Opened 22 months ago

Closed 22 months ago

#14440 closed defect (limitation)

Tried to add model but parent does not exist

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-13.4.1-arm64-arm-64bit
ChimeraX Version: 1.6rc202303292224 (2023-03-29 22:24:14 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6rc202303292224 (2023-03-29)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/SUNCHENG/zt/run_it200_class001.mrc

Opened run_it200_class001.mrc as #1, grid size 78,78,78, pixel 3.14, shown at
level 0.0423, step 1, values float32  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> molmap #1 30

No atoms specified  

> volume #1 level 0.08305

> ui mousemode right "tape measure"

> marker segment #2 position 123.1,163,128.8 toPosition 111.3,124.8,135.8
> color yellow radius 0.785 label 40.59 labelHeight 4.059 labelColor yellow

> marker segment #2 position 131.2,88.17,91.81 toPosition 107.5,114.1,142.9
> color yellow radius 0.785 label 62.02 labelHeight 6.202 labelColor yellow

> marker delete #2

> marker segment #2 position 110.7,139,130.6 toPosition 113,121.3,142.7 color
> yellow radius 0.785 label 21.57 labelHeight 2.157 labelColor yellow

> marker delete #2

> volume #1 level 0.0964

> volume #1 level 0.07193

> marker segment #2 position 147.2,80.12,97.52 toPosition 117.1,109.4,153.1
> color yellow radius 0.785 label 69.68 labelHeight 6.968 labelColor yellow

> marker segment #2 position 147.8,159.9,135.9 toPosition 129,123.2,145.4
> color yellow radius 0.785 label 42.3 labelHeight 4.23 labelColor yellow

> marker delete #2

> marker segment #2 position 138.6,164.4,137.8 toPosition 132.4,120.9,142.1
> color yellow radius 0.785 label 44.14 labelHeight 4.414 labelColor yellow

> marker segment #2 position 118,114.6,149.7 toPosition 144.8,77.47,97.91
> color yellow radius 0.785 label 69.13 labelHeight 6.913 labelColor yellow

> marker delete #2

> marker segment #2 position 139.2,164.5,136.8 toPosition 134.4,121.7,140.2
> color yellow radius 0.785 label 43.21 labelHeight 4.321 labelColor yellow

> marker segment #2 position 119,113.2,150.2 toPosition 145.1,78.05,97.05
> color yellow radius 0.785 label 68.83 labelHeight 6.883 labelColor yellow

> marker delete #2

> open "/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
> structure/em-change-B7H7/B7H7-monomer-V9-2.pdb"
> "/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
> structure/em-change-B7H7/B7H7-D2D3-monomer-V9.pdb"
> "/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
> structure/em-change-B7H7/B7H7-D1-monomer-V9.pdb"

Chain information for B7H7-monomer-V9-2.pdb #2  
---  
Chain | Description  
E | No description available  
F | No description available  
  
Chain information for B7H7-D2D3-monomer-V9.pdb #3  
---  
Chain | Description  
E | No description available  
  
Chain information for B7H7-D1-monomer-V9.pdb #4  
---  
Chain | Description  
F | No description available  
  

> hide #4 models

> show #4 models

> hide #3 models

> hide #2 models

> hide #4 models

> show #4 models

> hide #4 models

> show #3 models

> hide #3 models

> show #2 models

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  
Drag select of 61 residues  
Drag select of 40 residues  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

[Repeated 1 time(s)]

> ui mousemode right select

[Repeated 1 time(s)]

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0, steps = 24  
shifted from previous position = 0  
rotated from previous position = 0 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
1.00000000 0.00000000 0.00000000 0.00000000  
0.00000000 1.00000000 0.00000000 0.00000000  
0.00000000 0.00000000 1.00000000 0.00000000  
Axis 0.00000000 0.00000000 1.00000000  
Axis point 0.00000000 0.00000000 0.00000000  
Rotation angle (degrees) 0.00000000  
Shift along axis 0.00000000  
  

> hide #!1 models

> show #!1 models

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> hide #!1 models

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> show #!1 models

> view matrix models
> #1,1,0,0,67.943,0,1,0,32.118,0,0,1,39.159,#2,1,0,0,67.943,0,1,0,32.118,0,0,1,39.159

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #3

3076 atoms, 3112 bonds, 196 residues, 1 model selected  

> select subtract #3

Nothing selected  

> select add #4

1662 atoms, 1680 bonds, 103 residues, 1 model selected  

> select add #1

1662 atoms, 1680 bonds, 103 residues, 3 models selected  

> select subtract #4

2 models selected  

> select add #3

3076 atoms, 3112 bonds, 196 residues, 3 models selected  

> select subtract #3

2 models selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> view matrix models
> #1,1,0,0,106.15,0,1,0,-6.9464,0,0,1,17.024,#2,1,0,0,106.15,0,1,0,-6.9464,0,0,1,17.024

> ui mousemode right translate

> ui mousemode right rotate

> ui mousemode right translate

> ui mousemode right zoom

> ui mousemode right "move picked models"

> ui mousemode right "translate selected atoms"

> ui mousemode right "move picked models"

> ui mousemode right "rotate selected models"

> ui mousemode right "translate selected models"

> ui mousemode right pivot

[Repeated 2 time(s)]

> ui mousemode right "move picked models"

[Repeated 1 time(s)]

> ui mousemode right "rotate selected models"

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  
Drag select of 20 residues  
Drag select of 5 residues  

> view matrix models
> #2,0.9314,0.25493,0.25984,100.27,-0.29437,0.94739,0.1257,-16.312,-0.21412,-0.19356,0.95744,12.362

> view matrix models
> #2,0.95344,0.019691,0.30095,93.889,-0.14039,0.91213,0.38511,-25.896,-0.26692,-0.40943,0.87242,10.685

> view matrix models
> #2,0.86184,-0.090846,0.49898,82.558,0.30054,0.88397,-0.35815,8.3393,-0.40855,0.45863,0.78914,30.823

> view matrix models
> #2,0.97543,0.067014,-0.20985,115.8,-0.021231,0.97677,0.21323,-16.294,0.21927,-0.20354,0.9542,16.949

> ui mousemode right "translate selected models"

> view matrix models
> #2,0.97543,0.067014,-0.20985,160.21,-0.021231,0.97677,0.21323,22.671,0.21927,-0.20354,0.9542,42.049

> view matrix models
> #2,0.97543,0.067014,-0.20985,174.26,-0.021231,0.97677,0.21323,41.196,0.21927,-0.20354,0.9542,46.987

> view matrix models
> #2,0.97543,0.067014,-0.20985,186.09,-0.021231,0.97677,0.21323,92.065,0.21927,-0.20354,0.9542,68.426

> view matrix models
> #2,0.97543,0.067014,-0.20985,198.49,-0.021231,0.97677,0.21323,105.66,0.21927,-0.20354,0.9542,85.433

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0.01546, steps = 128  
shifted from previous position = 11.8  
rotated from previous position = 83 degrees  
atoms outside contour = 4767, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.26549510 -0.91230654 0.31178379 40.22502533  
0.94340909 0.31249193 0.11103187 122.86276409  
-0.19872502 0.26466125 0.94364336 78.65730093  
Axis 0.07956866 0.26440582 0.96112350  
Axis point -46.62741224 71.92564627 0.00000000  
Rotation angle (degrees) 74.88156148  
Shift along axis 111.28566231  
  

> view matrix models
> #2,0.2655,-0.91231,0.31178,206.26,0.94341,0.31249,0.11103,120.61,-0.19873,0.26466,0.94364,115.1

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0.1664, steps = 368  
shifted from previous position = 3.95  
rotated from previous position = 162 degrees  
atoms outside contour = 390, contour level = 0.071927  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.11635088 0.81202156 -0.57191211 166.78254804  
0.33453327 0.57421719 0.74723631 106.60414286  
0.93517376 -0.10438203 -0.33845890 145.63641140  
Axis -0.47425290 -0.83927250 -0.26590574  
Axis point 19.65553582 0.00000000 81.36033397  
Rotation angle (degrees) 116.12278742  
Shift along axis -207.29259026  
  

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select add #1

4767 atoms, 4821 bonds, 301 residues, 3 models selected  

> select subtract #1

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select subtract #2

Nothing selected  

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> show #!1 models

> transparency 50

> set bgColor white

> set bgColor gray

> set bgColor white

> transparency 0

> transparency 50

> color #1 #97bfbcff models

> color #1 #aebfb6ff models

> color #1 #b2a9bfff models

> color #1 #bdbfb9ff models

> color #1 #babbbfff models

> color #1 #a1afbfff models

> transparency 50

> volume #1 level 0.1127

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0.1664, steps = 44  
shifted from previous position = 0.0142  
rotated from previous position = 0.241 degrees  
atoms outside contour = 1034, contour level = 0.11272  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.12008637 0.81273277 -0.57012692 166.69966577  
0.33483090 0.57379104 0.74743034 106.57991207  
0.93459485 -0.10113991 -0.34103253 145.80128832  
Axis -0.47343040 -0.83950743 -0.26662881  
Axis point 19.82358765 0.00000000 81.32846696  
Rotation angle (degrees) 116.33788919  
Shift along axis -207.27014235  
  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0.1664, steps = 48  
shifted from previous position = 0.0186  
rotated from previous position = 0.108 degrees  
atoms outside contour = 1032, contour level = 0.11272  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.12109409 0.81352086 -0.56878822 166.66326512  
0.33466550 0.57291615 0.74817517 106.52614791  
0.93452406 -0.09975420 -0.34163412 145.83655385  
Axis -0.47339823 -0.83929793 -0.26734453  
Axis point 19.90260985 0.00000000 81.25698122  
Rotation angle (degrees) 116.41732664  
Shift along axis -207.29387497  
  

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> view matrix models
> #2,-0.12109,0.81352,-0.56879,273.23,0.33467,0.57292,0.74818,99.428,0.93452,-0.099754,-0.34163,161.75

> ui mousemode right "rotate selected models"

> view matrix models
> #2,-0.75617,0.60888,0.23975,229.36,0.47325,0.25582,0.84296,90.402,0.45193,0.75088,-0.4816,180.15

> view matrix models
> #2,-0.57461,0.75053,-0.32639,257.21,0.19235,0.51147,0.8375,92.986,0.7955,0.41846,-0.43825,175.09

> view matrix models
> #2,-0.7686,0.29899,0.56556,209.51,0.5969,0.017157,0.80213,88.356,0.23013,0.9541,-0.19166,170.31

> ui mousemode right "translate selected models"

> view matrix models
> #2,-0.7686,0.29899,0.56556,212.22,0.5969,0.017157,0.80213,85.778,0.23013,0.9541,-0.19166,166.93

> view matrix models
> #2,-0.7686,0.29899,0.56556,213.25,0.5969,0.017157,0.80213,86.092,0.23013,0.9541,-0.19166,169.57

> fitmap #2 inMap #1

Fit molecule B7H7-monomer-V9-2.pdb (#2) to map run_it200_class001.mrc (#1)
using 4767 atoms  
average map value = 0.1664, steps = 220  
shifted from previous position = 4.35  
rotated from previous position = 89.3 degrees  
atoms outside contour = 1034, contour level = 0.11272  
  
Position of B7H7-monomer-V9-2.pdb (#2) relative to run_it200_class001.mrc (#1)
coordinates:  
Matrix rotation and translation  
-0.12628569 0.81530247 -0.56509628 166.47772636  
0.33378404 0.57136479 0.74975362 106.42752549  
0.93415209 -0.09393696 -0.34429015 146.02204786  
Axis -0.47227098 -0.83923124 -0.26953860  
Axis point 20.19899548 0.00000000 81.09561692  
Rotation angle (degrees) 116.71837793  
Shift along axis -207.29848053  
  

> ui mousemode right "pick blobs"

> measure blob #!1.1 triangleNumber 1695 color #0000ccff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #872bd4ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #c1a422ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #45f12fff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #e27509ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #9bab6cff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #15fe09ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #6db68eff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #bf5d8dff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #7d11ddff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #86ac85ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #c15390ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #3486d3ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #bea908ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #4df30dff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1688 color #a764a5ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> transparency 50

> measure blob #!1.1 triangleNumber 1889 color #88d038ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2090 color #53c290ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2090 color #3bd67eff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2091 color #b351a2ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2091 color #f73623ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2091 color #2d8fcfff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2091 color #da801dff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 2091 color #14f543ff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> measure blob #!1.1 triangleNumber 1912 color #92c1baff outline true

Surface run_it200_class001.mrc #1.1 blob:  
volume = 58303  
area = 9649.7  
size = 92.08 52.622 35.302  
  

> transparency 0

> transparency 50

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> color #1 darkgrey models

> select subtract #2

Nothing selected  

> select add #2

4767 atoms, 4821 bonds, 301 residues, 1 model selected  

> select subtract #2

Nothing selected  

> volume #1 level 0.1517

> volume #1 level 0.112

> save "/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
> structure/em-change-B7H7/B7H7-EM-3D-initial model-monomer-V9.cxs"

> open "/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
> structure/em-change-B7H7/B7H7-EM-3D-initial model-monomer-V9.cxs" format
> session

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 614, in restore_snapshot  
m.add([model], _from_session=True)  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 760, in _parent_for_added_model  
raise ValueError('Tried to add model %s but parent #%s does not exist'  
ValueError: Tried to add model blob outline box #1.2 but parent #1 does not
exist  
  
opened ChimeraX session  

> open "/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
> structure/em-change-B7H7/B7H7-EM-3D-initial model-monomer-V9.cxs" format
> session

Error opening map
"/Users/sujin/Desktop/ZhouTing/CD28H/structure/figures/20231221-EM
structure/em-change-B7H7/B7H7-EM-3D-initial model-monomer-V9.cxs": File
B7H7-EM-3D-initial model-monomer-V9.cxs, format mrc  
MRC header value nsymbt (1953787962) is invalid  
  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeSurface" returned None  

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 614, in restore_snapshot  
m.add([model], _from_session=True)  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 699, in add  
p = self._parent_for_added_model(model, parent, root_model = root_model)  
File
"/Applications/ChimeraX-1.6-rc2023.03.29.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/models.py", line 760, in _parent_for_added_model  
raise ValueError('Tried to add model %s but parent #%s does not exist'  
ValueError: Tried to add model blob outline box #1.2 but parent #1 does not
exist  
  
opened ChimeraX session  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: Z16S00027CH/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 16 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 8422.121.1

Software:

    System Software Overview:

      System Version: macOS 13.4.1 (c) (22F770820d)
      Kernel Version: Darwin 22.5.0
      Time since boot: 5天12小时40分钟

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9
    ChimeraX-AddH: 2.2.4
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6rc202303292224
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.2
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.6
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.2.22
    imagesize: 1.4.1
    importlib-metadata: 6.1.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.2.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    zipp: 3.15.0

Change History (2)

comment:1 by Eric Pettersen, 22 months ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Tried to add model but parent does not exist

comment:2 by Tom Goddard, 22 months ago

Resolution: → limitation
Status: assigned → closed

The user saved a session with a volume where a blob outline box had been drawn which is a child of the volume model. When the restored the session the volume data file was missing and they did not provide a new location for the file. So the session restore code does not restore the volume. Then later when it tries to restore the blob outline model, it has no parent and produces an error.

I could try to fix this, but it has never been reported before, so I do not think it is worth the trouble. If it is reported by another user I will reconsider.

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