5 toPosition 74.36,193.4,138.2
> color yellow radius 0.24 label 92.29 labelHeight 9.229 labelColor yellow
> marker segment #7 position 129.1,120.2,182.6 toPosition 151.1,43.69,113.8
> color yellow radius 0.24 label 105.2 labelHeight 10.52 labelColor yellow
> marker delete #7
> marker segment #7 position 119,123.5,164.2 toPosition 146.1,144.7,111.1
> color yellow radius 0.24 label 63.21 labelHeight 6.321 labelColor yellow
> marker segment #7 position 120.3,123.7,163.2 toPosition 193.1,161.9,130.6
> color yellow radius 0.24 label 88.45 labelHeight 8.845 labelColor yellow
> marker delete #7
> ui mousemode right "play map series"
> ui mousemode right "pick blobs"
[Repeated 1 time(s)]
> ui mousemode right "map eraser"
[Repeated 1 time(s)]
> ui mousemode right "pick blobs"
> ui mousemode right "play map series"
> ui mousemode right "map eraser"
[Repeated 1 time(s)]
> ui mousemode right "pick blobs"
> ui mousemode right translate
> ui mousemode right "tape measure"
> marker segment #7 position 122.9,124.7,172.9 toPosition 192.7,168.8,123.1
> color yellow radius 0.24 label 96.38 labelHeight 9.638 labelColor yellow
> marker segment #7 position 122.2,124.9,172.9 toPosition 54.43,172,129.5
> color yellow radius 0.24 label 93.27 labelHeight 9.327 labelColor yellow
> marker segment #7 position 121.9,124.7,172.9 toPosition 54.09,74.88,122.9
> color yellow radius 0.24 label 97.92 labelHeight 9.792 labelColor yellow
> marker segment #7 position 122.5,124.5,172.9 toPosition 124.5,65.23,180.8
> color yellow radius 0.24 label 59.81 labelHeight 5.981 labelColor yellow
> marker segment #7 position 122.8,124.8,172.9 toPosition 173.3,52.13,125
> color yellow radius 0.24 label 100.6 labelHeight 10.06 labelColor yellow
> marker segment #7 position 122.7,125,172.9 toPosition 122,184.5,176.3 color
> yellow radius 0.24 label 59.56 labelHeight 5.956 labelColor yellow
> move y 90
> move y -90
> turn y 90
> turn y -90
> marker delete #7
> marker segment #7 position 125.7,125.6,92.39 toPosition 197.2,164.4,130.9
> color yellow radius 0.24 label 90.08 labelHeight 9.008 labelColor yellow
> marker segment #7 position 125.1,125.5,92.39 toPosition 120.2,175.2,155.4
> color yellow radius 0.24 label 80.36 labelHeight 8.036 labelColor yellow
> marker delete #7
> marker segment #7 position 120.1,120.9,137.2 toPosition 73.39,194.4,124
> color yellow radius 0.24 label 88.05 labelHeight 8.805 labelColor yellow
> marker segment #7 position 121.5,120.3,137.2 toPosition 45.86,163.4,98.01
> color yellow radius 0.24 label 95.49 labelHeight 9.549 labelColor yellow
> marker delete #7
> marker segment #7 position 126.4,125.4,92.39 toPosition 178.7,61.06,116.7
> color yellow radius 0.24 label 86.46 labelHeight 8.646 labelColor yellow
> marker delete #7
> marker segment #7 position 124.7,125.7,92.39 toPosition 192.2,169.5,122
> color yellow radius 0.24 label 85.75 labelHeight 8.575 labelColor yellow
> marker delete #7
> marker segment #7 position 121.1,120.8,137.2 toPosition 122.2,180.6,121.2
> color yellow radius 0.24 label 61.89 labelHeight 6.189 labelColor yellow
> marker delete #7
> marker segment #7 position 122,119.8,137.2 toPosition 198.4,163.6,146.1
> color yellow radius 0.24 label 88.49 labelHeight 8.849 labelColor yellow
> color #1,5,7 red
> undo
> marker delete #7
> marker segment #7 position 121.6,120,137.2 toPosition 196.6,163.5,146.1
> color yellow radius 0.24 label 87.22 labelHeight 8.722 labelColor yellow
> marker segment red
Missing or invalid "markerSet" argument: Expected a marker set or a model id
> labelColor red
Unknown command: labelColor red
> marker segment #7 position 121.2,120.2,137.2 toPosition 73.86,193.6,124.3
> color yellow radius 0.24 label 88.3 labelHeight 8.83 labelColor yellow
> marker segment #7 position 123,119.4,152.4 toPosition 124,59.66,135.5 color
> yellow radius 0.24 label 62.07 labelHeight 6.207 labelColor yellow
> marker segment #7 position 120.6,119.6,136.7 toPosition 46.37,83.19,145.8
> color yellow radius 0.24 label 83.21 labelHeight 8.321 labelColor yellow
> marker segment #7 position 124,119.6,151.5 toPosition 163.3,55.04,133.6
> color yellow radius 0.24 label 77.64 labelHeight 7.764 labelColor yellow
> marker segment #7 position 124.7,119.8,151.5 toPosition 198.4,86.11,143.2
> color yellow radius 0.24 label 81.52 labelHeight 8.152 labelColor yellow
> marker delete #7
> marker segment #7 position 119,189.9,93.05 toPosition 125.3,60.16,136 color
> yellow radius 0.24 label 136.8 labelHeight 13.68 labelColor yellow
> marker delete #7
> ui mousemode right "tape measure"
> marker segment #7 position 73.72,50.83,121 toPosition 189,168.7,112.6 color
> yellow radius 0.24 label 165 labelHeight 16.5 labelColor yellow
> marker segment #7 position 77.63,192.7,138 toPosition 172,53.49,124.8 color
> yellow radius 0.24 label 168.7 labelHeight 16.87 labelColor yellow
> color #1,5,7 orange
> undo
> marker delete #7
> marker segment #7 position 75.59,193.1,138.3 toPosition 171.9,52,123.8 color
> yellow radius 0.24 label 171.4 labelHeight 17.14 labelColor yellow
> ui mousemode right distance
> ui mousemode right "tape measure"
> tape measure red
Unknown command: tape measure red
> tape measure color red
Unknown command: tape measure color red
> tape measure colorred
Unknown command: tape measure colorred
> tape measure color
Unknown command: tape measure color
> tape measure red
Unknown command: tape measure red
> marker segment #7 position 75.59,193.1,138.3 toPosition 171.9,52,123.8 color
> yellow radius 0.24 label 171.4 labelHeight 17.14 labelColor red
> marker segment #7 position 75.59,193.1,138.3 toPosition 171.9,52,123.8 color
> red radius 0.24 label 171.4 labelHeight 17.14 labelColor red
[Repeated 1 time(s)]
> marker delete #7
> marker segment #7 position 128.2,122,166.1 toPosition 207.4,167.4,170.3
> color yellow radius 0.24 label 91.43 labelHeight 9.143 labelColor yellow
> marker segment #7 position 128.2,122,166.1 toPosition 207.4,167.4,170.3
> color red radius 2 label 91.43 labelHeight 15 labelColor red
> marker delete #7
> view
> ui tool show "Side View"
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B.cxs
> includeMaps true
——— End of log from Mon Nov 1 09:52:11 2021 ———
opened ChimeraX session
Showing atp_cytrate_lyase_flipped.seg - 402 regions, 60 surfaces
> hide #!6 models
> show #!6 models
> close #6
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B.cxs
> includeMaps true
——— End of log from Mon Nov 1 09:57:04 2021 ———
opened ChimeraX session
> hide #!5 models
> show #!5 models
> fitmap #5 inMap #1
Fit molecule 6uuz.pdb (#5) to map atp_cytrate_lyase_flipped.mrc (#1) using
31786 atoms
average map value = 0.2003, steps = 40
shifted from previous position = 0.00724
rotated from previous position = 0.0061 degrees
atoms outside contour = 22491, contour level = 0.3126
Position of 6uuz.pdb (#5) relative to atp_cytrate_lyase_flipped.mrc (#1)
coordinates:
Matrix rotation and translation
-0.00004443 0.00004035 1.00000000 122.88283770
0.00092117 0.99999958 -0.00004031 122.87635255
-0.99999958 0.00092117 -0.00004446 121.92691186
Axis 0.00048074 0.99999979 0.00044041
Axis point 122.34554813 0.00000000 -0.47272856
Rotation angle (degrees) 90.00255858
Shift along axis 122.98909877
> vop gaussian #1 sdev 2.88
Opened atp_cytrate_lyase_flipped.mrc gaussian as #6, grid size 256,256,256,
pixel 0.96, shown at step 1, values float32
> volume #6 level 0.1321
> hide #!6 models
> show #!1 models
> close #6
> ui mousemode right "mark maximum"
> view
> ui tool show "Side View"
> marker #6 position 118.6,123.9,106.5 color yellow radius 0.96
> marker #6 position 121.5,129.9,131.8 color yellow radius 0.96
> marker #6 position 121.7,131,131.3 color yellow radius 0.96
> ui mousemode right "mark plane"
> ui mousemode right "mark maximum"
> marker #6 position 128.8,126.7,167 color yellow radius 0.96
> color #6 #ff2600
> marker change #6:4 radius 5
> marker #6 position 130.6,125.6,167.4 color yellow radius 5
> undo
> hide #6 models
> show #6 models
> hide #6 models
> close #6
> marker #6 position 118.5,125.2,106.5 color yellow radius 5
> color #6 #ff2600
> ui mousemode right "move markers"
> marker change #6:1 position 117.7,120.2,106.3
> turn y 90
> marker change #6:1 position 121.2,122.2,124
> marker change #6:1 position 120.8,122.6,122
> turn y -90
> log metadata #5
No models had metadata
> log chains #5
Chain information for 6uuz.pdb #5
---
Chain | Description
A B C D | No description available
> marker change #6:1 position 121,121,121
> ui mousemode right "mark maximum"
> marker #6 position 192.2,168.6,123.1 color yellow radius 5
> color #5 #ff2600
> color #5 #fffb00
> undo
[Repeated 1 time(s)]
> marker #6 position 192,169.4,123.1 color yellow radius 5
> marker change #6:3 color #ff2600
> hide #6 models
> show #6 models
> ui tool show "Side View"
> ui mousemode right "move markers"
> marker change #6:2 position 218,165.1,117.8
> marker change #6:3 position 191.7,165.5,122.9
> marker change #6:2 position 218.6,165.1,117.6
> ui mousemode right "delete markers"
> marker delete #6:2
> ui mousemode right "link markers"
> marker link #6:3,1 color #659cef radius 0.48
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "link markers"
> turn y 90
> undo
> ui mousemode right "move markers"
> marker change #6:3 position 194.4,166.2,122.4
> marker change #6:3 position 189.6,170.8,123.7
> ui mousemode right "mark maximum"
> marker #6 position 83.07,52.69,128 color #ff2600 radius 5
> marker link #6:3,4 color #ff2600 radius 1
> marker #6 position 118.3,123.1,106 color #ff2600 radius 5
> marker link #6:4,5 color #ff2600 radius 1
> marker #6 position 193.9,165.9,163.4 color #ff2600 radius 5
> marker link #6:5,6 color #ff2600 radius 1
> marker #6 position 71.96,184.3,126.7 color #ff2600 radius 5
> marker link #6:6,7 color #ff2600 radius 1
> marker #6 position 119,123.6,106.2 color #ff2600 radius 5
> marker link #6:7,8 color #ff2600 radius 1
> marker #6 position 168.2,53.16,138.1 color #ff2600 radius 5
> marker link #6:8,9 color #ff2600 radius 1
> marker #6 position 193.9,166,153.9 color #ff2600 radius 5
> marker #6 position 191.7,167.2,154.4 color #ff2600 radius 5
> ui mousemode right "delete markers"
> marker delete #6:11
> marker delete #6:10
> marker delete #6:9
> marker delete #6:4
> turn y 90
> marker delete #6:5
> marker delete #6:8
> ui mousemode right "link markers"
> marker link #6:1,7 color #ff2600 radius 1
> turn y -90
> ui mousemode right "delete markers"
> marker delete #6:6
> ui mousemode right "move markers"
> ui mousemode right "link markers"
> marker link #6:3,7 color #ff2600 radius 1
> ui mousemode right "link markers"
> ui mousemode right "move markers"
> ui mousemode right "link markers"
> ui mousemode right "delete markers"
> marker delete #6:3
> ui mousemode right "mark maximum"
> marker #6 position 190.8,171.6,123.1 color #ff2600 radius 5
> marker link #6:1,12 color #ff2600 radius 1
> marker #6 position 70.9,185.9,126.5 color #ff2600 radius 5
> marker link #6:12,13 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:13
> ui mousemode right "link markers"
> marker link #6:7,12 color #ff2600 radius 1
> ui mousemode right "move markers"
> ui mousemode right "mark maximum"
> ui mousemode right "move markers"
> marker change #6:7 position 72.46,182.9,126.7
> marker change #6:12 position 188.1,170.9,123.5
> marker change #6:7 position 73.53,181.6,126.6
> marker change #6:12 position 187.4,173.5,123.5
> turn y 90
[Repeated 1 time(s)]
> marker change #6:7 position 50.63,164.7,129.7
> marker change #6:12 position 193,161.8,123
> marker change #6:7 position 49.45,162.2,129.9
> ui mousemode right "mark maximum"
> marker #6 position 155.3,190.9,99.42 color #ff2600 radius 5
> marker link #6:12,14 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:14
> ui mousemode right "mark maximum"
> marker #6 position 156.4,191.1,97.82 color #ff2600 radius 5
> marker #6 position 125.9,122,163.4 color #ff2600 radius 5
> marker link #6:15,16 color #ff2600 radius 1
> marker #6 position 78.65,192.8,116.5 color #ff2600 radius 5
> marker link #6:16,17 color #ff2600 radius 1
> turn y 90
> ui mousemode right "delete markers"
> marker delete #6:16
> ui mousemode right "mark maximum"
> ui mousemode right "move markers"
> marker change #6:15 position 160.3,190.8,128.7
> marker change #6:1 position 121,121,121
> ui mousemode right "link markers"
> marker link #6:17,1 color #ff2600 radius 1
> marker link #6:1,15 color #ff2600 radius 1
> turn y 90
> marker link #6:15,17 color #ff2600 radius 1
> ui mousemode right "move markers"
> marker change #6:7 position 53.16,160.8,129.5
> marker change #6:12 position 196,161.4,122.6
> marker change #6:17 position 74.93,191.3,116.9
> marker change #6:15 position 169.2,190.9,127.6
> ui mousemode right "mark maximum"
> marker #6 position 83.62,53.5,127.8 color #ff2600 radius 5
> marker link #6:17,18 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:18
> ui mousemode right "mark maximum"
> marker #6 position 84,53.31,127.3 color #ff2600 radius 5
> marker #6 position 119.3,124.3,106.5 color #ff2600 radius 5
> marker link #6:19,20 color #ff2600 radius 1
> turn y 90
> ui mousemode right "delete markers"
> marker delete #6:20
> turn y -90
> ui mousemode right "mark maximum"
> marker #6 position 159.9,52.98,130.5 color #ff2600 radius 5
> marker #6 position 50.89,83.61,144.7 color #ff2600 radius 5
> marker link #6:21,22 color #ff2600 radius 1
> marker #6 position 197.6,89.19,88.93 color #ff2600 radius 5
> marker link #6:22,23 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:21
> ui mousemode right "mark maximum"
> marker #6 position 164.7,56.56,145 color #ff2600 radius 5
> marker link #6:23,24 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:24
> ui mousemode right "mark maximum"
> marker #6 position 163.8,54.16,134 color #ff2600 radius 5
> ui mousemode right "link markers"
> marker link #6:25,1 color #ff2600 radius 1
> marker link #6:1,23 color #ff2600 radius 1
> marker link #6:23,19 color #ff2600 radius 1
> ui mousemode right "delete markers"
[Repeated 1 time(s)]
> marker delete #6:19
> ui mousemode right "mark maximum"
> marker #6 position 83.54,52.53,127.8 color #ff2600 radius 5
> ui mousemode right "link markers"
> marker link #6:26,1 color #ff2600 radius 1
> marker link #6:1,22 color #ff2600 radius 1
> marker link #6:22,25 color #ff2600 radius 1
> undo
> turn y -90
> ui mousemode right "delete markers"
> marker delete #6:22,25 linksOnly true
> ui mousemode right "link markers"
> marker link #6:25,26 color #ff2600 radius 1
> turn y 90
[Repeated 1 time(s)]
> ui mousemode right "move markers"
> marker change #6:22 position 49.82,86.41,144.7
> marker change #6:25 position 170.2,53.48,133.3
> marker change #6:26 position 76.51,53.5,128.6
> marker change #6:17 position 75.57,190.6,116.9
> marker change #6:15 position 171.5,192.1,127.2
> marker change #6:22 position 48.51,86.24,144.9
> marker change #6:23 position 195.7,89.1,89.18
> marker change #6:23 position 195.2,89.2,89.23
> turn y 90
[Repeated 5 time(s)]
> marker change #6:23 position 195.2,86.25,89.38
> marker change #6:7 position 53.72,160.1,129.4
> marker change #6:17 position 74.77,191.6,117
> marker change #6:15 position 170.2,190.9,127.5
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__1.cxs
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__1.cxs
> includeMaps true
> ui mousemode right "tape measure"
> ui mousemode right "rotate slab"
> ui mousemode right "tape measure"
> marker segment #7 position 170.2,190.9,127.5 toPosition 222.6,176.3,128.3
> color yellow radius 0.1 label 54.47 labelHeight 5.447 labelColor yellow
> marker segment #7 position 170.2,190.9,127.5 toPosition 121,121,121 color
> yellow radius 0.1 label 85.74 labelHeight 8.574 labelColor yellow
> marker delete #7
> marker segment #7 position 121,121,121 toPosition 170.2,190.9,127.5 color
> yellow radius 0.1 label 85.74 labelHeight 8.574 labelColor yellow
> marker segment #7 position 121,121,121 toPosition 170.2,190.9,127.5 color
> red radius 0.5 label 85.74 labelHeight 8.574 labelColor red
> marker segment #7 position 121,121,121 toPosition 170.2,190.9,127.5 color
> red radius 0.5 label 85.74 labelHeight 10 labelColor red
> marker delete #7
> marker segment #7 position 170.2,190.9,127.5 toPosition 121,121,121 color
> yellow radius 0.1 label 85.74 labelHeight 8.574 labelColor yellow
> marker delete #7
> ui tool show "Side View"
> view
> ui tool show "Side View"
[Repeated 1 time(s)]
> ui mousemode right select
> select clear
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__1.cxs
> includeMaps true
> ui mousemode right "link markers"
> marker link #6:22,26 color #ff2600 radius 1
> marker link #6:26,23 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:26,23 linksOnly true
> ui mousemode right "link markers"
> marker link #6:23,25 color #ff2600 radius 1
> marker link #6:25,15 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:25,15 linksOnly true
> ui mousemode right "link markers"
> marker link #6:15,12 color #ff2600 radius 1
> marker link #6:12,17 color #ff2600 radius 1
> ui mousemode right "delete markers"
> marker delete #6:12,17 linksOnly true
> ui mousemode right "link markers"
> marker link #6:17,7 color #ff2600 radius 1
> turn y 90
> turn y -90
> ui mousemode right "resize markers"
> ui mousemode right "move markers"
> marker change #6:26 position 79.17,54.33,128
> marker change #6:25 position 171,54.78,133.2
> marker change #6:17 position 73.95,192.2,117.2
> marker change #6:15 position 170.8,190.1,127.2
> marker change #6:7 position 54.46,158.8,129.1
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__1.cxs
> includeMaps true
——— End of log from Mon Nov 1 10:59:51 2021 ———
opened ChimeraX session
> hide #!6 models
> hide #!1 models
> show #!1 models
> rainbow #!5
> color #1 #ff9300 models
> scalebar
> show #!2 models
> hide #!2 models
> show #!6 models
> hide #!6 models
> show #4 models
> hide #4 models
> show #!3 models
> close #3
> scalebar
> hide #!5 models
> color #1 #ff7e79 models
> color #1 #ff9300 models
> color #1 #f4bc41 models
> color #1 #ff9300 models
> show #!5 models
> hide #!5 models
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/top__color_scale.tif
> width 3000 height 2334 supersample 4
> turn y 90
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/side__color_scale.tif
> width 3000 height 2334 supersample 4 transparentBackground true
> show #!5 models
> split
Split 6uuz.pdb (#5) into 4 models
Chain information for 6uuz.pdb A #5.1
---
Chain | Description
A | No description available
Chain information for 6uuz.pdb B #5.2
---
Chain | Description
B | No description available
Chain information for 6uuz.pdb C #5.3
---
Chain | Description
C | No description available
Chain information for 6uuz.pdb D #5.4
---
Chain | Description
D | No description available
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> hide #5.1.1 models
> show #5.1.1 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.1 models
> show #!5.1 models
> hide #!3 models
> show #!3 models
> hide #!1 models
> hide #!5 models
> show #!5 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> hide #!5.2 models
> show #!5.2 models
> split
Did not split 6uuz.pdb A, has only one piece
Did not split 6uuz.pdb B, has only one piece
Did not split 6uuz.pdb C, has only one piece
Did not split 6uuz.pdb D, has only one piece
> hide #!5.1 models
> show #!5.1 models
Drag select of 188 residues, 1 pseudobonds
> select up
2123 atoms, 2158 bonds, 1 pseudobond, 279 residues, 2 models selected
> select up
7947 atoms, 8119 bonds, 1 pseudobond, 1023 residues, 2 models selected
> select down
2123 atoms, 2158 bonds, 1 pseudobond, 279 residues, 2 models selected
Drag select of 312 residues, 1 pseudobonds
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 47, in
_make_color_callback
_color_callback(*args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 128, in _color_changed_cb
self.set_color(color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 191, in set_color
ColorButton.set_color(self, color)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color
self.setStyleSheet('background-color: %s' % hex_color_name(color))
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted
RuntimeError: wrapped C/C++ object of type MultiColorButton has been deleted
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/color_button.py", line 88, in set_color
self.setStyleSheet('background-color: %s' % hex_color_name(color))
See log for complete Python traceback.
> color (#!5.1 & sel) blue
> color (#!5.1 & sel) cyan
> ui tool show "Color Actions"
> color (#!5.1 & sel) #8efa00ff
> color (#!5.1 & sel) #00f900ff
> color (#!5.1 & sel) #00fa92ff
> color (#!5.1 & sel) #00fdffff
> undo
> select clear
Drag select of 3 atoms, 397 residues, 2 pseudobonds, 2 bonds
> select up
3041 atoms, 3091 bonds, 2 pseudobonds, 398 residues, 2 models selected
> select down
2996 atoms, 2 bonds, 2 pseudobonds, 398 residues, 2 models selected
> color (#!5.1 & sel) #00fa92ff
> color (#!5.1 & sel) #0096ffff
> color (#!5.1 & sel) #00fa92ff
> color (#!5.1 & sel) #00f900ff
> color (#!5.1 & sel) #00fa92ff
> select clear
Drag select of 31 atoms, 120 residues, 27 bonds
> color sel #00f900ff
> color sel #00fa92ff
Drag select of 49 residues
Drag select of 44 residues
Drag select of 1 residues
> select #5.1/A:830
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
69 atoms, 71 bonds, 8 residues, 1 model selected
> select up
7947 atoms, 8119 bonds, 1023 residues, 1 model selected
> select down
69 atoms, 71 bonds, 8 residues, 1 model selected
> color sel cyan
> color sel #00f900ff
> color sel #00fa92ff
Drag select of 5 residues
> select clear
Drag select of 59 residues
> select up
821 atoms, 830 bonds, 106 residues, 1 model selected
> color sel #00f900ff
> color sel #00fa92ff
Drag select of 2 residues
> select up
74 atoms, 78 bonds, 7 residues, 1 model selected
> color sel #00f900ff
> color sel #00fa92ff
> ui mousemode right select
> select clear
Drag select of 13 atoms, 154 residues, 8 bonds
> select up
1175 atoms, 641 bonds, 155 residues, 2 models selected
> color sel #00f900ff
> color sel #00fa92ff
> select clear
> undo
> redo
Drag select of 649 residues, 44 atoms, 2 pseudobonds, 40 bonds
> select up
4984 atoms, 5036 bonds, 2 pseudobonds, 650 residues, 3 models selected
> select up
5014 atoms, 5069 bonds, 2 pseudobonds, 650 residues, 3 models selected
> color (#!5.1-2 & sel) #00f900ff
> color (#!5.1-2 & sel) #00fa92ff
> select clear
Drag select of 6 residues
> select clear
Drag select of 3 residues
> select up
141 atoms, 146 bonds, 15 residues, 1 model selected
> color sel #00f900ff
> color sel #00fdffff
> color sel #00fa92ff
> select clear
Drag select of 265 residues
> color sel #00f900ff
> color sel #00fa92ff
Drag select of 49 atoms, 265 residues, 45 bonds
> select up
2010 atoms, 2029 bonds, 266 residues, 1 model selected
> select up
2035 atoms, 2058 bonds, 266 residues, 1 model selected
> select up
2762 atoms, 2808 bonds, 359 residues, 1 model selected
> color sel #00f900ff
> color sel #00fa92ff
> select clear
Drag select of 449 residues, 2 atoms, 1 pseudobonds, 2 bonds
> select clear
Drag select of 10 atoms, 590 residues, 2 pseudobonds, 9 bonds
> select up
4552 atoms, 4621 bonds, 2 pseudobonds, 592 residues, 3 models selected
> select up
4602 atoms, 4674 bonds, 2 pseudobonds, 592 residues, 3 models selected
> select down
4552 atoms, 4621 bonds, 2 pseudobonds, 592 residues, 3 models selected
> select up
4602 atoms, 4674 bonds, 2 pseudobonds, 592 residues, 3 models selected
> select up
5077 atoms, 5181 bonds, 2 pseudobonds, 656 residues, 3 models selected
> select up
15893 atoms, 16238 bonds, 2 pseudobonds, 2045 residues, 3 models selected
> select down
5077 atoms, 5181 bonds, 2 pseudobonds, 656 residues, 3 models selected
> color (#!5.3-4 & sel) #00f900ff
> color (#!5.3-4 & sel) #00fa92ff
> select clear
Drag select of 3 atoms, 83 residues, 1 bonds
> color sel #00f900ff
> color sel #00fa92ff
> select clear
Drag select of 15 residues
> select up
265 atoms, 266 bonds, 34 residues, 2 models selected
> select up
15893 atoms, 16238 bonds, 2045 residues, 2 models selected
> select down
265 atoms, 266 bonds, 34 residues, 2 models selected
> color sel #73fa79ff
> color sel #00f900ff
> color sel #00fa92ff
> select clear
Drag select of 5 atoms, 106 residues, 5 bonds
> select up
1473 atoms, 1499 bonds, 196 residues, 2 models selected
> color sel #00f900ff
> color sel #00fa92ff
> select clear
Drag select of 5 residues
> select up
141 atoms, 146 bonds, 15 residues, 1 model selected
> color sel #00f900ff
> color sel #00fa92ff
> select clear
Drag select of 28 atoms, 471 residues, 2 pseudobonds, 24 bonds
> select up
3602 atoms, 3654 bonds, 2 pseudobonds, 472 residues, 2 models selected
> select up
4288 atoms, 4368 bonds, 2 pseudobonds, 557 residues, 2 models selected
> select up
7946 atoms, 8119 bonds, 2 pseudobonds, 1022 residues, 2 models selected
> select down
4288 atoms, 4368 bonds, 2 pseudobonds, 557 residues, 2 models selected
> color (#!5.4 & sel) #8efa00ff
> color (#!5.4 & sel) #00f900ff
> color (#!5.4 & sel) #00fa92ff
> select clear
Drag select of 63 residues
> color sel #00f900ff
> color sel #00fdffff
> select clear
Drag select of 151 residues
> color sel #00fa92ff
> select clear
Drag select of 320 residues, 1 pseudobonds
> color (#!5.4 & sel) #00f900ff
> color (#!5.4 & sel) #00fdffff
> color (#!5.4 & sel) #00fa92ff
> color (#!5.4 & sel) #00fdffff
> color (#!5.4 & sel) #00fa92ff
> select clear
Drag select of 82 residues
> select up
1097 atoms, 1114 bonds, 134 residues, 1 model selected
> color sel #00f900ff
> color sel #00fa92ff
> select clear
Drag select of 129 residues
> select up
1949 atoms, 1979 bonds, 256 residues, 3 models selected
> color sel #0433ffff
> select up
23840 atoms, 24357 bonds, 3068 residues, 3 models selected
> select down
1949 atoms, 1979 bonds, 256 residues, 3 models selected
> select clear
Drag select of 1 atoms, 189 residues
> select up
2915 atoms, 2957 bonds, 380 residues, 4 models selected
> select down
1434 atoms, 189 residues, 4 models selected
> select up
2915 atoms, 2957 bonds, 380 residues, 4 models selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
Drag select of 422 residues, 1 atoms, 1 bonds
> select up
4547 atoms, 4620 bonds, 598 residues, 4 models selected
> select down
3147 atoms, 1 bond, 422 residues, 4 models selected
> select up
4547 atoms, 4620 bonds, 598 residues, 4 models selected
> color sel #0096ffff
> color sel #9437ffff
> color sel #7a81ffff
> color sel #0433ffff
> select clear
Drag select of 10 residues
> select up
499 atoms, 505 bonds, 63 residues, 3 models selected
> select down
89 atoms, 10 residues, 3 models selected
Drag select of 44 residues
> select up
848 atoms, 869 bonds, 106 residues, 4 models selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
Drag select of 21 residues
> select up
545 atoms, 555 bonds, 69 residues, 2 models selected
> color sel #0096ffff
> color sel #0433ffff
Drag select of 7 residues
> select up
153 atoms, 159 bonds, 17 residues, 2 models selected
> color sel #0096ffff
> color sel #9437ffff
> color sel #0433ffff
> select clear
Drag select of 3 residues
> select up
209 atoms, 210 bonds, 27 residues, 1 model selected
> select down
22 atoms, 3 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
Drag select of 65 residues
> color sel #0096ffff
> color sel #0433ffff
> select clear
Drag select of 1 residues
> select up
63 atoms, 64 bonds, 7 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
Drag select of 19 residues, 11 atoms, 12 bonds
> select up
176 atoms, 85 bonds, 21 residues, 4 models selected
> select up
223 atoms, 135 bonds, 21 residues, 4 models selected
> select down
176 atoms, 85 bonds, 21 residues, 4 models selected
> select clear
Drag select of 38 residues
Drag select of 222 residues
> color sel #0096ffff
> color sel #0433ffff
> select clear
> select #5.4/D:958
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
68 atoms, 69 bonds, 9 residues, 1 model selected
> select up
7946 atoms, 8119 bonds, 1022 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> undo
[Repeated 1 time(s)]
> select clear
Drag select of 75 residues, 5 atoms, 4 bonds
> color sel #0096ffff
> color sel #0433ffff
> select #5.4/D:966
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
170 atoms, 171 bonds, 22 residues, 1 model selected
> color sel #00fa92ff
> color sel #0433ffff
Drag select of 20 residues
> color sel #00fdffff
> color sel #0096ffff
> color sel #0433ffff
> select #5.4/D:1010
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
Drag select of 2 residues
> select up
39 atoms, 39 bonds, 5 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
> select #5.1/A:1021
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
39 atoms, 39 bonds, 5 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
> select #5.2/B:1021
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
39 atoms, 39 bonds, 5 residues, 1 model selected
> color sel #0096ffff
> color sel #0433ffff
> select clear
Drag select of 173 residues
> color sel #00fa92ff
> color sel #00fdffff
> color sel #00fa92ff
> select clear
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> select ::name="COA"
192 atoms, 200 bonds, 4 residues, 4 models selected
> color sel red
> select clear
> show #!1 models
> hide #!3 models
> show #!3 models
> hide #!5.1 models
> show #!5.1 models
> hide #!5 models
> ui tool show "Side View"
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/top__color_scale.tif
> width 3000 height 2334 supersample 4 transparentBackground true
> turn y 90
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/side__color_scale.tif
> width 3000 height 2334 supersample 4 transparentBackground true
> turn y -90
> show #!5 models
> ui tool show "Color Zone"
> select #5
31786 atoms, 32476 bonds, 8 pseudobonds, 4090 residues, 9 models selected
> color zone #1 near #5.1 distance 5.76
> color zone #1 near #5.2 distance 5.76
> combine
Exception ignored in: <function Drawing.__del__ at 0x7fab54fb5700>
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1183, in __del__
if not self.was_deleted:
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute 'was_deleted'
Traceback (most recent call last):
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/cmd.py", line 39, in combine_cmd
combination = structures[0].copy(name)
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 138, in copy
m = self.__class__(self.session, name = name,
TypeError: __init__() got an unexpected keyword argument 'c_pointer'
TypeError: __init__() got an unexpected keyword argument 'c_pointer'
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 138, in copy
m = self.__class__(self.session, name = name,
See log for complete Python traceback.
> hide #!5 models
> show #!5 models
> color zone #1 near #5.2 distance 5.76
> save
> /Users/daredevil/Documents/Invited__paper__/F5/5B/After_D/session_5B__2.cxs
> includeMaps true
——— End of log from Mon Nov 29 17:38:52 2021 ———
opened ChimeraX session
> ui mousemode right select
> select clear
> show #!6 models
> hide #!6 models
> combine
Exception ignored in: <function Drawing.__del__ at 0x7fe2a4fa8550>
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/drawing.py", line 1183, in __del__
if not self.was_deleted:
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 61, in _getattr_
return base.__getattr__(self, attr_name, look_in_class=base)
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 57, in _getattr_
return look_in_class._attr_registration.get_attr(attr_name)
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/attributes.py", line 85, in get_attr
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None
AttributeError: 'Structure' object has no attribute 'was_deleted'
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 297, in execute
cmd.run(cmd_text)
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run
result = ci.function(session, **kw_args)
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/cmd.py", line 39, in combine_cmd
combination = structures[0].copy(name)
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 140, in copy
m = self.__class__(self.session, name = name,
TypeError: __init__() got an unexpected keyword argument 'c_pointer'
TypeError: __init__() got an unexpected keyword argument 'c_pointer'
File
"/Applications/ChimeraX-1.3-rc2021.11.25.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/atomic/structure.py", line 140, in copy
m = self.__class__(self.session, name = name,
See log for complete Python traceback.
OpenGL version: 4.1 ATI-4.7.29
OpenGL renderer: AMD Radeon Pro 580 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3,8 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 16 GB
System Firmware Version: 447.40.12.0.0
OS Loader Version: 540.40.4~45
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 12.0.1 (21A559)
Kernel Version: Darwin 21.1.0
Time since boot: 5 days 7:48
Graphics/Displays:
Radeon Pro 580:
Chipset Model: Radeon Pro 580
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 8 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c0
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1X-025
EFI Driver Version: 01.00.931
Metal Family: Supported, Metal GPUFamily macOS 2
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
appnope: 0.1.2
Babel: 2.9.1
backcall: 0.2.0
blockdiag: 2.0.1
certifi: 2021.5.30
cftime: 1.5.1.1
charset-normalizer: 2.0.8
ChimeraX-AddCharge: 1.2.2
ChimeraX-AddH: 2.1.3
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.2.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.31
ChimeraX-AtomicLibrary: 4.2
ChimeraX-AtomSearch: 2.0
ChimeraX-AtomSearchLibrary: 1.0
ChimeraX-AxesPlanes: 2.0
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.0
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.6
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.2
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5
ChimeraX-CommandLine: 1.1.5
ChimeraX-ConnectStructure: 2.0
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.3rc202111250017
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.0
ChimeraX-DistMonitor: 1.1.5
ChimeraX-DistUI: 1.0
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.1
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.4
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.4
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.4
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.2.6
ChimeraX-ModelPanel: 1.2.1
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.7
ChimeraX-PDB: 2.6.5
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.0.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.4.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.6.1
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-Struts: 1.0
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1
ChimeraX-ToolshedUtils: 1.2
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.2.1
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.0.1
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
cxservices: 1.1
cycler: 0.11.0
Cython: 0.29.24
decorator: 5.1.0
docutils: 0.17.1
filelock: 3.0.12
funcparserlib: 0.3.6
grako: 3.16.5
h5py: 3.6.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.21
imagecodecs: 2021.4.28
imagesize: 1.3.0
ipykernel: 5.5.5
ipython: 7.23.1
ipython-genutils: 0.2.0
jedi: 0.18.0
Jinja2: 3.0.1
jupyter-client: 6.1.12
jupyter-core: 4.9.1
kiwisolver: 1.3.2
lxml: 4.6.3
lz4: 3.1.3
MarkupSafe: 2.0.1
matplotlib: 3.4.3
matplotlib-inline: 0.1.3
msgpack: 1.0.2
netCDF4: 1.5.7
networkx: 2.6.3
numexpr: 2.7.3
numpy: 1.21.2
openvr: 1.16.801
packaging: 21.0
ParmEd: 3.2.0
parso: 0.8.2
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 8.3.2
pip: 21.2.4
pkginfo: 1.7.1
prompt-toolkit: 3.0.23
psutil: 5.8.0
ptyprocess: 0.7.0
pycollada: 0.7.1
pydicom: 2.1.2
Pygments: 2.10.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.6
PyQt5-commercial: 5.15.2
PyQt5-sip: 12.8.1
PyQtWebEngine-commercial: 5.15.2
python-dateutil: 2.8.2
pytz: 2021.3
pyzmq: 22.3.0
qtconsole: 5.1.1
QtPy: 1.11.2
RandomWords: 0.3.0
requests: 2.26.0
scipy: 1.7.1
setuptools: 57.5.0
sfftk-rw: 0.7.1
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.2.0
sphinx-autodoc-typehints: 1.12.0
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 2.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-jurko: 0.6
tifffile: 2021.4.8
tinyarray: 1.2.3
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.7
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.0
wheel-filename: 1.3.0
Change History (6)
comment:1 by , 4 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Structure Editing |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → combine: 'was_deleted' attribute missing |
comment:2 by , 4 years ago
comment:3 by , 4 years ago
| Status: | accepted → feedback |
|---|
comment:4 by , 4 years ago
The problem is the marker set. You can get the combine to work by excluding the marker set with "combine #5".
comment:5 by , 4 years ago
In case you missed it because of the long, bogus "difference" text at the beginning, I commented:
The problem is the marker set. You can get the combine to work by excluding the marker set with "combine #5".
comment:6 by , 4 years ago
| Resolution: | → fixed |
|---|---|
| Status: | feedback → closed |
Fix committed for daily build, but not impending 1.3 release
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Hi Dmitry,
--Eric