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Opened 6 years ago
Closed 6 years ago
#2820 closed defect (duplicate)
SideVIew self.view.render is None
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Graphics | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-4.4.0-173-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-06-29)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 0.91 (2019-06-29)
© 2016-2019 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /data/disk3/modeling/gp10/capsid-tail-20200204.cxs
opened ChimeraX session
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!1 models
> surface dust #7 size 50
> surface dust #31 size 50
> lighting soft
> lighting soft
> lighting simple
> select clear
> save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!7 models
> show #!7 models
> hide #!23 models
> show #!23 models
> surface dust #23 size 50
> surface dust #26 size 50
> hide #!7 models
> show #!7 models
> hide #!11.1 models
> show #!11.1 models
> hide #!11.1 models
> hide #!11 models
> show #!11 models
> show #!11.1 models
> hide #!11 models
> show #!11 models
> surface dust #11 size 50
> hide #!7 models
> show #!7 models
> hide #!11.1 models
> hide #!11 models
> lighting soft
> lighting full
> lighting shadows false
> lighting flat
> lighting full
> lighting simple
> lighting shadows true
> lighting full
> lighting soft
> lighting flat
> set silhouettes false
> set silhouettes true
> lighting shadows true intensity 0.5
> lighting simple
> lighting full
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting simple
> surface dust #23 size 50
> surface dust #23 size 10
> surface dust #31 size 50
> surface dust #31 size 30
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting simple
> lighting flat
> lighting full
> lighting soft
> lighting simple
> save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> surface dust #31 size 100
> surface dust #31 size 50
> lighting flat
> select clear
> lighting simple
> lighting soft
> lighting full
> lighting shadows false
> lighting full
> lighting soft
> lighting flat
> lighting simple
> select clear
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> select up
Nothing selected
> save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!6 models
> hide #!6 models
> show #!11 models
> show #!11.1 models
> zoom 0.5
> save image /data/disk3/Paper-use/Figure1-20200205-2.tif pixelSize 0.1
supersample 10 transparentBackground true
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> save image /data/disk3/Paper-use/Figure1-20200205-2.tif pixelSize 0.1
supersample 10 transparentBackground true
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> save image /data/disk3/Paper-use/Figure1-20200205-3.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!23 models
> show #!23 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> show #!11 models
> transparency #11 70
> transparency #11 40
> transparency #11 0
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!23 models
> show #!23 models
> hide #!23 models
> show #!23 models
> transparency #23 70
> transparency #7 70
> lighting soft
> toolshed show "Side View"
> hide #!9 models
> hide #!7 models
> show #!7 models
> hide #!15 models
> hide #!16 models
> hide #!17 models
> hide #!19 models
> ui mousemode rightMode "rotate selected models"
> view cofr false
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting soft
> lighting full
> lighting soft
> hide #!11 models
> show #!11 models
> hide #!23 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> hide #!26 models
> save image /data/disk3/Paper-use/Figure1-20200205-4.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!26 models
> lighting soft
> save image /data/disk3/Paper-use/Figure1-20200205-5.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting soft
> lighting simple
> save image /data/disk3/Paper-use/Figure1-20200205-5.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure1-20200205-5.tif pixelSize 0.1
supersample 10 transparentBackground true
> view name portal
> show #!23 models
> view name gp8
> view name gp8
> save image /data/disk3/Paper-use/Figure1-20200205-4.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!7 models
> select clear
> save image /data/disk3/Paper-use/Figure1-20200205-6.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure1-20200205-6.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting flat
> lighting soft
> lighting soft
> lighting flat
> lighting simple
> lighting soft
> lighting simple
Expected an objects specifier or a view name or a keyword
> show #!13 models
> hide #!13 models
> show #!9 models
> hide #!9 models
> show #!4 models
> hide #!4 models
> show #!177 models
> hide #!177 models
> hide #!7 models
> show #!7 models
> save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure1-20200205-7.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!7 models
> show #!7 models
> hide #!7 models
> show #!7 models
> hide #!7 models
> hide #!31 models
> show #!31 models
> hide #!23 models
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure2-20200205-2.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting full
> lighting simple
> lighting soft
> lighting full
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting full
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting shadows false
> save image /data/disk3/Paper-use/Figure2-20200205-2.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!17 models
> hide #!16 models
> hide #!15 models
> hide #!19 models
> hide #!9 models
> show #!23 models
> show #!27 models
> show #!7 models
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> lighting soft
> lighting soft
> show #!9 models
> hide #!9 models
> save image /data/disk3/Paper-use/Figure2-20200205-3.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!5 models
> hide #!31 models
> show #!31 models
> select #31
3 models selected
> ~select #31
Nothing selected
> hide #!31 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> show selAtoms ribbons
> select clear
> ui mousemode rightMode "translate selected models"
> lighting soft
> lighting simple
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> show #!31 models
> hide #!31 models
> show #!31 models
> transparency #31 70
> transparency #31 50
> select clear
> select clear
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> show #!26 models
> show #!14 models
> hide #!14 models
> show #!3 models
> hide #!3 models
> show #!14 models
> select #14
76410 atoms, 77460 bonds, 3 models selected
> show selAtoms ribbons
> select clear
> hide #!11 models
> show #!11 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!23 models
> hide #!14 models
> hide #!7 models
> surface dust #13 size 50
> surface dust #13 size 100
> surface dust #13 size 150
> surface dust #13 size 100
> transparency #13 80
> transparency #13 40
> save image /data/disk3/Paper-use/Figure2-20200205-4.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!11 models
> show #!11 models
> surface dust #13 size 150
> surface dust #13 size 200
> surface dust #13 size 300
> surface dust #13 size 500
> surface dust #13 size 400
> surface dust #13 size 300
> hide #!5 models
> save image /data/disk3/Paper-use/Figure2-20200205-4.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!11 models
> show #!11 models
> hide #!11 models
> hide #!13 models
> show #!13 models
> hide #!13 models
> show #!13 models
> hide #!11.1 models
> hide #!31 models
> hide #!26 models
> show #!26 models
> hide #!26 models
> hide #!27 models
> show #!27 models
> hide #!27 models
> save image /data/disk3/Paper-use/Figure2-20200205-5.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!11 models
> show #!11.1 models
> select up
Nothing selected
> transparency #13 40
> lighting flat
> show #!26 models
> hide #!26 models
> show #!31 models
> lighting soft
> show #!26 models
> hide #!26 models
> lighting flat
> lighting full
> lighting simple
> lighting simple
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-6.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting flat
> show #!29 models
> hide #!13 models
> hide #!29 models
> lighting soft
> open /data/disk3/modeling/gp8/gp8-C12-clean.mrc
Opened gp8-C12-clean.mrc, grid size 400,400,400, pixel 1.05, shown at level
-4.87e-06, step 2, values float32
> hide #!11 models
> hide #!11.1 models
> lighting flat
> hide #!20 models
> show #!20 models
> select #20
2 models selected
> ui mousemode rightMode "translate selected models"
> hide #!20 models
> show #!20 models
> ui mousemode rightMode "translate selected models"
> hide #!20 models
> show #!20 models
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> hide #!20 models
> show #!20 models
> fitmap #20 inMap #31
Fit map gp8-C12-clean.mrc in map gp8-Res2.9-clean.mrc using 28724 points
correlation = 0.9108, correlation about mean = 0.7448, overlap = 15.77
steps = 104, shift = 2.16, angle = 7.73 degrees
Position of gp8-C12-clean.mrc (#20) relative to gp8-Res2.9-clean.mrc (#31)
coordinates:
Matrix rotation and translation
-0.40431498 0.91461981 -0.00002575 102.83950342
0.91461981 0.40431498 0.00006074 -66.98431350
0.00006596 0.00000101 -1.00000000 420.15908783
Axis -0.54577749 -0.83793015 -0.00001475
Axis point 73.22767612 0.00000000 210.08181233
Rotation angle (degrees) 179.99686465
Shift along axis -0.00550679
> show #!30 models
> hide #!30 models
> show #!26 models
> show #!11 models
> show #!11.1 models
> hide #!31 models
> select clear
> lighting flat
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> hide #!11 models
> show #!11 models
> hide #!11 models
> lighting soft
> show #!1 models
> surface dust #1 size 400
> surface dust #1 size 40
> hide #!20 models
> show #!20 models
> hide #!26 models
> show #!26 models
> hide #!1 models
> hide #!26 models
> show #!26 models
> lighting flat
> zoom 0.5
> lighting flat
> lighting soft
> hide #!20 models
> show #!20 models
> hide #!26 models
> show #!26 models
> surface dust #26 size 40
> surface dust #26 size 80
> surface dust #26 size 60
> surface dust #26 size 70
> hide #!26 models
> show #!26 models
> hide #!20 models
> show #!20 models
> surface dust #20 size 70
> show #!11 models
> hide #!11 models
> show #!11 models
> show #!23 models
> show #!7 models
> hide #!11 models
> select clear
> lighting flat
> lighting flat
> lighting soft
> lighting simple
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting simple
> select clear
> lighting flat
> lighting soft
> lighting simple
> save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure1-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!11 models
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting soft
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting flat
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting full
> lighting soft
> view name 1
> save image /data/disk3/Paper-use/Figure2-20200205-1.tif pixelSize 0.1
supersample 10 transparentBackground true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> show #!14 models
> close #14
> show #!5 models
> hide #!5 models
> show #!5 models
> show #!10 models
> select #10
18336 atoms, 18660 bonds, 1 model selected
> select clear
> hide #!5 models
> show #!5 models
> hide #!20 models
> hide selAtoms ribbons
> hide selAtoms ribbons
> show #!20 models
> open /data/disk3/modeling/gp10/3j7w-C5-C6-pentamer-V.pdb
Chain information for 3j7w-C5-C6-pentamer-V.pdb #14
---
Chain | Description
B D L M N O T U V W | No description available
F b c e | No description available
d | No description available
> hide #!5 models
> show #!5 models
> hide #!14 models
> show #!14 models
> select #14
37263 atoms, 37783 bonds, 1 model selected
> close #14
> open /data/disk3/modeling/gp10/3j7w-C5-C6-pentamer-1.pdb
/data/disk3/modeling/gp10/3j7w-C5-C6-pentamer-2.pdb
Chain information for 3j7w-C5-C6-pentamer-1.pdb #14.1
---
Chain | Description
A C E H I J K P Q R S X Y Z a | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb #14.2
---
Chain | Description
B D F L M N O T U V W b c d e | No description available
> select #14
76410 atoms, 77460 bonds, 3 models selected
> ~select #14.1
38205 atoms, 38730 bonds, 2 models selected
> ~select #14.2
1 model selected
> select #14.1
38205 atoms, 38730 bonds, 1 model selected
> select #14
76410 atoms, 77460 bonds, 3 models selected
> hide selAtoms
> show selAtoms ribbons
> show selAtoms
> show selAtoms ribbons
> hide selAtoms
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> hide #!14 models
> show #!14 models
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.003277, steps = 184
shifted from previous position = 13
rotated from previous position = 8.82 degrees
atoms outside contour = 33158, contour level = 0.014
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87077427 0.44074248 0.21794086 -255.17401789
0.44300176 -0.89557672 0.04113117 341.22465748
0.21331102 0.06073222 -0.97509487 421.71636726
Axis 0.96715335 0.22844510 0.11147749
Axis point 0.00000000 199.60859977 226.53103304
Rotation angle (degrees) 179.41939043
Shift along axis -121.82942344
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.00301, steps = 176
shifted from previous position = 8.24
rotated from previous position = 8.69 degrees
atoms outside contour = 33669, contour level = 0.014
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.88858723 0.39914992 0.22603554 -254.94469240
0.40067124 -0.91529584 0.04118342 356.75744205
0.22332776 0.05397088 -0.97324809 420.44709225
Axis 0.97174749 0.20577055 0.11560839
Axis point 0.00000000 204.63507213 226.03657012
Rotation angle (degrees) 179.62301282
Shift along axis -125.72447641
> lighting flat
> view cofr false
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.003896, steps = 124
shifted from previous position = 8.5
rotated from previous position = 4.92 degrees
atoms outside contour = 32300, contour level = 0.014
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.91098479 0.38597423 0.14536367 -230.26877151
0.38664508 -0.92189595 0.02476749 373.85349728
0.14356980 0.03364134 -0.98906823 460.38543728
Axis 0.97749291 0.19760269 0.07389709
Axis point 0.00000000 209.65694133 239.35760756
Rotation angle (degrees) 179.73992877
Shift along axis -117.19049440
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.003879, steps = 96
shifted from previous position = 5.46
rotated from previous position = 2.73 degrees
atoms outside contour = 32342, contour level = 0.014
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.88041990 0.43828982 0.18100501 -246.92143020
0.43340100 -0.89863979 0.06789759 333.77575063
0.19241714 0.01866936 -0.98113562 446.82207444
Axis -0.96963925 -0.22478250 -0.09629411
Axis point 0.00000000 198.51001869 233.30835046
Rotation angle (degrees) 178.54540104
Shift along axis 121.37142807
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.004629, steps = 160
shifted from previous position = 13
rotated from previous position = 5.29 degrees
atoms outside contour = 31217, contour level = 0.014
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.86597982 0.42442861 0.26446038 -258.59400689
0.41367029 -0.90513039 0.09806047 339.76900742
0.28099081 0.02448101 -0.95939817 410.82950911
Axis -0.96590142 -0.21700025 -0.14122794
Axis point 0.00000000 203.14840431 220.71640569
Rotation angle (degrees) 177.81716196
Shift along axis 118.02575589
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 128
shifted from previous position = 6.68
rotated from previous position = 6.31 degrees
atoms outside contour = 21091, contour level = 0.014
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87105169 0.43180772 0.23411755 -259.31100606
0.43088566 -0.90055103 0.05783932 345.21826870
0.23581028 0.05049685 -0.97048626 417.79531053
Axis -0.96722557 -0.22298304 -0.12146302
Axis point 0.00000000 202.92431247 224.81402889
Rotation angle (degrees) 179.78252577
Shift along axis 123.08773570
> select clear
> hide #!11 models
> hide #!5 models
> show #!5 models
> hide #!14 models
> hide #!20 models
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms
> hide selAtoms ribbons
> hide selAtoms ribbons
> show #!11 models
> show #!14 models
> hide #!5 models
> select #11
3 models selected
> select #14.1
38205 atoms, 38730 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 104
shifted from previous position = 11.5
rotated from previous position = 2.95 degrees
atoms outside contour = 17054, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87266983 0.43809630 0.21568259 -240.34437556
0.42481187 -0.89892619 0.10708207 343.62425563
0.24079500 -0.00182277 -0.97057428 446.57565351
Axis -0.96761791 -0.22312336 -0.11803200
Axis point 0.00000000 206.19802213 232.61159406
Rotation angle (degrees) 176.77399198
Shift along axis 103.18070608
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 96
shifted from previous position = 9.67
rotated from previous position = 1.44 degrees
atoms outside contour = 17069, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87165040 0.44382963 0.20794429 -246.40304653
0.43574272 -0.89597161 0.08580871 351.05434471
0.22439664 0.01581501 -0.97436955 441.53038546
Axis -0.96736971 -0.22738480 -0.11176760
Axis point 0.00000000 208.72980426 231.48417700
Rotation angle (degrees) 177.92673932
Shift along axis 109.18962883
> select #14.2
38205 atoms, 38730 bonds, 1 model selected
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 92
shifted from previous position = 10.2
rotated from previous position = 1.68 degrees
atoms outside contour = 17709, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87154036 0.43231440 0.23134747 -247.82239723
0.42424380 -0.90143033 0.08625865 348.94881293
0.24583450 0.02296983 -0.96903962 435.65959681
Axis -0.96734324 -0.22142808 -0.12335580
Axis point 0.00000000 206.63567257 230.47650121
Rotation angle (degrees) 178.12536568
Shift along axis 108.72111917
> select #23
4 models selected
> select clear
> lighting soft
> lighting soft
> hide #!23 models
> hide #!26 models
> show #!26 models
> hide #!10 models
> hide #!11.1 models
> show #!11.1 models
> hide #!11 models
> show #!11 models
> hide #!26 models
> select #14.1
38205 atoms, 38730 bonds, 1 model selected
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 52
shifted from previous position = 0.516
rotated from previous position = 0.722 degrees
atoms outside contour = 17051, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87141650 0.43979498 0.21728700 -248.28937285
0.43369597 -0.89770555 0.07766951 351.17649597
0.22921841 0.02655400 -0.97301274 435.34455599
Axis -0.96731431 -0.22579111 -0.11541833
Axis point 0.00000000 207.62667240 229.91596728
Rotation angle (degrees) 178.48599181
Shift along axis 110.63459153
> select #14.2
38205 atoms, 38730 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 76
shifted from previous position = 3.04
rotated from previous position = 0.834 degrees
atoms outside contour = 17716, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87175271 0.43856635 0.21841873 -246.90795772
0.42950250 -0.89856792 0.09001831 346.42211180
0.23574307 0.01533768 -0.97169437 439.08637210
Axis -0.96739466 -0.22441532 -0.11741097
Axis point 0.00000000 206.35965402 230.82439841
Rotation angle (degrees) 177.78789990
Shift along axis 109.56145253
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 52
shifted from previous position = 1.9
rotated from previous position = 0.417 degrees
atoms outside contour = 17692, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87147552 0.44032347 0.21597603 -246.54997704
0.43271422 -0.89761051 0.08398675 348.78865188
0.23084370 0.02026350 -0.97277982 437.67284585
Axis -0.96732636 -0.22569295 -0.11550933
Axis point 0.00000000 206.99054785 230.37700702
Rotation angle (degrees) 178.11246041
Shift along axis 109.21985671
> select #14
76410 atoms, 77460 bonds, 3 models selected
> select clear
> ui mousemode rightMode "translate selected models"
> lighting soft
> select clear
> hide #!7 models
> select #14.1
38205 atoms, 38730 bonds, 1 model selected
> ~select #14.1
Nothing selected
> select #14.2
38205 atoms, 38730 bonds, 1 model selected
> ~select #14.2
Nothing selected
> select #14.1
38205 atoms, 38730 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 48
shifted from previous position = 1.35
rotated from previous position = 0.36 degrees
atoms outside contour = 17052, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87152575 0.43744295 0.22155475 -248.08390878
0.43059629 -0.89890364 0.08098810 349.84460221
0.23458405 0.02481743 -0.97177899 435.45368809
Axis -0.96734135 -0.22438373 -0.11790947
Axis point 0.00000000 207.06052433 230.03528537
Rotation angle (degrees) 178.33626741
Shift along axis 110.13827118
> select clear
> hide #!14.2 models
> show #!14.2 models
> sequence chain #14.3
Chains must have same sequence
> sequence chain #14.2
Alignment identifier is 1
2 headers
> select clear
> select clear
> select clear
> hide #!14 models
> show #!14 models
> hide #!14.1 models
> show #!14.1 models
> hide #!14.2 models
> show #!14.2 models
> color #14.2/B-W:2-28 red
> color #14.2/b-e:2-28 red
> select clear
> color #14.2/W:2-28 red
> color #14.2/B:2-28 red
> color #14.2/D:2-28 red
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random' or a keyword
> color #14.2/W:2-28 red
> color #14.2/V:2-28 red
> color #14.2/U:2-28 red
> color #14.2/T:2-28 red
> color #14.2/O:2-28 red
> color #14.2/L:2-28 red
> color #14.2/M:2-28 red
> color #14.2/N:2-28 red
> color #14.2/D:2-28 red
> color #14.2/F:2-28 red
> color #14.2/F,b-e:2-28 red
> select clear
> select clear
> select clear
> save session /data/disk3/modeling/gp10/capsid-tail-20200205.cxs
> save image /data/disk3/Paper-use/Figure2-20200205-2.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!5 models
> show #!20 models
> show #!10 models
> show #!26 models
> toolshed show "Side View"
> lighting flat
> hide #!10 models
> show #!10 models
> sequence chain #10
Alignment identifier is 2
2 headers
> hide #10/A-L:4-10
> hide selAtoms ribbons
> select clear
> lighting flat
> view cofr false
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-3.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!10 models
> hide #!26 models
> save image /data/disk3/Paper-use/Figure2-20200205-3.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!20 models
> show #!20 models
> show #!10 models
> show #!26 models
> save image /data/disk3/Paper-use/Figure2-20200205-4.tif pixelSize 0.1
supersample 10 transparentBackground true
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> hide selAtoms ribbons
> select #14.1/X:2
5 atoms, 4 bonds, 1 model selected
> show selAtoms
> style selAtoms sphere
Changed 120 atom styles
> style selAtoms stick
Changed 120 atom styles
> style selAtoms ball
Changed 120 atom styles
> color selAtoms byhetero
> style selAtoms ball
Changed 120 atom styles
> color selAtoms byhetero
> style selAtoms sphere
Changed 120 atom styles
> color #14.2/b-e,F:29 red
> color #14.2/b-e,F:29 magenta
> select clear
> save image /data/disk3/Paper-use/Figure2-20200205-8.tif pixelSize 0.1
supersample 10 transparentBackground true
> show #!23 models
> show #!7 models
> hide #!7 models
> hide #!20 models
> show #!20 models
> hide #!23 models
> save image /data/disk3/Paper-use/Figure2-20200205-9.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting flat
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-9.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!10 models
> hide #!26 models
> save image /data/disk3/Paper-use/Figure2-20200205-10.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!5 models
> hide #!20 models
> save image /data/disk3/Paper-use/Figure2-20200205-11.tif pixelSize 0.1
supersample 10 transparentBackground true
> toolshed show "Side View"
> show #!10 models
> show #!26 models
> show #!5 models
> show #!20 models
> show #!23 models
> show #!7 models
> save image /data/disk3/Paper-use/Figure2-20200205-12.tif pixelSize 0.1
supersample 10 transparentBackground true
> view cofr false
> hide #!23 models
> hide #!7 models
> save image /data/disk3/Paper-use/Figure2-20200205-13.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure2-20200205-14.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting flat
> hide #!5 models
> show #!5 models
> sequence chain #5
Alignment identifier is 3
2 headers
> select #5/K:351
11 atoms, 10 bonds, 1 model selected
> select #5/K:352
8 atoms, 7 bonds, 1 model selected
> select #5/K:370
7 atoms, 6 bonds, 1 model selected
> hide selAtoms ribbons
> hide selAtoms ribbons
> select clear
> hide selAtoms ribbons
> show selAtoms ribbons
> hide selAtoms
> select clear
> hide #!14 models
> show #!14 models
> hide #!11 models
> show #!11 models
> save image /data/disk3/Paper-use/Figure2-20200205-15.tif pixelSize 0.1
supersample 10 transparentBackground true
> save image /data/disk3/Paper-use/Figure2-20200205-15.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!20 models
> lighting soft
> show #!13 models
> hide #!13 models
> show #!20 models
> save image /data/disk3/Paper-use/Figure2-20200205-15.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting flat
> hide #!20 models
> hide #!11 models
> hide #!14 models
> hide selAtoms ribbons
> show #!14 models
> view cofr false
> show #!11 models
> lighting soft
> lighting flat
> lighting simple
> lighting flat
> lighting flat
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-16.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!5 models
> hide #!14 models
> show #!14 models
> select #14
76410 atoms, 77460 bonds, 3 models selected
> hbonds selAtoms
4619 hydrogen bonds found
> show selAtoms
> style selAtoms stick
Changed 76410 atom styles
> style selAtoms ball
Changed 76410 atom styles
> style selAtoms ball
Changed 76410 atom styles
> show #!5 models
> hide #!5 models
> select clear
> show #!5 models
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> color selAtoms byhetero
> style selAtoms sphere
Changed 76410 atom styles
> style selAtoms ball
Changed 76410 atom styles
> style selAtoms sphere
Changed 76410 atom styles
> select clear
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> style selAtoms ball
Changed 76410 atom styles
> select clear
> style selAtoms sphere
Changed 257163 atom styles
> select clear
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> style selAtoms stick
Changed 76410 atom styles
> style selAtoms ball
Changed 76410 atom styles
> hide #!11 models
> select clear
> select #14.2/N:295
11 atoms, 10 bonds, 1 model selected
> select #14.2/N:295
11 atoms, 10 bonds, 1 model selected
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
> style selAtoms sphere
Changed 11 atom styles
> select #14.2/d:240
11 atoms, 10 bonds, 1 model selected
> select #14.2/d:240
11 atoms, 10 bonds, 1 model selected
> select #14.2/O:53
11 atoms, 10 bonds, 1 model selected
> select #14.2/O:63@CE2
1 atom, 1 model selected
> select #14.2/O:53
11 atoms, 10 bonds, 1 model selected
> select #5/B:203
4 atoms, 3 bonds, 1 model selected
> select #26
4 models selected
> select #5/C:200
4 atoms, 3 bonds, 1 model selected
> select #14.1/K:197@CG
1 atom, 1 model selected
> select #14.2/e:240
11 atoms, 10 bonds, 1 model selected
> select #14.2/e:240
11 atoms, 10 bonds, 1 model selected
> select #14.2/e:241
8 atoms, 7 bonds, 1 model selected
> style selAtoms sphere
Changed 165 atom styles
> select #14.2/e:329
10 atoms, 10 bonds, 1 model selected
> select #14.2/e:329
10 atoms, 10 bonds, 1 model selected
> select #5/D:206@CE
1 atom, 1 model selected
> select clear
> select #14.1/A:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/A:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/A:235
9 atoms, 8 bonds, 1 model selected
> select #14.1/A:186
5 atoms, 4 bonds, 1 model selected
> select #14.1/A:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/A:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/A:235@CA
1 atom, 1 model selected
> lighting flat
> select #14.2/L:295@CA
1 atom, 1 model selected
> select #14.1/X:235
9 atoms, 8 bonds, 1 model selected
> select #14.1/X:236
9 atoms, 8 bonds, 1 model selected
> select clear
> select #14.2/b:53@CA
1 atom, 1 model selected
> select #14.2/b:53
11 atoms, 10 bonds, 1 model selected
> select #14.2/M:53
11 atoms, 10 bonds, 1 model selected
> select #14.2/M:53
11 atoms, 10 bonds, 1 model selected
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/I:241
8 atoms, 7 bonds, 1 model selected
> select #14.1/I:241
8 atoms, 7 bonds, 1 model selected
> select #14.1/I:241@CA
1 atom, 1 model selected
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> hide #!14.1 models
> show #!14.1 models
> hide #!14.2 models
> select #14.1/I:290
4 atoms, 3 bonds, 1 model selected
> select #14.1/I:239
8 atoms, 7 bonds, 1 model selected
> sequence chain #14.2
Alignment identifier is 2
2 headers
> select #14.1
38205 atoms, 38730 bonds, 2125 pseudobonds, 2 models selected
> select clear
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/H:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/H:240@CA
1 atom, 1 model selected
> sequence chain #14.1
Alignment identifier is 1
2 headers
> hide #!14 models
> show #!14 models
> hide #!14.1 models
> show #!14.1 models
> select #14.1/H:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/E:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/A:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/K:35
9 atoms, 8 bonds, 1 model selected
> select #14.1/K:35
9 atoms, 8 bonds, 1 model selected
> select #14.1/Z:236
9 atoms, 8 bonds, 1 model selected
> select #14.1/I:240
11 atoms, 10 bonds, 1 model selected
> select #14.1/I:35
9 atoms, 8 bonds, 1 model selected
> hide #!14.1 models
> show #!14.2 models
> sequence chain #14.2
Alignment identifier is 1
2 headers
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> style selAtoms ball
Changed 38205 atom styles
> select clear
> select #14.2/d:295
11 atoms, 10 bonds, 1 model selected
> select clear
> select #14.2/O:53
11 atoms, 10 bonds, 1 model selected
> select #14.2/e:240@CA
1 atom, 1 model selected
> select #10/I:78
8 atoms, 7 bonds, 1 model selected
> select #14.2/F:295
11 atoms, 10 bonds, 1 model selected
> select #14.2/F:295
11 atoms, 10 bonds, 1 model selected
> select #14.2/F:295
11 atoms, 10 bonds, 1 model selected
> select #14.2/L:295
11 atoms, 10 bonds, 1 model selected
> select #14.2/b:240@CA
1 atom, 1 model selected
> hide #!11.1 models
> show #!14.1 models
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> hide selAtoms
> hide selAtoms
> select #14.1
38205 atoms, 38730 bonds, 2125 pseudobonds, 2 models selected
> hide selAtoms
> select #14.2/b:240
11 atoms, 10 bonds, 1 model selected
> style selAtoms ball
Changed 11 atom styles
> show selAtoms
> show #!11 models
> show #!11.1 models
> show selAtoms
> style selAtoms sphere
Changed 165 atom styles
> style selAtoms ball
Changed 165 atom styles
> show selAtoms
> style selAtoms ball
Changed 165 atom styles
> color selAtoms byhetero
> style selAtoms sphere
Changed 165 atom styles
> style selAtoms stick
Changed 165 atom styles
> select #5/C:204@OE1
1 atom, 1 model selected
> select #5/C:204@OE1
1 atom, 1 model selected
> toolshed show Distances
Exactly two atoms must be selected!
> select #5/C:204@OE1
1 atom, 1 model selected
> select #5/C:204@OE1
1 atom, 1 model selected
> distance #5/C:204@OE1 #14.2/e:240@NH2
Distance between gp8-WCY-C12-coot-basedon-newdata.pdb #5/C GLU 204 OE1 and
3j7w-C5-C6-pentamer-2.pdb #14.2/e ARG 240 NH2: 4.049Å
> hide #!22.1 models
> select #5/C:204@OE2
1 atom, 1 model selected
> hide #!22 models
> select #5/C:204@OE2
1 atom, 1 model selected
Exactly two atoms must be selected!
> select #5/C:204@OE2
1 atom, 1 model selected
> select #5/C:204@OE2
1 atom, 1 model selected
Exactly two atoms must be selected!
> select #5/C:204@OE2
1 atom, 1 model selected
> select #5/C:204@OE2
1 atom, 1 model selected
> select #5/C:204@OE2
1 atom, 1 model selected
> select #5/C:204@OE2
1 atom, 1 model selected
> distance #5/C:204@OE2 #14.2/e:240@NH2
Distance between gp8-WCY-C12-coot-basedon-newdata.pdb #5/C GLU 204 OE2 and
3j7w-C5-C6-pentamer-2.pdb #14.2/e ARG 240 NH2: 2.925Å
> select #14.2/e:240@NH1
1 atom, 1 model selected
> distance #5/C:204@OE1 #14.2/e:240@NH1
Distance between gp8-WCY-C12-coot-basedon-newdata.pdb #5/C GLU 204 OE1 and
3j7w-C5-C6-pentamer-2.pdb #14.2/e ARG 240 NH1: 4.688Å
> show #!16 models
> hide #!16 models
> show #!22 models
> ~distance #5/C:204@OE1 #14.2/e:240@NH1
> ~distance #5/C:204@OE1 #14.2/e:240@NH2
> distance #5/C:204@OE1 #14.2/e:240@NH1
Distance between gp8-WCY-C12-coot-basedon-newdata.pdb #5/C GLU 204 OE1 and
3j7w-C5-C6-pentamer-2.pdb #14.2/e ARG 240 NH1: 4.688Å
> distance style dashes 8
> distance style dashes 8
> distance style dashes 7
> distance style dashes 7
> distance style dashes 6
> distance style dashes 6
> distance style dashes 5
> distance style dashes 5
> distance style dashes 4
> distance style dashes 4
> distance style dashes 5
> distance style dashes 5
> distance style dashes 6
> distance style dashes 6
> distance style dashes 7
> distance style dashes 7
> distance style dashes 8
> distance style dashes 8
> distance style dashes 9
> distance style dashes 9
> distance style dashes 10
> distance style dashes 10
> distance style dashes 11
> distance style dashes 11
> distance style dashes 10
> distance style dashes 10
> distance style decimalPlaces 2
> distance style decimalPlaces 2
> distance style decimalPlaces 1
> distance style decimalPlaces 1
> distance style dashes 11
> distance style dashes 11
> distance style dashes 10
> distance style dashes 10
> select #11
3 models selected
> select #11
3 models selected
> show selAtoms
> style selAtoms ball
Changed 165 atom styles
> style selAtoms ball
Changed 165 atom styles
> show selAtoms
> view cofr false
> select clear
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> hide selAtoms
> select clear
> hide #!11 models
> select #14.2/M:53
11 atoms, 10 bonds, 1 model selected
> show selAtoms
> style selAtoms stick
Changed 11 atom styles
> style selAtoms ball
Changed 11 atom styles
> select #11
3 models selected
> show #!11 models
> select #5/I:204@OE2
1 atom, 1 model selected
> distance #5/I:204@OE2 #14.2/M:53@NH2
Distance between gp8-WCY-C12-coot-basedon-newdata.pdb #5/I GLU 204 OE2 and
3j7w-C5-C6-pentamer-2.pdb #14.2/M ARG 53 NH2: 5.9Å
> hide #!14.2 models
> show #!14.2 models
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 52
shifted from previous position = 2.54
rotated from previous position = 0.208 degrees
atoms outside contour = 17720, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87138327 0.43921749 0.21858449 -247.77189922
0.43221758 -0.89807533 0.08153928 348.82697723
0.23211883 0.02342409 -0.97240535 435.88410414
Axis -0.96730403 -0.22527357 -0.11651066
Axis point 0.00000000 206.74972457 229.96217930
Rotation angle (degrees) 178.27858857
Shift along axis 110.30411243
> hide #!11 models
> show #!11 models
> select #5/I:204@CA
1 atom, 1 model selected
> style selAtoms ball
Changed 1 atom style
> style selAtoms stick
Changed 4 atom styles
> select #5/I:204@CD
1 atom, 1 model selected
> style selAtoms stick
Changed 2 atom styles
> color selAtoms byhetero
> style selAtoms ball
Changed 2 atom styles
> select #11
3 models selected
Exactly two atoms must be selected!
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> select #11
3 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 96
shifted from previous position = 1.55
rotated from previous position = 3.99 degrees
atoms outside contour = 17700, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87148234 0.43837591 0.21987515 -247.85931691
0.43117512 -0.89849757 0.08240215 349.95752656
0.23368041 0.02299267 -0.97204156 436.66396600
Axis -0.96732930 -0.22478294 -0.11724612
Axis point 0.00000000 207.34548244 230.37888387
Rotation angle (degrees) 178.24028527
Shift along axis 109.89994340
> select clear
> view name test1
> view 1
> lighting flat
> lighting flat
> view cofr false
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> style selAtoms sphere
Changed 76410 atom styles
> show selAtoms
> select clear
> hide #!11 models
> show #!12 models
> hide #!12 models
> show #!11 models
> hide #!14 models
> show #!14 models
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> select #11
3 models selected
Exception ignored in: <function Buffer.__del__ at 0x7f208a172840>
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2421, in __del__
% self.shader_variable_name)
chimerax.core.graphics.opengl.OpenGLError: OpenGL buffer "None" was not
deleted before core.graphics.Buffer destroyed
> lighting soft
> select clear
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> hide selAtoms
> select clear
> select #14.1
38205 atoms, 38730 bonds, 2125 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> view 1
> lighting flat
> view cofr false
> select clear
> hide #!14.1 models
> hide #!14.2 models
> show #!14.1 models
> hide #!14.1 models
> show #!14.2 models
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 108
shifted from previous position = 10.1
rotated from previous position = 3.98 degrees
atoms outside contour = 17717, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87091133 0.44912114 0.19950850 -249.05015986
0.44598272 -0.89282019 0.06301999 356.96050653
0.20642883 0.03409252 -0.97786749 434.46693254
Axis -0.96718766 -0.23138082 -0.10493305
Axis point 0.00000000 209.99566642 229.26287539
Rotation angle (degrees) 179.14314274
Shift along axis 112.69448947
> select clear
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 124
shifted from previous position = 4.81
rotated from previous position = 5.48 degrees
atoms outside contour = 17720, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87129336 0.41599505 0.26037661 -257.28977606
0.41178535 -0.90833124 0.07326100 350.51476012
0.26698443 0.04338745 -0.96272366 423.31360835
Axis -0.96728629 -0.21395696 -0.13630717
Axis point 0.00000000 205.46549904 228.28685222
Rotation angle (degrees) 179.11520685
Shift along axis 116.17712263
> ~select #14.2
Nothing selected
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ~select #14.2
Nothing selected
> select clear
> show #!14.1 models
> select clear
> hide #!14.2 models
> show #!14.2 models
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 112
shifted from previous position = 10.3
rotated from previous position = 1.75 degrees
atoms outside contour = 17714, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87159491 0.43814570 0.21988780 -249.61671958
0.43000777 -0.89869519 0.08625694 340.10695396
0.23540522 0.01937235 -0.97170422 433.58062956
Axis -0.96735631 -0.22442955 -0.11769941
Axis point 0.00000000 203.00433533 228.70748801
Rotation angle (degrees) 178.01884366
Shift along axis 114.10607516
> select clear
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "rotate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 172
shifted from previous position = 15.4
rotated from previous position = 8.84 degrees
atoms outside contour = 17698, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87184000 0.43723832 0.22072076 -249.90849103
0.44656783 -0.89470985 0.00845289 367.54255552
0.20117697 0.09119722 -0.97530041 406.71865152
Axis 0.96741444 0.22849834 0.10907705
Axis point 0.00000000 208.65111851 221.79837124
Rotation angle (degrees) 177.54895804
Shift along axis -113.41854652
> select clear
> hide #!10 models
> hide #!5 models
> hide #!26 models
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 100
shifted from previous position = 4.26
rotated from previous position = 4.37 degrees
atoms outside contour = 17690, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87120479 0.42141686 0.25181347 -252.76393125
0.41774086 -0.90581591 0.07064060 354.50912237
0.25786580 0.04365034 -0.96519422 426.11286820
Axis -0.96726376 -0.21690033 -0.13173859
Axis point 0.00000000 207.18419345 228.90369050
Rotation angle (degrees) 179.20059109
Shift along axis 111.46073747
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 88
shifted from previous position = 3.56
rotated from previous position = 2.17 degrees
atoms outside contour = 17687, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87205934 0.43387864 0.22641073 -247.94276153
0.42276280 -0.90091402 0.09810980 345.40390070
0.24654435 0.01016046 -0.96907824 441.26862530
Axis -0.96746916 -0.22147595 -0.12227768
Axis point 0.00000000 206.42464516 231.95916403
Rotation angle (degrees) 177.39482017
Shift along axis 109.42101455
> select clear
> hide #!14.1 models
> show #!14.1 models
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ~select #14.2
Nothing selected
> hide #!14.2 models
> show #!14.2 models
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 112
shifted from previous position = 4.24
rotated from previous position = 4.23 degrees
atoms outside contour = 17697, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87308056 0.44501036 0.19923881 -240.59886299
0.43043610 -0.89542262 0.11376773 341.08918763
0.22903077 -0.01356882 -0.97332461 452.52991272
Axis -0.96771455 -0.22640872 -0.11075942
Axis point 0.00000000 206.58884638 233.82368800
Rotation angle (degrees) 176.22764770
Shift along axis 105.48350372
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 80
shifted from previous position = 6.15
rotated from previous position = 2.1 degrees
atoms outside contour = 17718, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87128804 0.44644826 0.20381630 -247.95612848
0.43996900 -0.89456004 0.07867398 350.24003807
0.21744979 0.02112515 -0.97584287 438.40792550
Axis -0.96727956 -0.22915139 -0.10890317
Axis point 0.00000000 207.95590734 230.27177816
Rotation angle (degrees) 178.29532634
Shift along axis 111.84089162
> select #14.1
38205 atoms, 38730 bonds, 2125 pseudobonds, 2 models selected
> ui mousemode rightMode "translate selected models"
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 52
shifted from previous position = 3
rotated from previous position = 0.18 degrees
atoms outside contour = 17055, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87158544 0.43795856 0.22029777 -248.58859429
0.43040165 -0.89873277 0.08386784 350.06108992
0.23471947 0.02171853 -0.97182049 437.44196871
Axis -0.96735522 -0.22447409 -0.11762343
Axis point 0.00000000 207.61333052 230.72151109
Rotation angle (degrees) 178.15915293
Shift along axis 110.44040290
> hide #!14.1 models
> show #!14.1 models
> ui mousemode rightMode "translate selected models"
> fitmap #14.1 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-1.pdb (#14.1) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 48
shifted from previous position = 1.21
rotated from previous position = 0.0897 degrees
atoms outside contour = 17044, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb (#14.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87158559 0.43864627 0.21892466 -248.14087257
0.43111073 -0.89840505 0.08373712 349.18672906
0.23341400 0.02139669 -0.97214201 437.16833974
Axis -0.96735520 -0.22483552 -0.11693120
Axis point 0.00000000 207.17912501 230.46611881
Rotation angle (degrees) 178.15349006
Shift along axis 110.41216567
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 80
shifted from previous position = 3.27
rotated from previous position = 1.05 degrees
atoms outside contour = 17716, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87123479 0.43869772 0.22021406 -249.08363602
0.43347029 -0.89810677 0.07421413 351.80127500
0.23033332 0.03079831 -0.97262430 433.25103671
Axis -0.96726896 -0.22544876 -0.11646295
Axis point 0.00000000 207.51703025 229.43458391
Rotation angle (degrees) 178.71403287
Shift along axis 111.16001359
> select clear
> select #14.2
38205 atoms, 38730 bonds, 2079 pseudobonds, 2 models selected
> fitmap #14.2 inMap #11
Fit molecule 3j7w-C5-C6-pentamer-2.pdb (#14.2) to map capsid-c5-res3.2-tail-
vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 56
shifted from previous position = 2.46
rotated from previous position = 0.523 degrees
atoms outside contour = 17718, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb (#14.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.87141140 0.43680228 0.22326199 -247.81275063
0.42975169 -0.89922241 0.08193010 349.56089679
0.23654945 0.02455239 -0.97130919 435.43342616
Axis -0.96731149 -0.22400876 -0.11886360
Axis point 0.00000000 206.91284874 230.07403216
Rotation angle (degrees) 178.30045319
Shift along axis 109.65023609
> select clear
> view name good
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> select clear
> hide #!21 models
> show #!21 models
> show #!15 models
> hide #!15 models
> hide #!14.1 models
> show #!14.1 models
> hide #!14.1 models
> show #!14.1 models
> show #!5 models
> save image /data/disk3/Paper-use/Figure2-20200205-17.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-17.tif pixelSize 0.1
supersample 10 transparentBackground true
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> show selAtoms
> style selAtoms ball
Changed 76410 atom styles
> color selAtoms byhetero
> style selAtoms ball
Changed 76410 atom styles
> style selAtoms sphere
Changed 76410 atom styles
> select clear
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> style selAtoms ball
Changed 76410 atom styles
> select clear
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> style selAtoms sphere
Changed 76410 atom styles
> select clear
> lighting flat
> lighting full
> lighting soft
> lighting soft
> lighting soft
> lighting simple
> lighting soft
> select clear
> save image /data/disk3/Paper-use/Figure2-20200205-18.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!5 models
> show #!5 models
> sequence chain #5
Alignment identifier is 2
2 headers
> select #5/K:205
9 atoms, 8 bonds, 1 model selected
> select #5/K:205
9 atoms, 8 bonds, 1 model selected
> hide selAtoms
> hide selAtoms
> style selAtoms ball
Changed 588 atom styles
> color #5/A-Y:198 red
> color #5/A-Y: 201-207 red
> color #5/A-Y: 201-207 green
> color #5/A-Y: 201-207 magenta
> style selAtoms sphere
Changed 588 atom styles
> show selAtoms
> color selAtoms byhetero
> lighting flat
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> lighting soft
> lighting full
> show #!26 models
> show #!27 models
> hide #!27 models
> show #!29 models
> hide #!29 models
> show #!29 models
> hide #!26 models
> hide #!29 models
> view cofr false
> select clear
> save image /data/disk3/Paper-use/Figure2-20200205-19.tif pixelSize 0.1
supersample 10 transparentBackground true
> color #5/A-Y: 201-207 green
> style selAtoms ball
Changed 588 atom styles
> style selAtoms sphere
Changed 588 atom styles
> color selAtoms byhetero
> select clear
> lighting flat
> select clear
> save image /data/disk3/Paper-use/Figure2-20200205-19.tif pixelSize 0.1
supersample 10 transparentBackground true
> toolshed show "Side View"
> hide selAtoms ribbons
> hide selAtoms
> save session /data/disk3/modeling/gp10/capsid-tail-20200205.cxs
> view orient cofr false
> view cofr false
> hide #!5.2 models
> hide #!5.3 models
> hide #!5.4 models
> hide #!5.5 models
> hide #!5.6 models
> hide #!5.7 models
> hide #!5.8 models
> hide #!5.9 models
> hide #!5.10 models
> hide #!5.11 models
> hide #!5.12 models
> show #!5.2 models
> show #!5.3 models
> hide #!5.3 models
> show #!5.4 models
> show #!5.5 models
> show #!5.6 models
> show #!5.7 models
> show #!5.9 models
> show #!5.10 models
> show #!5.11 models
> show #!5.12 models
> hide #!5.11 models
> hide #!5.10 models
> hide #!5.9 models
> show #!5.8 models
> show #!5.3 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> hide selAtoms ribbons
> hide #!5.1 models
> show #!5.1 models
> view good
> show #!5.9 models
> show #!5.10 models
> show #!5.11 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select clear
> select #5.1
4084 atoms, 1 model selected
> show selAtoms ribbons
> hide #!14 models
> hide #!11 models
> select #14.1
38205 atoms, 38730 bonds, 2125 pseudobonds, 2 models selected
> show #!14 models
> select #14
76410 atoms, 77460 bonds, 4204 pseudobonds, 4 models selected
> hide selAtoms
> hide #!14 models
> show #!14 models
> split #14
Chain information for 3j7w-C5-C6-pentamer-1.pdb A #14.1.1
---
Chain | Description
A | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb C #14.1.2
---
Chain | Description
C | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb E #14.1.3
---
Chain | Description
E | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb H #14.1.4
---
Chain | Description
H | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb I #14.1.5
---
Chain | Description
I | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb J #14.1.6
---
Chain | Description
J | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb K #14.1.7
---
Chain | Description
K | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb P #14.1.8
---
Chain | Description
P | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb Q #14.1.9
---
Chain | Description
Q | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb R #14.1.10
---
Chain | Description
R | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb S #14.1.11
---
Chain | Description
S | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb X #14.1.12
---
Chain | Description
X | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb Y #14.1.13
---
Chain | Description
Y | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb Z #14.1.14
---
Chain | Description
Z | No description available
Chain information for 3j7w-C5-C6-pentamer-1.pdb a #14.1.15
---
Chain | Description
a | No description available
Split 3j7w-C5-C6-pentamer-1.pdb (#14.1) into 15 models
Chain information for 3j7w-C5-C6-pentamer-2.pdb B #14.2.1
---
Chain | Description
B | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb D #14.2.2
---
Chain | Description
D | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb F #14.2.3
---
Chain | Description
F | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb L #14.2.4
---
Chain | Description
L | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb M #14.2.5
---
Chain | Description
M | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb N #14.2.6
---
Chain | Description
N | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb O #14.2.7
---
Chain | Description
O | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb T #14.2.8
---
Chain | Description
T | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb U #14.2.9
---
Chain | Description
U | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb V #14.2.10
---
Chain | Description
V | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb W #14.2.11
---
Chain | Description
W | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb b #14.2.12
---
Chain | Description
b | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb c #14.2.13
---
Chain | Description
c | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb d #14.2.14
---
Chain | Description
d | No description available
Chain information for 3j7w-C5-C6-pentamer-2.pdb e #14.2.15
---
Chain | Description
e | No description available
Split 3j7w-C5-C6-pentamer-2.pdb (#14.2) into 15 models
> select clear
> hide #!14.1 models
> select #14.1.1
2547 atoms, 2582 bonds, 1 model selected
> show #!14.1 models
> hide #!14.1 models
> select #14.2
38205 atoms, 38730 bonds, 16 models selected
> view good
> show #!14.1 models
> show #!6 models
> hide #!14 models
> hide #!14.1 models
> hide #!14.2 models
> show #!14 models
> show #!14.1 models
> show #!14.2 models
> select #14
76410 atoms, 77460 bonds, 33 models selected
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> view good
> hide #!6 models
> show #!11 models
> view good
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecules 3j7w-C5-C6-pentamer-2.pdb B (#14.2.1), 3j7w-C5-C6-pentamer-2.pdb
D (#14.2.2), 3j7w-C5-C6-pentamer-2.pdb F (#14.2.3), 3j7w-C5-C6-pentamer-2.pdb
L (#14.2.4), 3j7w-C5-C6-pentamer-2.pdb M (#14.2.5), 3j7w-C5-C6-pentamer-2.pdb
N (#14.2.6), 3j7w-C5-C6-pentamer-2.pdb O (#14.2.7), 3j7w-C5-C6-pentamer-2.pdb
T (#14.2.8), 3j7w-C5-C6-pentamer-2.pdb U (#14.2.9), 3j7w-C5-C6-pentamer-2.pdb
V (#14.2.10), 3j7w-C5-C6-pentamer-2.pdb W (#14.2.11),
3j7w-C5-C6-pentamer-2.pdb b (#14.2.12), 3j7w-C5-C6-pentamer-2.pdb c
(#14.2.13), 3j7w-C5-C6-pentamer-2.pdb d (#14.2.14), 3j7w-C5-C6-pentamer-2.pdb
e (#14.2.15) to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 136
shifted from previous position = 10.8
rotated from previous position = 5.77 degrees
atoms outside contour = 17692, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb B (#14.2.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb D (#14.2.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb F (#14.2.3) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb L (#14.2.4) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb M (#14.2.5) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb N (#14.2.6) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb O (#14.2.7) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb T (#14.2.8) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb U (#14.2.9) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb V (#14.2.10) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb W (#14.2.11) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb b (#14.2.12) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb c (#14.2.13) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb d (#14.2.14) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
Position of 3j7w-C5-C6-pentamer-2.pdb e (#14.2.15) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90412262 0.39791771 0.15563988 -219.81490867
0.38112787 -0.91572915 0.12720719 356.10518779
0.19314197 -0.05569220 -0.97958897 465.89495430
Axis -0.97568210 -0.20005601 -0.08956586
Axis point 0.00000000 212.02081586 233.97685470
Rotation angle (degrees) 174.62183028
Shift along axis 101.50020615
> fitmap #14.1 inMap #11
Fit molecules 3j7w-C5-C6-pentamer-1.pdb A (#14.1.1), 3j7w-C5-C6-pentamer-1.pdb
C (#14.1.2), 3j7w-C5-C6-pentamer-1.pdb E (#14.1.3), 3j7w-C5-C6-pentamer-1.pdb
H (#14.1.4), 3j7w-C5-C6-pentamer-1.pdb I (#14.1.5), 3j7w-C5-C6-pentamer-1.pdb
J (#14.1.6), 3j7w-C5-C6-pentamer-1.pdb K (#14.1.7), 3j7w-C5-C6-pentamer-1.pdb
P (#14.1.8), 3j7w-C5-C6-pentamer-1.pdb Q (#14.1.9), 3j7w-C5-C6-pentamer-1.pdb
R (#14.1.10), 3j7w-C5-C6-pentamer-1.pdb S (#14.1.11),
3j7w-C5-C6-pentamer-1.pdb X (#14.1.12), 3j7w-C5-C6-pentamer-1.pdb Y
(#14.1.13), 3j7w-C5-C6-pentamer-1.pdb Z (#14.1.14), 3j7w-C5-C6-pentamer-1.pdb
a (#14.1.15) to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 164
shifted from previous position = 10.9
rotated from previous position = 5.56 degrees
atoms outside contour = 17057, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb A (#14.1.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb C (#14.1.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb E (#14.1.3) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb H (#14.1.4) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb I (#14.1.5) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb J (#14.1.6) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb K (#14.1.7) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb P (#14.1.8) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb Q (#14.1.9) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb R (#14.1.10) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb S (#14.1.11) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb X (#14.1.12) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb Y (#14.1.13) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb Z (#14.1.14) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
Position of 3j7w-C5-C6-pentamer-1.pdb a (#14.1.15) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90410872 0.39830342 0.15473138 -220.18344512
0.38190127 -0.91563955 0.12552139 356.48312308
0.19167378 -0.05439288 -0.97995029 465.29463583
Axis -0.97568029 -0.20033970 -0.08894933
Axis point 0.00000000 212.07767068 233.76042608
Rotation angle (degrees) 174.70985067
Shift along axis 102.02327881
> hide #!14.1 models
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecules 3j7w-C5-C6-pentamer-2.pdb B (#14.2.1), 3j7w-C5-C6-pentamer-2.pdb
D (#14.2.2), 3j7w-C5-C6-pentamer-2.pdb F (#14.2.3), 3j7w-C5-C6-pentamer-2.pdb
L (#14.2.4), 3j7w-C5-C6-pentamer-2.pdb M (#14.2.5), 3j7w-C5-C6-pentamer-2.pdb
N (#14.2.6), 3j7w-C5-C6-pentamer-2.pdb O (#14.2.7), 3j7w-C5-C6-pentamer-2.pdb
T (#14.2.8), 3j7w-C5-C6-pentamer-2.pdb U (#14.2.9), 3j7w-C5-C6-pentamer-2.pdb
V (#14.2.10), 3j7w-C5-C6-pentamer-2.pdb W (#14.2.11),
3j7w-C5-C6-pentamer-2.pdb b (#14.2.12), 3j7w-C5-C6-pentamer-2.pdb c
(#14.2.13), 3j7w-C5-C6-pentamer-2.pdb d (#14.2.14), 3j7w-C5-C6-pentamer-2.pdb
e (#14.2.15) to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 84
shifted from previous position = 3.48
rotated from previous position = 2.11 degrees
atoms outside contour = 17714, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb B (#14.2.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb D (#14.2.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb F (#14.2.3) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb L (#14.2.4) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb M (#14.2.5) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb N (#14.2.6) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb O (#14.2.7) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb T (#14.2.8) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb U (#14.2.9) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb V (#14.2.10) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb W (#14.2.11) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb b (#14.2.12) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb c (#14.2.13) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb d (#14.2.14) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
Position of 3j7w-C5-C6-pentamer-2.pdb e (#14.2.15) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90326229 0.41056332 0.12471963 -213.59419953
0.39799605 -0.91026699 0.11407518 351.08822205
0.16036326 -0.05340190 -0.98561243 474.95846557
Axis -0.97546999 -0.20760624 -0.07319805
Axis point 0.00000000 208.90464138 237.29386571
Rotation angle (degrees) 175.07542281
Shift along axis 100.70058991
> show #!14.1 models
> hide #!14.2 models
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "rotate selected models"
> show #!14.2 models
> ui mousemode rightMode "translate selected models"
> fitmap #14.2 inMap #11
Fit molecules 3j7w-C5-C6-pentamer-2.pdb B (#14.2.1), 3j7w-C5-C6-pentamer-2.pdb
D (#14.2.2), 3j7w-C5-C6-pentamer-2.pdb F (#14.2.3), 3j7w-C5-C6-pentamer-2.pdb
L (#14.2.4), 3j7w-C5-C6-pentamer-2.pdb M (#14.2.5), 3j7w-C5-C6-pentamer-2.pdb
N (#14.2.6), 3j7w-C5-C6-pentamer-2.pdb O (#14.2.7), 3j7w-C5-C6-pentamer-2.pdb
T (#14.2.8), 3j7w-C5-C6-pentamer-2.pdb U (#14.2.9), 3j7w-C5-C6-pentamer-2.pdb
V (#14.2.10), 3j7w-C5-C6-pentamer-2.pdb W (#14.2.11),
3j7w-C5-C6-pentamer-2.pdb b (#14.2.12), 3j7w-C5-C6-pentamer-2.pdb c
(#14.2.13), 3j7w-C5-C6-pentamer-2.pdb d (#14.2.14), 3j7w-C5-C6-pentamer-2.pdb
e (#14.2.15) to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 38205 atoms
average map value = 0.01396, steps = 80
shifted from previous position = 3.48
rotated from previous position = 0.925 degrees
atoms outside contour = 17703, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-2.pdb B (#14.2.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb D (#14.2.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb F (#14.2.3) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb L (#14.2.4) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb M (#14.2.5) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb N (#14.2.6) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb O (#14.2.7) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb T (#14.2.8) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb U (#14.2.9) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb V (#14.2.10) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb W (#14.2.11) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb b (#14.2.12) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb c (#14.2.13) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb d (#14.2.14) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
Position of 3j7w-C5-C6-pentamer-2.pdb e (#14.2.15) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90202583 0.41195977 0.12899043 -215.17900329
0.40164131 -0.91043041 0.09899861 357.17624225
0.15822026 -0.03749143 -0.98669181 467.89587909
Axis -0.97516808 -0.20883575 -0.07372144
Axis point 0.00000000 210.16714926 235.28757026
Rotation angle (degrees) 175.98699912
Shift along axis 100.75056582
> fitmap #14.1 inMap #11
Fit molecules 3j7w-C5-C6-pentamer-1.pdb A (#14.1.1), 3j7w-C5-C6-pentamer-1.pdb
C (#14.1.2), 3j7w-C5-C6-pentamer-1.pdb E (#14.1.3), 3j7w-C5-C6-pentamer-1.pdb
H (#14.1.4), 3j7w-C5-C6-pentamer-1.pdb I (#14.1.5), 3j7w-C5-C6-pentamer-1.pdb
J (#14.1.6), 3j7w-C5-C6-pentamer-1.pdb K (#14.1.7), 3j7w-C5-C6-pentamer-1.pdb
P (#14.1.8), 3j7w-C5-C6-pentamer-1.pdb Q (#14.1.9), 3j7w-C5-C6-pentamer-1.pdb
R (#14.1.10), 3j7w-C5-C6-pentamer-1.pdb S (#14.1.11),
3j7w-C5-C6-pentamer-1.pdb X (#14.1.12), 3j7w-C5-C6-pentamer-1.pdb Y
(#14.1.13), 3j7w-C5-C6-pentamer-1.pdb Z (#14.1.14), 3j7w-C5-C6-pentamer-1.pdb
a (#14.1.15) to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 38205 atoms
average map value = 0.01449, steps = 68
shifted from previous position = 2.24
rotated from previous position = 1.99 degrees
atoms outside contour = 17061, contour level = 0.01
Position of 3j7w-C5-C6-pentamer-1.pdb A (#14.1.1) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb C (#14.1.2) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb E (#14.1.3) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb H (#14.1.4) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb I (#14.1.5) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb J (#14.1.6) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb K (#14.1.7) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb P (#14.1.8) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb Q (#14.1.9) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb R (#14.1.10) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb S (#14.1.11) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb X (#14.1.12) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb Y (#14.1.13) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb Z (#14.1.14) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
Position of 3j7w-C5-C6-pentamer-1.pdb a (#14.1.15) relative to
capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
0.90332793 0.41019503 0.12545390 -213.70255761
0.39769156 -0.91048172 0.11342158 352.59308566
0.16074846 -0.05256493 -0.98559467 474.29314802
Axis -0.97548766 -0.20742292 -0.07348174
Axis point 0.00000000 209.53849569 237.03828422
Rotation angle (degrees) 175.11944738
Shift along axis 100.47643420
> select clear
> hide #!5 models
> show #!5 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> rainbow selAtoms
> color selAtoms byhetero
> show #!20 models
> hide #!5 models
> show #!5 models
> hide #!20 models
> show #!20 models
> fitmap #8 inMap #20
Fit map gp7.3-240-hp-20200116.mrc in map gp8-C12-clean.mrc using 941087 points
correlation = 0.4483, correlation about mean = 0.2246, overlap = 112.7
steps = 80, shift = 0.0626, angle = 0.0332 degrees
Position of gp7.3-240-hp-20200116.mrc (#8) relative to gp8-C12-clean.mrc (#20)
coordinates:
Matrix rotation and translation
0.40376834 -0.91486126 -0.00005871 274.40343192
-0.91486126 -0.40376833 -0.00005039 376.15301669
0.00002239 0.00007406 -0.99999999 337.58395180
Axis 0.83779012 -0.54599241 -0.00000172
Axis point 0.00000000 277.48413584 168.80089077
Rotation angle (degrees) 179.99574456
Shift along axis 24.51521272
> fitmap #8 inMap #20
Fit map gp7.3-240-hp-20200116.mrc in map gp8-C12-clean.mrc using 941087 points
correlation = 0.4483, correlation about mean = 0.2246, overlap = 112.7
steps = 116, shift = 0.0033, angle = 0.00248 degrees
Position of gp7.3-240-hp-20200116.mrc (#8) relative to gp8-C12-clean.mrc (#20)
coordinates:
Matrix rotation and translation
0.40379390 -0.91484998 -0.00002985 274.39300896
-0.91484998 -0.40379390 -0.00006641 376.15489783
0.00004870 0.00005412 -0.99999999 337.58154298
Axis 0.83779791 -0.54598046 0.00001504
Axis point 0.00000000 277.47912849 168.79667037
Rotation angle (degrees) 179.99587837
Shift along axis 24.51774041
> select clear
> hide #!5 models
> show #!5 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> ui mousemode rightMode "translate selected models"
> fitmap #8 inMap #20
Fit map gp7.3-240-hp-20200116.mrc in map gp8-C12-clean.mrc using 941087 points
correlation = 0.4483, correlation about mean = 0.2246, overlap = 112.7
steps = 80, shift = 0.00811, angle = 0.00396 degrees
Position of gp7.3-240-hp-20200116.mrc (#8) relative to gp8-C12-clean.mrc (#20)
coordinates:
Matrix rotation and translation
0.40379566 -0.91484920 -0.00009885 274.39459778
-0.91484920 -0.40379566 -0.00006929 376.15113824
0.00002347 0.00011841 -0.99999999 337.57556037
Axis 0.83779664 -0.54598240 -0.00001645
Axis point 0.00000000 277.47418119 168.80349390
Rotation angle (degrees) 179.99358198
Shift along axis 24.50941966
> select clear
> hide #!20 models
> hide #!14 models
> show #!14 models
> hide #!14.1 models
> show #!14.1 models
> hide #!11 models
> select clear
> select #14.1.6/J:236
9 atoms, 8 bonds, 1 model selected
> show selAtoms
> style selAtoms stick
Changed 9 atom styles
> style selAtoms sphere
Changed 9 atom styles
> show #!11 models
> select #14.1.6/J:236@NZ
1 atom, 1 model selected
> toolshed show Distances
> distance #5/L:204@OE2 #14.1.6/J:236@NZ
Distance between gp8-WCY-C12-coot-basedon-newdata.pdb #5/L GLU 204 OE2 and
3j7w-C5-C6-pentamer-1.pdb J #14.1.6/J LYS 236 NZ: 7.2Å
> view orient cofr false
> select #11
2 models selected
> select #14.2.14/d:204
8 atoms, 7 bonds, 1 model selected
> select #11
2 models selected
> select #11
2 models selected
> select #14.2.14/d:204
8 atoms, 7 bonds, 1 model selected
> show selAtoms
> style selAtoms sphere
Changed 8 atom styles
> hide selAtoms
> open /data/disk3/modeling/gp10/capsid-c5-res3.2-tail-vertex-new-for-capsid-
interaction.pdb
Chain information for capsid-c5-res3.2-tail-vertex-new-for-capsid-
interaction.pdb #9
---
Chain | Description
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z a b c d | No description
available
> hide #!5 models
> show #!5 models
> hide #!9 models
> show #!9 models
> matchmaker #9 to #14
Specify a single 'to' model only
> matchmaker #9 to #14.1
Specify a single 'to' model only
> select #9
76410 atoms, 77460 bonds, 1 model selected
> ui mousemode rightMode "rotate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> ui mousemode rightMode "translate selected models"
> fitmap #9 inMap #11
Fit molecule capsid-c5-res3.2-tail-vertex-new-for-capsid-interaction.pdb (#9)
to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 76410 atoms
average map value = 0.01519, steps = 104
shifted from previous position = 6.59
rotated from previous position = 3.8 degrees
atoms outside contour = 32262, contour level = 0.01
Position of capsid-c5-res3.2-tail-vertex-new-for-capsid-interaction.pdb (#9)
relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
-0.80901097 0.58779350 -0.00002886 256.46270723
-0.58779350 -0.80901098 -0.00003014 503.34416331
-0.00004107 -0.00000742 0.99999998 0.01250340
Axis 0.00001933 0.00001039 -1.00000000
Axis point 210.00598970 210.00646592 0.00000000
Rotation angle (degrees) 143.99941534
Shift along axis -0.00231776
> hide #!14 models
> hide #!14.1 models
> hide #!14.2 models
> hide selAtoms ribbons
> show selAtoms ribbons
> hide selAtoms
> hide selAtoms
> fitmap #9 inMap #11
Fit molecule capsid-c5-res3.2-tail-vertex-new-for-capsid-interaction.pdb (#9)
to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 76410 atoms
average map value = 0.01519, steps = 28
shifted from previous position = 0.0131
rotated from previous position = 0.00602 degrees
atoms outside contour = 32259, contour level = 0.01
Position of capsid-c5-res3.2-tail-vertex-new-for-capsid-interaction.pdb (#9)
relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
-0.80907275 0.58770847 -0.00002842 256.49516320
-0.58770846 -0.80907276 -0.00002908 503.33279436
-0.00004009 -0.00000683 0.99999998 0.02350935
Axis 0.00001893 0.00000993 -1.00000000
Axis point 210.00574835 210.00296007 0.00000000
Rotation angle (degrees) 144.00543769
Shift along axis -0.01365570
> ui mousemode rightMode "translate selected models"
> fitmap #9 inMap #11
Fit molecule capsid-c5-res3.2-tail-vertex-new-for-capsid-interaction.pdb (#9)
to map capsid-c5-res3.2-tail-vertex.mrc (#11) using 76410 atoms
average map value = 0.01518, steps = 52
shifted from previous position = 0.784
rotated from previous position = 0.000969 degrees
atoms outside contour = 32278, contour level = 0.01
Position of capsid-c5-res3.2-tail-vertex-new-for-capsid-interaction.pdb (#9)
relative to capsid-c5-res3.2-tail-vertex.mrc (#11) coordinates:
Matrix rotation and translation
-0.80908235 0.58769525 -0.00002979 256.50003099
-0.58769524 -0.80908236 -0.00002488 503.32712240
-0.00003873 -0.00000263 0.99999998 -0.00623959
Axis 0.00001894 0.00000761 -1.00000000
Axis point 210.00498855 210.00049120 0.00000000
Rotation angle (degrees) 144.00637347
Shift along axis 0.01492684
> hide #!9 models
> show #!9 models
> hide #!9 models
> show #!14 models
> show #!14.1 models
> show #!14.2 models
> ~select #9
Nothing selected
> hide #!11 models
> hide #!14.1.1 models
> show #!14.1.1 models
> hide #!14.1 models
> hide #!14.1.1 models
> show #!14.1.1 models
> hide #!14.1.1 models
> show #!14.1.1 models
> hide #!14.1 models
> show #!14.1 models
> hide #!14.1.1 models
> hide #!14.1.2 models
> hide #!14.1.3 models
> hide #!14.1.4 models
> hide #!14.1.5 models
> hide #!14.1.6 models
> hide #!14.1.7 models
> hide #!14.1.8 models
> hide #!14.1.9 models
> hide #!14.1.10 models
> hide #!14.1.11 models
> hide #!14.1.12 models
> hide #!14.1.13 models
> hide #!14.1.14 models
> hide #!14.1.15 models
> show #!14.1.1 models
> show #!14.1.2 models
> hide #!14.1.2 models
> hide #!14.1.1 models
> show #!14.1.1 models
> show #!14.1.3 models
> hide #!14.1.3 models
> show #!14.1.4 models
> show #!14.1.5 models
> show #!14.1.6 models
> show #!14.1.7 models
> hide #!14.1.1 models
> show #!14.1.1 models
> hide #!14.1.4 models
> show #!14.1.4 models
> hide #!14.1.4 models
> show #!14.1.4 models
> hide #!14.2 models
> show #!14.1.8 models
> hide #!14.1.8 models
> show #!14.1.8 models
> show #!14.1.9 models
> hide #!14.1.9 models
> hide #14.2.1-15 target m
> show #!14.2 models
> show #!14.2.1 models
> hide #!14.2.1 models
> show #!14.2.2 models
> hide #!14.2.2 models
> show #!14.2.2 models
> hide #!14.2.2 models
> show #!14.2.15 models
> show #!14.2.14 models
> show #!14.2.13 models
> show #!14.2.12 models
> show #!14.2.11 models
> hide #!14.2.11 models
> show #!14.2.10 models
> hide #!14.2.10 models
> show #!14.2.10 models
> show #!14.2.9 models
> hide #!14.2.9 models
> show #!14.2.9 models
> hide #!14.2.9 models
> hide #!14.2.10 models
> hide #!14.1.1 models
> show #!14.1.1 models
> hide #!14.1.1 models
> show #!14.1.1 models
> hide #!14.1.8 models
> show #!14.2.11 models
> hide #!14.2.11 models
> show #!14.2.10 models
> hide #!14.2.10 models
> show #!14.2.9 models
> hide #!14.2.9 models
> show #!14.2.9 models
> hide #!14.2.9 models
> show #!14.2.8 models
> hide #!14.2.8 models
> show #!14.2.8 models
> hide #!14.2.8 models
> show #!14.2.7 models
> hide #!14.2.7 models
> show #!14.2.6 models
> hide #!14.2.6 models
> show #!14.2.5 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.3 models
> hide #!14.2.12 models
> show #!14.2.12 models
> hide #!14.2.12 models
> show #!14.2.12 models
> hide #!14.2.5 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> show #!14.2.5 models
> show #!14.2.6 models
> show #!14.2.7 models
> show #!14.2.8 models
> hide #!14.2.8 models
> show #!14.2.9 models
> hide #!14.2.9 models
> show #!14.2.9 models
> hide #!14.2.9 models
> show #!14.2.10 models
> hide #!14.2.10 models
> show #!14.2.11 models
> hide #!14.2.11 models
> show #!14.2.1 models
> hide #!14.2.3 models
> hide #!14.2.4 models
> show #!14.2.4 models
> show #!14.2.3 models
> hide #!14.2.1 models
> show #!14.2.1 models
> hide #!14.2.1 models
> show #!14.2.1 models
> hide #!14.2.3 models
> show #!14.2.3 models
> hide #!14.2.3 models
> show #!14.2.3 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.4 models
> show #!14.2.4 models
> hide #!14.2.5 models
> show #!14.2.5 models
> hide #!14.2.6 models
> show #!14.2.6 models
> hide #!14.2.6 models
> show #!14.2.6 models
> hide #!14.2.6 models
> show #!14.2.6 models
> hide #!14.2.7 models
> show #!14.2.7 models
> hide #!14.2.7 models
> show #!14.2.7 models
> hide #!14.2.12 models
> show #!14.2.12 models
> hide #!14.2.12 models
> show #!14.2.12 models
> hide #!22 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> show selAtoms ribbons
> hide selAtoms ribbons
> color selAtoms byhetero
> preset cartoons/nucleotides cylinders/stubs
Changed 333573 atom styles
Preset expands to these ChimeraX commands:
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> rainbow selAtoms
> lighting soft
> preset cartoons/nucleotides licorice/ovals
Changed 0 atom styles
Preset expands to these ChimeraX commands:
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh default arrows f x round width 1 thick 1
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides tube/slab shape ellipsoid
> preset cartoons/nucleotides ribbons/slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> show #!5.1 models
> ~select #5
12 models selected
> select #5
49008 atoms, 49740 bonds, 1 model selected
> hide #!5 models
> hide #!5.1 models
> hide selAtoms ribbons
> show #!5 models
> style selAtoms sphere
Changed 49179 atom styles
> color selAtoms byhetero
> color selAtoms byhetero
> select clear
> lighting soft
> lighting soft
> hide selAtoms
> select clear
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> hide selAtoms ribbons
> lighting simple
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> select clear
> hide #!5 models
> show #!5 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> show selAtoms ribbons
> hide #!6.1 models
> show #!6.1 models
> hide #!6.1 models
> hide #!11.1 models
> show #!11.1 models
> hide #!11.1 models
> hide #!11 models
> hide #!14 models
> show #!14 models
> hide #!14.1 models
> hide #!14.2 models
> hide selAtoms ribbons
> hide selAtoms ribbons
> show #!14.2 models
> show #!14.1 models
> show #!12 models
> hide #!12 models
> show #!11 models
> show #!11.1 models
internal error: void QXcbWindow::setNetWmStateOnUnmappedWindow() called on
mapped window
> lighting soft
> transparency #11 90
> hide #!11.1 models
> hide #!11 models
> hide #!14 models
> show #!14 models
> hide #!5 models
> show #!5 models
> select #5
49008 atoms, 49740 bonds, 1 model selected
> hide selAtoms ribbons
> select clear
> select clear
> save image /data/disk3/Paper-use/Figure2-20200205-20.tif pixelSize 0.1
supersample 10 transparentBackground true
> hide #!14 models
> hide #!14.2 models
> show #!14.2 models
> hide #!14.1 models
> hide #!14.2 models
> show #!11 models
> show #!11.1 models
> hide #!5 models
> save image /data/disk3/Paper-use/Figure2-20200205-21.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting soft
> lighting soft
> lighting simple
> lighting full
> lighting shadows false
> lighting shadows true
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting full
> lighting soft
> save image /data/disk3/Paper-use/Figure2-20200205-21.tif pixelSize 0.1
supersample 10 transparentBackground true
> lighting soft
> lighting full
> lighting shadows false
> hide #!11 models
> show #!14 models
> show #!14.1 models
> show #!14.2 models
> show #!5 models
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 116, in exposeEvent
self.render()
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
AttributeError: 'NoneType' object has no attribute 'use_shared_context'
File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-
packages/chimerax/sideview/tool.py", line 139, in render
mvwin = self.view.render.use_shared_context(self, width, height)
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 384.130
OpenGL renderer: Quadro K2200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Change History (2)
comment:1 by , 6 years ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Graphics |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → SideVIew self.view.render is None |
comment:2 by , 6 years ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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