The following bug report has been submitted:
Platform: Windows-10-10.0.18362
ChimeraX Version: 0.93 (2020-03-23)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\20201210\585_ligand_detail2.cxs" format
> session
Log from Wed Dec 30 12:23:57 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\20201210\585_ligand_interaction.cxs"
> format session
Log from Sun Dec 13 10:25:37 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\20201210\585_ligand_detail.cxs" format
> session
Log from Thu Dec 10 16:32:53 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\figure_20201127\overall_map_1_20201128.cxs"
> format session
Log from Sat Nov 28 10:45:54 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\figure_recolor\20201022_map_overall2.cxs"
> format session
Log from Thu Oct 22 17:11:02 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\figure_recolor\20201022_map_overall.cxs"
> format session
Log from Thu Oct 22 15:01:06 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\figure_recolor\20201022_map_overall.cxs"
> format session
Log from Thu Oct 22 14:03:14 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\20201006_overall_2.cxs" format session
Log from Tue Oct 6 14:48:11 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\20201006_overall.cxs" format session
Log from Tue Oct 6 11:33:07 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open "F:\Experiment\onedrive2\OneDrive -
> case.edu\CWRU\CWRU\AdeJ_manuscript\20201006_overall.cxs" format session
Log from Tue Oct 6 11:12:20 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open F:\Experiment\OneDrive\CWRU\AdeJ_presentation\20200925_4.cxs format
> session
Log from Fri Sep 25 15:01:42 2020UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
> open F:\Experiment\OneDrive\CWRU\AdeJ_presentation\20200921_3.cxs format
> session
Log from Mon Sep 21 18:04:55 2020 Startup Messages
---
warning | 'clip' is a prefix of an existing command 'clipper'
UCSF ChimeraX version: 0.93 (2020-03-23)
© 2016-2020 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open D:/phenix/AdeJ/EVA/20200915/AdeJ_era_J409_20200915-coot-25.pdb
Summary of feedback from opening
D:/phenix/AdeJ/EVA/20200915/AdeJ_era_J409_20200915-coot-25.pdb
---
warning | Ignored bad PDB record found on line 49291
END
Chain information for AdeJ_era_J409_20200915-coot-25.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> close
> open D:/phenix/AdeJ/EVA/20200915/AdeJ_era_J409_20200915-coot-26.pdb
Summary of feedback from opening
D:/phenix/AdeJ/EVA/20200915/AdeJ_era_J409_20200915-coot-26.pdb
---
warning | Ignored bad PDB record found on line 50053
END
Chain information for AdeJ_era_J409_20200915-coot-26.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> set bgColor white
> color #1/B light pink
> color #1/A snow
> color #1/C gainsboro
> color #1/A dark goldenrod
> color #1/A dodger blue
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921.cxs
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> save C:\Users\HP\Desktop\image1.png supersample 3
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.tif
> width 1340 height 788
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.tif
> width 2600 height 1529
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.tif
> width 3900 height 2293
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.png
> width 2600 height 1529
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #1 byhetero
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.tif
> width 3900 height 2293
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.png
> width 2600 height 1529
> select #1
49041 atoms, 49512 bonds, 1 model selected
> ~select #1
Nothing selected
> select #1
49041 atoms, 49512 bonds, 1 model selected
> ~select #1
Nothing selected
> color #1/D sandy brown
> color #1/D byhetero
> open D:/phenix/AdeJ/EVA/20200915/cryosparc_P33_J409_005_volume_map_sharp.mrc
Opened cryosparc_P33_J409_005_volume_map_sharp.mrc, grid size 400,400,400,
pixel 1.08, shown at level 0.124, step 2, values float32
> volume #2 step 1
> volume #2 level 0.2336
> volume zone #2 nearAtoms #3/D range 2
no atoms specified for zone
> volume zone #2 nearAtoms #1/D range 2
> volume #2 level 0.2611
> volume #3 level 0.07326
> volume #3 style mesh
> volume #3 color blue
> volume #3 color #550000
> volume #3 color blue
> volume #3 color #0055ff
> volume #3 color #55ff00
> volume #3 color cyan
> volume #3 color #aaffff
> volume #3 color lime
> volume #3 color #5555ff
> volume #3 subdivideSurface true
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_1.cxs
> volume #3 subdivisionLevels 2
> volume #3 subdivisionLevels 3
> volume #3 subdivisionLevels 1
Invalid "subdivisionLevels" argument: Expected an integer
Invalid "subdivisionLevels" argument: Expected an integer
> volume #3 level 0.04921
> volume #3 level 0.0476
> volume #3 level 0.05402
> select #1/B: 675,327,674,627,616,618,621,274,629,573,613,277,570
223 atoms, 217 bonds, 1 model selected
> color sel green
> color #1/B@ca light pink
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_2.cxs
> volume #3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.2
> surface undust #3
Expected fewer arguments
Expected fewer arguments
Expected fewer arguments
> volume #3 level 0.0476
> color sel byhetero
> select #1
49041 atoms, 49512 bonds, 1 model selected
> ~select #1
Nothing selected
> select #2
2 models selected
> ~select #2
Nothing selected
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_2.tif
> width 3900 height 2293
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_2.png
> width 2600 height 1529
> select #1
49041 atoms, 49512 bonds, 1 model selected
> ~select #1
Nothing selected
> select #2
2 models selected
> ~select #2
Nothing selected
> select #3
2 models selected
> ~select #3
Nothing selected
> select #3
2 models selected
> ~select #3
Nothing selected
> select #1/B: 675,327,674,627,616,618,621,274,629,573,613,277,570
223 atoms, 217 bonds, 1 model selected
> color sel lime green
> color sel byhetero
> color #1/B@ca light pink
> select #2
2 models selected
> ~select #2
Nothing selected
> color #1/D magenta
> color #1/D byhetero
> volume #3 color cyan
> volume #3 color #aaffff
> volume #3 color #55aa7f
> volume #3 color #ff5500
> volume #3 color #55aaff
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> volume #3 color #aaff00
> volume #3 color #aaff7f
> volume #3 color #55ffff
> volume #3 color white
> volume #3 color #00557f
> volume #3 color #aa007f
> volume #3 color #aa557f
> volume #3 color #00557f
> volume #3 color blue
> volume #3 color #5500ff
> volume #3 color #ff55ff
> volume #3 color #5555ff
> volume #3 color #55aaff
> volume #3 color #5555ff
> volume #3 color #55aaff
> color #1/D violet
> volume #3 color #5500ff
> color #1/D dark orange
> color #1/D byhetero
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_2.png
> width 2600 height 1529
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_3.tif
> width 3900 height 2293
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_3.png
> width 2600 height 1529
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_3.cxs
opened ChimeraX session
> close #1
> open
> F:/Experiment/OneDrive/CWRU/AdeJ_manuscript/AdeJ_era_J409_20200915-coot-29_try.pdb
Summary of feedback from opening
F:/Experiment/OneDrive/CWRU/AdeJ_manuscript/AdeJ_era_J409_20200915-coot-29_try.pdb
---
warning | Ignored bad PDB record found on line 49289
END
Chain information for AdeJ_era_J409_20200915-coot-29_try.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #!3 models
> show #!3 models
> close #3
> color #1/D dark orange
> color #1/D byhetero
> select up
Nothing selected
> select up
Nothing selected
> volume zone #1 nearAtoms #2/D range 2
no atoms specified for zone
> color #1/B light pink
> color #1/A snow
> color #1/C gainsboro
> color #1/A dark goldenrod
> color #1/A dodger blue
> color #1 byhetero
> volume zone #2 nearAtoms #1/D range 2
> volume #3 subdivideSurface true
> volume #3 subdivisionLevels 2
> volume #2 style mesh
> volume #2 level 0.1923
> volume #3 style mesh
> volume #3 color #5555ff
> volume #3 color #5500ff
> volume #3 level 0.09069
> volume #3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.2
> surface undust #3
> volume #3 level 0.09456
Expected fewer arguments
Expected fewer arguments
> volume zone #2 nearAtoms #1/D range 1.5
> volume #4 level 0.09229
> volume #4 color #5500ff
> volume #3 subdivideSurface true
No volumes specified
> volume #3 subdivisionLevels 2
No volumes specified
> volume #3 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.2
No volumes specified
> volume #4 subdivisionLevels 2
> volume #4 subdivideSurface true
> volume #4 subdivisionLevels 2
> volume #4 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.2
> volume #4 level 0.07509
> select #1/B: 327,627,616,618,621,274,629,573,613,277,570,87,176,139,611,178
284 atoms, 275 bonds, 1 model selected
> color sel lime green
> color sel byhetero
> color #1/B@ca light pink
> volume #4 level 0.04538
> volume #4 level 0.04538
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200921_4.cxs
> hide #1 models
> show #1 models
> select #1
49041 atoms, 49512 bonds, 1 model selected
> ~select #1
Nothing selected
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> volume #4 color #5555ff
> volume #4 surfaceSmoothing true smoothingIterations 8 smoothingFactor 0.2
> volume #4 surfaceSmoothing true smoothingIterations 6 smoothingFactor 0.2
> volume #4 surfaceSmoothing true smoothingIterations 4 smoothingFactor 0.2
> volume #4 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.2
> volume #4 surfaceSmoothing true smoothingIterations 20 smoothingFactor 0.2
> volume #4 surfaceSmoothing true smoothingIterations 10 smoothingFactor 0.2
> volume #4 surfaceSmoothing true smoothingIterations 20 smoothingFactor 0.2
> volume #4 subdivisionLevels 1
Invalid "subdivisionLevels" argument: Expected an integer
> volume #4 subdivisionLevels 2
> volume #4 color #55ffff
> volume #4 color white
> volume #4 color red
> volume #4 color #550000
> volume #4 color blue
> volume #4 color #00007f
> volume #4 color #0055ff
> volume #4 color #00aaff
> volume #4 color #55aaff
> volume #4 color #5555ff
> volume #4 color lime
> volume #4 color #aaaa00
> volume #4 color #aa5500
> volume #4 color #005500
> volume #4 color #aaffff
> volume #4 color cyan
> volume #4 color #5555ff
> color #1/D dark orange
> color #1/D byhetero
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/2020095_1.png width
> 3900 height 2293
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200925_2.png
> width 3900 height 2293
> show #1 target m
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #1/B surfaces
> toolshed show "Side View"
> transparency #1.1 50
> transparency #1.1 0
> transparency #1.1 50
Expected a keyword
> volume #1 transparency 30
No volumes specified
> transparency #3/b 80 surfaces
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> transparency #1/b 80 surfaces
> transparency #1/b 50 surfaces
> transparency #1/b 30 surfaces
> transparency #1/b 20 surfaces
> transparency #1/b 10 surfaces
> transparency #1.1 0
> transparency #1.1 50
> transparency #1/b 10 surfaces
> transparency #1.1 0
> transparency #1.1 50
> transparency #1.1 0
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200925_3.png
> width 3900 height 2293
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200925_3.cxs
> transparency #1.1 50
> transparency #1.1 0
Expected a density maps specifier or a keyword
> hide surfaces
> hide #!1 models
> show #!2 models
> volume #2 style surface
> volume #2 level 0.2209
> volume #2 level 0.1876
> volume #2 level 0.2162
> volume #2 level 0.159
> surface undust #2
Expected fewer arguments
Expected fewer arguments
> surface undust #2
> volume #2 style image
> volume #2 style surface
> volume #2 change image level -0.04259,0 level 0.1234,0.8 level 1.719,1
> volume #2 level 0.1876
Expected fewer arguments
Expected fewer arguments
Expected fewer arguments
Expected fewer arguments
> volume zone #2 nearAtoms #1 range 2
> volume zone #2 nearAtoms #1 range 5
> volume zone #2 nearAtoms #1 range 2
> volume #3 level 0.1876
> volume zone #2 nearAtoms #1/a range 2
QWindowsWindow::setGeometry: Unable to set geometry 1920x1044+0+29 (frame:
1938x1091-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9
minimum size: 565x1044 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=583,1091
maxtrack=0,0)
> volume zone #2 nearAtoms #1/b range 2
QWindowsWindow::setGeometry: Unable to set geometry 1920x1044+0+29 (frame:
1938x1091-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9
minimum size: 565x1044 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=583,1091
maxtrack=0,0)
> volume zone #2 nearAtoms #1/c range 2
QWindowsWindow::setGeometry: Unable to set geometry 1920x1044+0+29 (frame:
1938x1091-9-9) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1001+0+29 (frame: 1938x1048-9-9) margins: 9, 38, 9, 9
minimum size: 565x1044 MINMAXINFO maxSize=0,0 maxpos=0,0 mintrack=583,1091
maxtrack=0,0)
> volume #3 color #0055ff
> volume #3 color #00aaff
> volume #5 color #ffaaff
> volume #5 color magenta
> volume #5 color #ff55ff
> volume #5 color #ffaaff
> volume #6 color white
> volume #6 color #d5d5d5
> save image F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200925_4.png
> width 1300 height 764
> save session F:/Experiment/OneDrive/CWRU/AdeJ_presentation/20200925_4.cxs
opened ChimeraX session
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!3 models
> show #!3 models
> show #!2 models
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> hide #!6 models
> hide #!3 models
> show #!2 models
> show #!1 models
> volume #2 level 0.1876
> hide #!1 models
> show #!1 models
> volume zone #2 nearAtoms #1 range 1.5
> volume subtract #2 #7
> volume #8 level 0.1876
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> surface undust #8
> surface dust #8
> volume #8 level 0.1637
> volume zone #2 nearAtoms #1 range 2
> volume zone #2 nearAtoms #1 range 2.5
> volume subtract #2 #8
Missing or invalid "surfaces" argument: invalid surfaces specifier
> surface dust #7
> volume #7 level 0.1359
> volume #7 level 0.141
> volume #7 level 0.15
> volume #7 level 0.155
> volume #7 level 0.16
> volume #7 color white
> volume #7 color #747474
> volume #7 color #828282
> volume #7 color #959595
> volume #7 color #969696
> volume #7 color #989898
> volume #7 color #afafaf
> volume #7 color #cecece
> show #!3 models
> show #!5 models
> show #!6 models
> volume #6 color #ffff7f
> volume #7 level 0.1445
> volume #7 level 0.135
> volume #7 transparency 60
> volume #7 transparency 50
> volume #7 transparency 40
> volume #7 transparency 10
> volume #7 transparency 80
> volume #7 transparency 30
> transparency #1.1#3.1#5.1#6.1#7.1 0
> volume #7 transparency 30
> transparency #1.1#3.1#5.1#6.1#7.1 0
> transparency #1.1#3.1#5.1#6.1#7.1 50
> transparency #1.1#3.1#5.1#6.1#7.1 0
> volume #7 transparency 50
> volume #7 transparency 3
> transparency #1.1#3.1#5.1#6.1#7.1 0
> transparency #1.1#3.1#5.1#6.1#7.1 50
> transparency #1.1#3.1#5.1#6.1#7.1 0
> volume #7 transparency 3
> volume #7 transparency 50
> volume #7 color #a3a3a300
> volume #7 color #a5a5a500
> volume #7 color #bdbdbd00
> volume #7 color #bebebe00
> volume #7 color #cbcbcb00
> transparency #1.1#3.1#5.1#6.1#7.1 0
> volume #7 transparency 50
> show #!8 models
> hide #!8 models
> show #!8 models
> hide #!8 models
> hide #!7 models
> show #!7 models
> select #7
3 models selected
> volume #7 transparency 50
> ~select #7
Nothing selected
> select #7
3 models selected
> ~select #7
Nothing selected
> select #7
3 models selected
> ~select #7
Nothing selected
> volume #7 transparency 0.5
> volume #7 transparency 0.3
> volume #7 transparency 0.6
> volume #7 color #d8d8d866
> volume #7 transparency 0.6
> volume #7 color #e5e5e566
> transparency #1.1#3.1#5.1#6.1#7.1 0
> volume #7 transparency 0.6
> volume #7 transparency 0.8
> volume #7 transparency 0.7
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201006_overall.cxs"
opened ChimeraX session
> hide #!1 models
> show #!1 models
> color #1/C khaki
> color #6 khaki
> volume zone #2 nearAtoms #1 range 15
> volume zone #2 nearAtoms #1 range 20
> surface dust #7
> volume #6 level 0.1261
> volume #6 level 0.2018
> volume #7 level 0.07802
> volume #7 level 0.08755
> volume subtract #7 #8
> surface dust #9
> volume #9 level 0.09531
> volume #9 level 0.1057
> volume #9 level 0.133
> volume #9 color white
> volume #9 color #dddddd
> transparency #1.1#3.1#5.1#6.1#9.1 50
> transparency #1.1#3.1#5.1#6.1#9.1 0
> volume #9 transparency 0.7
> volume #9 level 0.145
> hide #!1 models
> volume #9 level 0.14
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201006_overall.cxs"
opened ChimeraX session
> surface dust #9
> hide #!3 models
> show #!3 models
> color #3 lawngreen
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201006_overall_2.cxs"
opened ChimeraX session
> hide #!9 models
> show #!9 models
> surface dust #9
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!3 models
> show #!3 models
> color #5 purple
> color #5 dark violet
> color #7 yellow
> color #7 gold
> hide #!6 models
> show #!6 models
> color #6 gold
> color #6 yellow
QFileSystemWatcher::removePaths: list is empty
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/figure_recolor/20201022_map_overall.cxs"
> hide #!5 models
> show #!5 models
> color #5 blue violet
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/figure_recolor/20201022_map_overall.cxs"
opened ChimeraX session
> hide #!6 models
> show #!6 models
> color #6 tomato
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/figure_recolor/20201022_map_overall.cxs"
opened ChimeraX session
> hide #!9 models
> show #!9 models
> surface dust #9
> hide #!3 models
> show #!3 models
> color #3 tomato
> color #6 lawngreen
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/figure_recolor/20201022_map_overall2.cxs"
opened ChimeraX session
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> graphics silhouettes false
> graphics silhouettes true
> surface dust #2
> select up
Nothing selected
> surface dust #9
> volume #2 level -0.3827
> volume #2 level 0.2508
> volume #2 level 0.3175
> volume #9 level 0.1374
QFileSystemWatcher::removePaths: list is empty
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/figure_20201127/overall_map_1_20201128.cxs"
opened ChimeraX session
> close session
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/J577_denmod_map.ccp4"
Opened J577_denmod_map.ccp4, grid size 133,131,160, pixel 1.08, shown at level
0.982, step 1, values float32
> volume #1 level 0.192
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting soft
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_J577_20201203-coot-21.pdb"
Summary of feedback from opening F:/Experiment/onedrive2/OneDrive -
case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_J577_20201203-coot-21.pdb
---
warning | Ignored bad PDB record found on line 49226
END
Chain information for AdeJ_J577_20201203-coot-21.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A:1-1049
16127 atoms, 16286 bonds, 1 model selected
> volume zone #1 nearAtoms #2/A range 2
> volume zone #1 nearAtoms #2/B range 2
> volume zone #1 nearAtoms #2/C range 2
> color #3 tomato
> color #4 violet
> color #4 darkviolet
> color #5 lawngreen
> select #2
48979 atoms, 49446 bonds, 1 model selected
> ~select #2
Nothing selected
> hide #2 models
> surface dust #3
> surface dust #4
> surface dust #5
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/577_MAP.cxs"
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/577_MAP.tif" width 3900 height
> 2295
> close session
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/J585_denmod_map.ccp4"
Opened J585_denmod_map.ccp4, grid size 133,130,160, pixel 1.08, shown at level
0.969, step 1, values float32
> volume #1 level 0.1903
> volume #1 level 0.2241
> volume #1 level 0.2326
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_585_aligned-coot-29.pdb"
Summary of feedback from opening F:/Experiment/onedrive2/OneDrive -
case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_585_aligned-coot-29.pdb
---
warning | Ignored bad PDB record found on line 49298
END
Chain information for AdeJ_585_aligned-coot-29.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
> volume zone #1 nearAtoms #2/A range 2
> volume zone #1 nearAtoms #2/B range 2
> volume zone #1 nearAtoms #2/C range 2
> color #3 tomato
> color #4 violet
> color #4 darkviolet
> color #5 lawngreen
> surface dust #3
> surface dust #4
> surface dust #5
> hide #2 models
> volume #1 level 0.2157
> hide #!1 models
> volume #3 level 0.216
> volume #4 level 0.216
> volume #5 level 0.216
> surface dust #5
> surface dust #5
> surface dust #4
> surface dust #3
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_MAP.cxs"
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_MAP.tif" width 3900 height
> 2295
> show #2 models
> transparency #3.1#4.1#5.1 50
> hide #2 models
> close session
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_J577_20201203-coot-21.pdb"
Summary of feedback from opening F:/Experiment/onedrive2/OneDrive -
case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_J577_20201203-coot-21.pdb
---
warning | Ignored bad PDB record found on line 49226
END
Chain information for AdeJ_J577_20201203-coot-21.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A:1-1049
16127 atoms, 16286 bonds, 1 model selected
> color #1/A tomato
> color #1/B darkviolet
> color #1/C lawngreen
> select /A:1-1049
16127 atoms, 16286 bonds, 1 model selected
> hide #1 models
> show #1 models
> select #1
48979 atoms, 49446 bonds, 1 model selected
> ~select #1
Nothing selected
> color #1/D gold
> select #1/D
Nothing selected
Unknown command: seleect #1/D
> select #1/D
Nothing selected
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/577_all.cxs"
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/577_all.tif" width 3900 height
> 2295
> preset "overall look" publication
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
> close session
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_585_aligned-coot-29.pdb"
Summary of feedback from opening F:/Experiment/onedrive2/OneDrive -
case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/AdeJ_585_aligned-coot-29.pdb
---
warning | Ignored bad PDB record found on line 49298
END
Chain information for AdeJ_585_aligned-coot-29.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> color #1/A tomato
> color #1/B darkviolet
> color #1/C lawngreen
> color #1/D gold
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_all.cxs"
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_all.tif" width 3900 height
> 2295
> select #1/D
71 atoms, 75 bonds, 1 model selected
> color #1/D byhetero
> select #1
49051 atoms, 49522 bonds, 1 model selected
> ~select #1
Nothing selected
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_all.tif" width 3900 height
> 2295
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_all.cxs"
> color #1/B byhetero
> toolshed show "Side View"
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/J585_denmod_map.ccp4"
Opened J585_denmod_map.ccp4, grid size 133,130,160, pixel 1.08, shown at level
0.969, step 1, values float32
> volume zone #2 nearAtoms #1/D range 2
> hide #!3 models
> close #3
> volume zone #2 nearAtoms #1/D range 2
> volume #3 level 0.1066
> volume #3 level 0.1136
> transparency #3.1 50
> volume #3 subdivideSurface true
> volume #3 subdivisionLevels 2
> volume #3 color #ffff7f80
> volume #3 color #efef7780
> volume #3 color #f3f37980
> volume #3 color #ffffff80
> volume #3 color #ebebeb80
> volume #3 color #d5d5d580
> volume #3 color #d4d4d480
> volume #3 color #d3d3d380
> volume #3 color #c5c5c580
> close #3
> volume zone #2 nearAtoms #1/D range 1.5
> volume #3 level 0.05228
> transparency #3.1 50
> volume #3 level 0.0794
> volume zone #2 nearAtoms #1/D range 1
> volume #4 level 0.04243
> transparency #4.1 50
> volume #4 level 0.03021
> volume #4 color #ffffff80
> volume #4 color #e6e6e680
> volume #4 color #e5e5e580
> volume #4 color #d8d8d880
> volume #4 color #cccccc80
> volume #4 color #ffff7f80
> volume #4 color #e8e87380
> volume #4 color #eeee7680
> lighting soft
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting simple
> volume #4 style mesh
> volume #4 style surface
> select #1/B: 136, 327, 629, 326, 611, 613, 618, 616, 274, 178
181 atoms, 179 bonds, 1 model selected
> ui mousemode rightMode select
> select /B:155@CE
1 atom, 1 model selected
> hide sel atoms
> show sel atoms
> select /B:155@CG
1 atom, 1 model selected
> ui mousemode rightMode select
> select /B:155@NZ
1 atom, 1 model selected
> select /B:155@CE
1 atom, 1 model selected
> select #1/B: 155
22 atoms, 21 bonds, 1 model selected
> hide sel atoms
> select #1/B: 136, 327, 629, 326, 611, 613, 618, 616, 274, 178
181 atoms, 179 bonds, 1 model selected
> color sel cyan
> color sel byhetero
> undo
> undo
> color sel cyan target a
> color sel byhetero
> select #1
49051 atoms, 49522 bonds, 1 model selected
> ~select #1
Nothing selected
> select #1/B: 136, 327, 629, 326, 611, 613, 618, 616, 274, 178, 277
201 atoms, 199 bonds, 1 model selected
> color sel cyan target a
> color sel byhetero
> select #1
49051 atoms, 49522 bonds, 1 model selected
> ~select #1
Nothing selected
> select up
Nothing selected
> select up
Nothing selected
> select #1/B: 136, 327, 629, 326, 611, 613, 618, 616, 274, 178, 277,139
217 atoms, 214 bonds, 1 model selected
> select up
803 atoms, 809 bonds, 1 model selected
> select up
16091 atoms, 16249 bonds, 1 model selected
> select up
49051 atoms, 49522 bonds, 1 model selected
> select up
49051 atoms, 49522 bonds, 5 models selected
> color sel cyan target a
> undo
> select #1/B: 136, 327, 629, 326, 611, 613, 618, 616, 274, 178, 277,139
217 atoms, 214 bonds, 1 model selected
> color sel cyan target a
> color sel byhetero
> select #1
49051 atoms, 49522 bonds, 1 model selected
> ~select #1
Nothing selected
> select #1/B: 615,616,617,618,619,620,621
95 atoms, 96 bonds, 1 model selected
> color sel lightpink target c
> select #1
49051 atoms, 49522 bonds, 1 model selected
> ~select #1
Nothing selected
> volume #4 color #ffffff80
> volume #4 color #f3f3f380
> volume #4 color #f1f1f180
> volume #4 color #f0f0f080
> volume #4 color #e7e7e780
> volume #4 color #c3c3c380
> volume #4 color #9d9d9d80
> volume #4 color #ff007f80
> volume #4 color #aaff7f80
> volume #4 color #aa55ff80
> volume #4 color #0055ff80
> volume #4 color #00aaff80
> volume #4 color #ff55ff80
> volume #4 color #5500ff80
> volume #4 color #55007f80
> volume #4 color #55000080
> volume #4 color #00000080
> volume #4 color #ffff0080
> volume #4 color #ffffff80
> volume #4 color #ffff7f80
> volume #4 color #ffffff80
> volume #4 color #91919180
> volume #4 color #acacac80
> volume #4 color #ffff7f80
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_detail.cxs"
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_detail.cxs"
opened ChimeraX session
> hide #!4 models
> ui mousemode rightMode distance
> distance /D:1@N26 /B:327@OH
Distance between /D ERA 1 N26 and /B TYR 327 OH: 3.372Å
> ui mousemode rightMode select
Drag select of
> ui mousemode rightMode select
> ui mousemode rightMode select
> toolshed show "Side View"
> ui mousemode rightMode distance
> distance /D:1@C03 /B:139@CG2
Distance between /D ERA 1 C03 and /B VAL 139 CG2: 4.569Å
> distance /D:1@C03 /B:139@CG1
Distance between /D ERA 1 C03 and /B VAL 139 CG1: 4.500Å
> distance /D:1@C01 /B:139@CG1
Distance between /D ERA 1 C01 and /B VAL 139 CG1: 3.883Å
> distance /D:1@C01 /B:139@CG2
Distance between /D ERA 1 C01 and /B VAL 139 CG2: 4.336Å
> distance /B:139@CG1 /D:1@C03
Distance already exists; modify distance properties with 'distance style'
> ~distance /D:1@C03 /B:139@CG1
> ~distance /D:1@C03 /B:139@CG2
> distance /D:1@F40 /B:613@CG1
Distance between /D ERA 1 F40 and /B VAL 613 CG1: 3.712Å
> ~distance /D:1@F40 /B:613@CG1
> distance /B:277@CE2 /D:1@C39
Distance between /B PHE 277 CE2 and /D ERA 1 C39: 4.032Å
> distance /B:277@CE1 /D:1@C11
Distance between /B PHE 277 CE1 and /D ERA 1 C11: 5.297Å
> ~distance /B:277@CE1 /D:1@C11
> ui mousemode rightMode "mark point"
> marker #5 226,170.1,223.1 color yellow radius 1
> ui mousemode rightMode "move markers"
> marker change #5:1 position 217.5,165.8,230.4
> marker change #5:1 position 211.7,166.5,222.2
> marker change #5 radius 0.5
> marker change #5 radius 0.1
> marker change #5:1 position 210.2,167.3,223.5
> ui mousemode rightMode "move markers"
> ui mousemode rightMode "mark point"
> marker #5 217.6,173.6,225.8 color yellow radius 0.1
> marker #5 212.7,169.3,223.1 color yellow radius 0.1
> ui mousemode rightMode "move markers"
> marker change #5:3 position 211.3,171.6,222.4
> marker change #5:3 position 211.2,171.3,222.3
> marker change #5:3 position 211.1,171.3,222.4
> marker change #5:3 position 211.1,171.3,222.4
> ui mousemode rightMode distance
> distance #5/M:1@M #5/M:3@M
Distance between markers #5/M mark 1 M and mark 3 M: 4.242Å
> ui mousemode rightMode "move markers"
> marker change #5:2 position 221.2,167.4,218.8
> marker change #5:2 position 218.3,165.1,219.5
> marker change #5:2 position 217.7,166.4,218.5
> marker change #5:2 position 217.1,166.2,218.3
> marker change #5:2 position 217.1,166.1,218.4
> ui mousemode rightMode distance
> distance #5/M:2@M #1/D:1@C04
Distance between markers #5/M mark 2 M and AdeJ_585_aligned-coot-29.pdb #1/D
ERA 1 C04: 3.376Å
> distance #5/M:2@M #1/D:1@C20
Distance between markers #5/M mark 2 M and AdeJ_585_aligned-coot-29.pdb #1/D
ERA 1 C20: 4.622Å
> ~distance #5/M:2@M #1/D:1@C20
> ui mousemode rightMode "mark point"
> marker #5 226,170.8,206.9 color yellow radius 0.1
> ui mousemode rightMode "move markers"
> marker change #5:4 position 221,175.7,215.4
> marker change #5:4 position 215.3,170.9,212.7
> marker change #5:4 position 214,168.4,215.7
> marker change #5:4 position 214,168.6,215.3
> marker change #5:4 position 215,167.9,216.1
> marker change #5:4 position 215.2,168.2,216.6
> marker change #5:4 position 215.3,168.8,216.2
> ui mousemode rightMode distance
> distance #5/M:2@M #5/M:4@M
Distance between markers #5/M mark 2 M and mark 4 M: 3.943Å
> ~distance #5/M:2@M #1/D:1@C04
> marker change #5:4 color #55ff00
> ui mousemode rightMode "mark point"
> marker #5 232.1,178.4,218.9 color #55ff00 radius 0.1
> ui mousemode rightMode "move markers"
> marker change #5:5 position 226.7,178.8,227
> marker change #5:5 position 223.9,170.7,219.8
> marker change #5:5 position 219.8,171.3,221.4
> marker change #5:5 position 220.3,171,221.9
> marker change #5:5 position 220.4,170.9,222
> marker change #5:5 position 220.3,171.1,222.3
> ui mousemode rightMode distance
> distance #5/M:5@M #1/D:1@C01
Distance between markers #5/M mark 5 M and AdeJ_585_aligned-coot-29.pdb #1/D
ERA 1 C01: 4.705Å
> ~distance #5/M:5@M #1/D:1@C01
> distance #1/B:326@CB #1/D:1@C03
Distance between AdeJ_585_aligned-coot-29.pdb #1/B ALA 326 CB and /D ERA 1
C03: 4.455Å
> ~distance #1/B:326@CB #1/D:1@C03
> distance #1/D:1@C08 #1/B:178@CD2
Distance between AdeJ_585_aligned-coot-29.pdb #1/D ERA 1 C08 and /B PHE 178
CD2: 4.475Å
> ~distance #1/D:1@C08 #1/B:178@CD2
> ui mousemode rightMode "move markers"
> marker change #5:5 position 216.8,176.7,221.6
> marker change #5:5 position 217,174.3,221.3
> marker change #5:5 position 214.5,174.1,219.7
> marker change #5:5 position 214.7,174.4,219.6
> marker change #5:5 position 214.6,174.5,219.6
> ui mousemode rightMode "mark point"
> marker #5 215.2,164.9,223.4 color #55ff00 radius 0.1
> ui mousemode rightMode "move markers"
> marker change #5:6 position 216.5,169.6,223.4
> marker change #5:6 position 212.7,171,220.2
> marker change #5:6 position 212.6,170.6,220.2
> marker change #5:6 position 212.5,170.7,220.3
> marker change #5:6 position 212.5,170.5,220.3
> marker change #5:6 position 212.4,170.6,220.2
> ui mousemode rightMode distance
> distance #5/M:6@M #5/M:5@M
Distance between markers #5/M mark 6 M and mark 5 M: 4.503Å
> hide #!3 models
> show #!3 models
> hide #3.1 models
> show #3.1 models
> select #3
7 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> distance #1/D:1@C38 #1/B:274@CB
Distance between AdeJ_585_aligned-coot-29.pdb #1/D ERA 1 C38 and /B ASN 274
CB: 4.565Å
> ~distance #1/D:1@C38 #1/B:274@CB
> distance #1/B:618@CE1 #1/D:1@C17
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 618 CE1 and /D ERA 1
C17: 4.835Å
> ~distance #1/B:618@CE1 #1/D:1@C17
> distance #1/B:326@CB #1/D:1@C03
Distance between AdeJ_585_aligned-coot-29.pdb #1/B ALA 326 CB and /D ERA 1
C03: 4.455Å
> select #3
8 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> ~distance #5/M:2@M #5/M:4@M
> distance #1/B:136@CE2 #5/M:4@M
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 136 CE2 and markers
#5/M mark 4 M: 4.625Å
> distance #5/M:2@M #5/M:4@M
Distance between markers #5/M mark 2 M and mark 4 M: 3.943Å
> ~distance #1/B:136@CE2 #5/M:4@M
> select #3
8 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> distance #1/B:611@CD1 #1/D:1@C01
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 611 CD1 and /D ERA 1
C01: 4.203Å
> select #3
9 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> hide #3.1 models
> transparency #1 80 cartoons
> transparency #1 100 cartoons
> transparency #1 50 cartoons
> transparency #1 0 cartoons
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_interaction.cxs"
> transparency #1 95 cartoons
> transparency #1 100 cartoons
> select H
24784 atoms, 3 pseudobonds, 3 models selected
> hide sel atoms
> select #1
49051 atoms, 49522 bonds, 6 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> select #3
9 pseudobonds, 2 models selected
> undo
> undo
> undo
> undo
> ~select #5
24778 atoms, 1 model selected
> select #1
49051 atoms, 49522 bonds, 6 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> select H
24784 atoms, 3 pseudobonds, 3 models selected
> select #3
9 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> select H
24784 atoms, 3 pseudobonds, 3 models selected
> hide sel cartoons
> undo
> hide sel atoms
> hide sel atoms
> show sel atoms
> hide sel atoms
> select #1
49051 atoms, 49522 bonds, 6 pseudobonds, 2 models selected
> ~select #1
Nothing selected
> select #3
9 pseudobonds, 2 models selected
> show #3.1 models
> hide #3.1 models
> select #5
6 atoms, 3 pseudobonds, 2 models selected
> show sel atoms
> select #3
9 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> ui mousemode rightMode distance
> ui mousemode rightMode distance
> distance #1/B:618@CZ #1/D:1@C16
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 618 CZ and /D ERA 1
C16: 5.503Å
> show #3.1 models
> distance #1/B:618@CE1 #1/D:1@C16
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 618 CE1 and /D ERA 1
C16: 5.379Å
> distance #1/B:618@CZ #1/D:1@C17
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 618 CZ and /D ERA 1
C17: 4.767Å
> distance #1/B:618@CZ #1/D:1@C06
Distance between AdeJ_585_aligned-coot-29.pdb #1/B PHE 618 CZ and /D ERA 1
C06: 6.039Å
> ~distance #1/B:618@CZ #1/D:1@C17
> ~distance #1/B:618@CZ #1/D:1@C16
> ~distance #1/B:618@CZ #1/D:1@C06
> ~distance #1/B:618@CE1 #1/D:1@C16
> hide #3.1 models
> ui mousemode rightMode select
> color sel green
> color sel lawngreen
> color sel lightgreen
> color sel yellowgreen
> color sel lime
> select #3
9 pseudobonds, 2 models selected
> ~select #3
Nothing selected
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_interaction.cxs"
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_interaction.tif"
> width 3900 height 2293
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_interaction.tif"
> width 3900 height 2293
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_interaction.cxs"
opened ChimeraX session
> lighting soft
> lighting flat
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting soft
> save image "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_detail2.tif" width
> 2000 height 1176
> save session "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/585_ligand_detail2.cxs"
opened ChimeraX session
> open "F:/Experiment/onedrive2/OneDrive -
> case.edu/CWRU/CWRU/AdeJ_manuscript/20201210/J1634_final_4_DONE.pdb"
Chain information for J1634_final_4_DONE.pdb #6
---
Chain | Description
A B C | No description available
Traceback (most recent call last):
File "D:\ChimeraX\bin\lib\site-packages\chimerax\core\triggerset.py", line
130, in invoke
return self._func(self._name, data)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\structure.py", line
1545, in _update_graphics_if_needed
s[i]._update_graphics_if_needed()
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\structure.py", line
300, in _update_graphics_if_needed
self._create_ribbon_graphics()
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\structure.py", line
554, in _create_ribbon_graphics
ribbons_drawing.compute_ribbons(self)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 524,
in compute_ribbons
_make_ribbon_graphics(structure, self)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 136,
in _make_ribbon_graphics
geometry)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 414,
in _ribbon_geometry
back_c, back_t, back_n = ribbon.segment(i, Ribbon.FIRST_HALF, next_cap)
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 1763,
in segment
flip_mode = FLIP_MINIMIZE if self.ignore_flip_mode[seg] else
self._flip_mode[seg]
AttributeError: 'Ribbon' object has no attribute '_flip_mode'
Error processing trigger "graphics update":
AttributeError: 'Ribbon' object has no attribute '_flip_mode'
File "D:\ChimeraX\bin\lib\site-packages\chimerax\atomic\ribbon.py", line 1763,
in segment
flip_mode = FLIP_MINIMIZE if self.ignore_flip_mode[seg] else
self._flip_mode[seg]
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 452.41
OpenGL renderer: GeForce GTX 960M/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: HP
Model: HP Pavilion Notebook
OS: Microsoft Windows 10 家庭中文版 (Build 18363)
Memory: 17,064,304,640
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz"
![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
You are using old ChimeraX version 0.93. The current version is ChimeraX 1.1 and very likely does not have the reported bug because the ribbon flip_mode variable that is causing the problem does not even exist in the version 1.1 code. Please update ChimeraX.