Session save failed: AttributeError: 'Sequence' object has no attribute 'structure'

[ciji.lim@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-10-10)
Description
I saved a large session, and now I could not open it.

Log:
UCSF ChimeraX version: 0.91 (2019-10-10)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure4.cxs" format
session

opened ChimeraX session  

> show sel atoms

> color sel green

> style sel stick

Changed 8 atom styles  

> style sel stick

Changed 8 atom styles  

> color sel byhetero

> style sel stick

Changed 12 atom styles  

> show sel atoms

> color sel green

> color sel byhetero

> show sel atoms

> color sel green

> color sel byhetero

> show sel atoms

> color sel yellow

> color sel byhetero

> show sel atoms

> color sel yellow

> color sel byhetero

> select /F:4@P

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 2 models selected  

> select up

85 atoms, 95 bonds, 2 models selected  

> hide sel atoms

> show sel atoms

> select clear

> toolshed show "Side View"

> select /F:4@P

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 2 models selected  

> select up

85 atoms, 95 bonds, 2 models selected  

> nucleotides sel fill

> style nucleic & sel stick

Changed 85 atom styles  

> select clear

> undo

> nucleotides sel slab

> style nucleic & sel stick

Changed 85 atom styles  

> nucleotides sel tube/slab shape ellipsoid

> nucleotides sel fill

> style nucleic & sel stick

Changed 85 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 85 atom styles  

> view sel

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting full

> lighting soft

> lighting flat

> lighting soft

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure4D.tif" width 1104
height 858

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure4E-1.tif" width
1104 height 858

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure4E-2.tif" width
1104 height 858

> color /A medium orchid

> select /A

7197 atoms, 7385 bonds, 9 pseudobonds, 2 models selected  

> hide sel atoms

> select clear

> color /F gold

> select /C

1264 atoms, 1292 bonds, 1 pseudobond, 2 models selected  

> show sel cartoons

> select /D

1350 atoms, 1374 bonds, 1 pseudobond, 2 models selected  

> show sel cartoons

> select /E

938 atoms, 956 bonds, 1 model selected  

> show sel cartoons

> select clear

> show sel atoms

> color sel green

> color sel hotpink

> color sel green

> show sel atoms

> color sel green

> show sel atoms

> color sel green

> select clear

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure4H.tif" width 1104
height 858

> hide #!3 models

> close #4

> show #!3 models

> lighting soft

> lighting soft

> show #!1 models

Exception ignored in: <function Framebuffer.__del__ at 0x114249170>  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 2031, in __del__  
% self.name)  
chimerax.core.graphics.opengl.OpenGLError: OpenGL framebuffer "offscreen" was
not deleted before core.graphics.Framebuffer destroyed  

> surface dust #1 size 10

> surface dust #1 size 10

> open
/Users/cijilim/Downloads/ccpem-1.3.0/W33combine_refine1_seg_monomer_smallbox/model_20191014_refinement/CTC1_143-1205-PolyA-
STN1-TEN1-DNA-Zn-coot-refine3-manual7-annotated.pdb

Summary of feedback from opening
/Users/cijilim/Downloads/ccpem-1.3.0/W33combine_refine1_seg_monomer_smallbox/model_20191014_refinement/CTC1_143-1205-PolyA-
STN1-TEN1-DNA-Zn-coot-refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 VAL A 271 ALA A 275
1 5  
Start residue of secondary structure not found: HELIX 2 2 SER A 452 ARG A 461
1 10  
Start residue of secondary structure not found: HELIX 3 3 LEU A 465 CYS A 483
1 19  
End residue of secondary structure not found: HELIX 4 4 HIS A 489 LEU A 493 1
5  
Start residue of secondary structure not found: HELIX 5 5 LEU A 503 ALA A 516
1 14  
Start residue of secondary structure not found: HELIX 6 6 HIS A 526 LEU A 530
1 5  
Start residue of secondary structure not found: HELIX 7 7 LEU A 553 SER A 567
1 15  
Start residue of secondary structure not found: HELIX 8 8 PRO A 570 LEU A 573
1 4  
Start residue of secondary structure not found: HELIX 9 9 PRO A 583 LEU A 591
1 9  
8 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 18 18 HIS A 1092 ALA A
1097 1 6  
Start residue of secondary structure not found: HELIX 19 19 PRO A 1102 GLN A
1113 1 12  
Start residue of secondary structure not found: HELIX 20 20 MET A 1141 THR A
1148 1 8  
Start residue of secondary structure not found: SHEET 4 4 4 GLN A 224 LEU A
234 0  
Start residue of secondary structure not found: SHEET 5 5 5 LEU A 237 LYS A
239 0  
Start residue of secondary structure not found: SHEET 6 6 6 TYR A 245 GLN A
265 0  
39 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #4  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> select #4

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ui mousemode rightMode "translate selected models"

> fitmap #4 inMap #1

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#4) to map
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) using 11050 atoms  
average map value = 0.2944, steps = 68  
shifted from previous position = 0.938  
rotated from previous position = 1.67 degrees  
atoms outside contour = 8418, contour level = 0.52045  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#4) relative to
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99997884 -0.00426839 0.00491000 232.45546707  
0.00412691 0.99958605 0.02847291 333.99883094  
-0.00502950 -0.02845204 0.99958251 236.07639526  
Axis -0.97486171 0.17021774 0.14377263  
Axis point 0.00000000 9165.74034511 -12409.10313256  
Rotation angle (degrees) 1.67306971  
Shift along axis -135.81808546  
  

> hide #!3 models

> close #2

> fitmap #4 inMap #1

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#4) to map
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) using 11050 atoms  
average map value = 1.281, steps = 60  
shifted from previous position = 2.48  
rotated from previous position = 1.67 degrees  
atoms outside contour = 2245, contour level = 0.52045  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#4) relative to
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999998 0.00021431 -0.00003713 227.47328764  
-0.00021430 0.99999997 0.00010016 333.09177331  
0.00003715 -0.00010016 0.99999999 239.32342779  
Axis -0.41828819 -0.15510134 -0.89497406  
Axis point 1293077.06997560 -356687.20917006 0.00000000  
Rotation angle (degrees) 0.01371968  
Shift along axis -361.00062779  
  

> ~select #4

Nothing selected  

> open
/Users/cijilim/Downloads/ccpem-1.3.0/W33combine_refine1_seg_monomer_smallbox/model_20191014_refinement/CTC1_143-1205-PolyA-
STN1-TEN1-DNA-Zn-coot-refine3-manual7-annotated.pdb

Summary of feedback from opening
/Users/cijilim/Downloads/ccpem-1.3.0/W33combine_refine1_seg_monomer_smallbox/model_20191014_refinement/CTC1_143-1205-PolyA-
STN1-TEN1-DNA-Zn-coot-refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 VAL A 271 ALA A 275
1 5  
Start residue of secondary structure not found: HELIX 2 2 SER A 452 ARG A 461
1 10  
Start residue of secondary structure not found: HELIX 3 3 LEU A 465 CYS A 483
1 19  
End residue of secondary structure not found: HELIX 4 4 HIS A 489 LEU A 493 1
5  
Start residue of secondary structure not found: HELIX 5 5 LEU A 503 ALA A 516
1 14  
Start residue of secondary structure not found: HELIX 6 6 HIS A 526 LEU A 530
1 5  
Start residue of secondary structure not found: HELIX 7 7 LEU A 553 SER A 567
1 15  
Start residue of secondary structure not found: HELIX 8 8 PRO A 570 LEU A 573
1 4  
Start residue of secondary structure not found: HELIX 9 9 PRO A 583 LEU A 591
1 9  
8 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 18 18 HIS A 1092 ALA A
1097 1 6  
Start residue of secondary structure not found: HELIX 19 19 PRO A 1102 GLN A
1113 1 12  
Start residue of secondary structure not found: HELIX 20 20 MET A 1141 THR A
1148 1 8  
Start residue of secondary structure not found: SHEET 4 4 4 GLN A 224 LEU A
234 0  
Start residue of secondary structure not found: SHEET 5 5 5 LEU A 237 LYS A
239 0  
Start residue of secondary structure not found: SHEET 6 6 6 TYR A 245 GLN A
265 0  
39 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show #!2,4 cartoons

> hide #!2,4 atoms

> select #4

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #4

Nothing selected  

> select #3

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #3

6 models selected  

> close #3

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 517, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
KeyError: <chimerax.atomic.molobject.Sequence object at 0x12e3a6450>  
  
Error processing trigger "modified":  
KeyError:  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 517, in _mmap_mod_cb  
self.disassociate(self._sseq_to_chain[match_map.struct_seq], demotion=True)  
  
See log for complete Python traceback.  
  

> select #4

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #4

Nothing selected  

> select #2

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> select #4

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> close #4

> close #2

> open
/Users/cijilim/Downloads/ccpem-1.3.0/W33combine_refine1_seg_monomer_smallbox/model_20191014_refinement/CTC1_143-1205-PolyA-
STN1-TEN1-DNA-Zn-coot-refine3-manual7-annotated.pdb

Summary of feedback from opening
/Users/cijilim/Downloads/ccpem-1.3.0/W33combine_refine1_seg_monomer_smallbox/model_20191014_refinement/CTC1_143-1205-PolyA-
STN1-TEN1-DNA-Zn-coot-refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 1 1 VAL A 271 ALA A 275
1 5  
Start residue of secondary structure not found: HELIX 2 2 SER A 452 ARG A 461
1 10  
Start residue of secondary structure not found: HELIX 3 3 LEU A 465 CYS A 483
1 19  
End residue of secondary structure not found: HELIX 4 4 HIS A 489 LEU A 493 1
5  
Start residue of secondary structure not found: HELIX 5 5 LEU A 503 ALA A 516
1 14  
Start residue of secondary structure not found: HELIX 6 6 HIS A 526 LEU A 530
1 5  
Start residue of secondary structure not found: HELIX 7 7 LEU A 553 SER A 567
1 15  
Start residue of secondary structure not found: HELIX 8 8 PRO A 570 LEU A 573
1 4  
Start residue of secondary structure not found: HELIX 9 9 PRO A 583 LEU A 591
1 9  
8 messages similar to the above omitted  
End residue of secondary structure not found: HELIX 18 18 HIS A 1092 ALA A
1097 1 6  
Start residue of secondary structure not found: HELIX 19 19 PRO A 1102 GLN A
1113 1 12  
Start residue of secondary structure not found: HELIX 20 20 MET A 1141 THR A
1148 1 8  
Start residue of secondary structure not found: SHEET 4 4 4 GLN A 224 LEU A
234 0  
Start residue of secondary structure not found: SHEET 5 5 5 LEU A 237 LYS A
239 0  
Start residue of secondary structure not found: SHEET 6 6 6 TYR A 245 GLN A
265 0  
39 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> select #2

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> select #1

2 models selected  

> select #2

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #2

Nothing selected  

> close #2

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> select #2

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> fitmap #2 inMap #1

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#2) to map
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) using 11050 atoms  
average map value = 1.281, steps = 56  
shifted from previous position = 2.46  
rotated from previous position = 0.0172 degrees  
atoms outside contour = 2240, contour level = 0.52045  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#2) relative to
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999997 0.00025025 -0.00006698 227.47329717  
-0.00025024 0.99999996 0.00015030 333.08823548  
0.00006702 -0.00015028 0.99999999 239.31602528  
Axis -0.50179330 -0.22370015 -0.83556072  
Axis point 983675.19564242 -129602.35145071 0.00000000  
Rotation angle (degrees) 0.01716004  
Shift along axis -388.61953622  
  

> ~select #2

Nothing selected  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> select #3

11050 atoms, 11316 bonds, 11 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 #3 inMap #1

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) to map
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) using 11050 atoms  
average map value = 0.1617, steps = 440  
shifted from previous position = 29.7  
rotated from previous position = 28.9 degrees  
atoms outside contour = 10575, contour level = 0.52045  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) relative to
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.45862285 -0.86534560 0.20209423 131.72019241  
0.55207477 0.45566802 0.69826936 300.77915563  
-0.69633220 -0.20867116 0.68671524 179.48592016  
Axis -0.47544492 0.47098158 0.74305348  
Axis point -60.90036102 307.01764377 0.00000000  
Rotation angle (degrees) 72.51217976  
Shift along axis 212.40338255  
  

> 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"

> ui mousemode rightMode "translate selected models"

> fitmap #3 inMap #1

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) to map
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) using 11050 atoms  
average map value = 0.1617, steps = 148  
shifted from previous position = 14.2  
rotated from previous position = 12.4 degrees  
atoms outside contour = 10467, contour level = 0.45626  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) relative to
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.30718291 -0.94030286 0.14652373 114.25255485  
0.55641417 0.30237142 0.77393462 294.90601053  
-0.77203752 -0.15621160 0.61608117 178.71237124  
Axis -0.46806136 0.46223165 0.75316696  
Axis point -31.87964958 253.23077269 0.00000000  
Rotation angle (degrees) 83.52222787  
Shift along axis 217.43794021  
  

> fitmap #3 inMap #1

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) to map
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) using 11050 atoms  
average map value = 0.1643, steps = 308  
shifted from previous position = 15.9  
rotated from previous position = 16.5 degrees  
atoms outside contour = 10521, contour level = 0.45626  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) relative to
cryosparc_P43_J356_009_volume_map_sharp.mrc (#1) coordinates:  
Matrix rotation and translation  
0.15919467 -0.98559603 0.05707471 101.07721180  
0.75723825 0.15899476 0.63349104 281.73912349  
-0.63344084 -0.05762924 0.77164213 195.25680552  
Axis -0.34590924 0.34560657 0.87229748  
Axis point -31.44003540 211.05543723 0.00000000  
Rotation angle (degrees) 87.42564926  
Shift along axis 232.72936917  
  

> open
/Users/cijilim/Downloads/W33_seg_masks/cryosparc_P43_J356_009_volume_map.mrc

Opened cryosparc_P43_J356_009_volume_map.mrc, grid size 400,400,400, pixel
1.08, shown at level 0.222, step 2, values float32  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #3 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.2738, steps = 2000  
shifted from previous position = 11.8  
rotated from previous position = 15 degrees  
atoms outside contour = 9951, contour level = 0.45607  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#3) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.30182691 -0.95336178 -0.00135408 106.96874403  
0.95328579 0.30182029 -0.01227681 262.32000328  
0.01211293 0.00241465 0.99992372 238.80408928  
Axis 0.00770497 -0.00706280 0.99994537  
Axis point -127.68419292 203.78670892 0.00000000  
Rotation angle (degrees) 72.43512637  
Shift along axis 237.76252173  
  

> fitmap #2 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#2) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.6698, steps = 40  
shifted from previous position = 0.0171  
rotated from previous position = 0.00866 degrees  
atoms outside contour = 3421, contour level = 0.45607  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#2) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.99999999 0.00014110 -0.00002692 227.45592966  
-0.00014109 0.99999999 0.00005360 333.10238808  
0.00002693 -0.00005360 1.00000000 239.31483186  
Axis -0.34961338 -0.17562341 -0.92028632  
Axis point 1914974.96697796 -724215.15802853 0.00000000  
Rotation angle (degrees) 0.00878437  
Shift along axis -358.26037821  
  

> ~select #3

Nothing selected  

> close #1

> hide #!4 models

> show #!4 models

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> select #1

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ui mousemode rightMode "translate selected models"

> lighting flat

> 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"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #1 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#1) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.3949, steps = 224  
shifted from previous position = 9.05  
rotated from previous position = 19.5 degrees  
atoms outside contour = 8333, contour level = 0.49077  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#1) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.32717698 -0.94475647 -0.01975971 108.31427764  
-0.94475626 -0.32747132 0.01407659 166.69773846  
-0.01976968 0.01406257 -0.99970566 192.66817198  
Axis -0.81459246 0.57990752 0.01209965  
Axis point 0.00000000 121.90378814 97.13809239  
Rotation angle (degrees) 179.99950711  
Shift along axis 10.76849664  
  

> ~select #1

Nothing selected  

> hide #!4 models

> show #!4 models

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #5  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> select #5

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> show sel cartoons

> hide sel atoms

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> surface dust #4 size 10

> 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 "translate selected models"

> fitmap #5 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#5) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.3001, steps = 216  
shifted from previous position = 6.38  
rotated from previous position = 19.6 degrees  
atoms outside contour = 10162, contour level = 0.58618  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#5) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
0.30831819 0.95115952 0.01534448 331.85629453  
-0.95126992 0.30835926 -0.00032799 240.46344898  
-0.00504359 -0.01449562 0.99988221 238.23506592  
Axis -0.00744649 0.01071595 -0.99991486  
Axis point 332.15982035 -105.48631256 0.00000000  
Rotation angle (degrees) 72.04440420  
Shift along axis -238.10915276  
  

> ~select #5

Nothing selected  

> hide #!4 models

> lighting soft

> show #!4 models

> lighting flat

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #6  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show atoms

> hide atoms

> show cartoons

> select #6

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #6 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.1543, steps = 596  
shifted from previous position = 35.2  
rotated from previous position = 21.5 degrees  
atoms outside contour = 10943, contour level = 0.58618  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.69541373 -0.50780696 -0.50846027 118.46579942  
-0.38865505 0.86092506 -0.32826102 295.80525182  
0.60443941 -0.03066156 -0.79606085 225.89549567  
Axis 0.25696136 -0.96092991 0.10288136  
Axis point 57.35067404 0.00000000 158.28055299  
Rotation angle (degrees) 144.61453797  
Shift along axis -230.56654415  
  

> 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 #6 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.1734, steps = 312  
shifted from previous position = 30.6  
rotated from previous position = 35.8 degrees  
atoms outside contour = 10853, contour level = 0.58618  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.65117442 0.27368956 -0.70786009 168.58398127  
0.73470943 0.46108278 -0.49759896 356.76045847  
0.19019445 -0.84409519 -0.50132761 136.17249897  
Axis -0.32465150 -0.84143701 0.43195504  
Axis point -29.90191226 0.00000000 172.10641624  
Rotation angle (degrees) 147.74804633  
Shift along axis -296.10210083  
  

> 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 #6 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.1511, steps = 296  
shifted from previous position = 22.8  
rotated from previous position = 26.3 degrees  
atoms outside contour = 10905, contour level = 0.58618  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.87307713 0.20863882 -0.44068829 163.13607954  
0.41501003 0.79241193 -0.44704587 355.09663198  
0.25593554 -0.57319559 -0.77842394 160.88366148  
Axis -0.17106912 -0.94467774 0.27985590  
Axis point 24.13456081 0.00000000 144.03120090  
Rotation angle (degrees) 158.36393216  
Shift along axis -318.33518650  
  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #6 inMap #4

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) to map
cryosparc_P43_J356_009_volume_map.mrc (#4) using 11050 atoms  
average map value = 0.255, steps = 1856  
shifted from previous position = 30.6  
rotated from previous position = 32.4 degrees  
atoms outside contour = 10578, contour level = 0.53414  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#6) relative to
cryosparc_P43_J356_009_volume_map.mrc (#4) coordinates:  
Matrix rotation and translation  
-0.80488595 -0.59334531 -0.00999768 136.07478842  
-0.59342906 0.80474972 0.01482686 303.39066062  
-0.00075182 0.01786684 -0.99984010 194.68923199  
Axis 0.31233269 -0.94993382 -0.00860428  
Axis point 117.66730642 0.00000000 96.24383300  
Rotation angle (degrees) 179.72116444  
Shift along axis -247.37560363  
  

> ~select #6

Nothing selected  

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5.cxs"

> lighting soft

> select #1

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #1

Nothing selected  

> select #3

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> select #2

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> select #3

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #3

Nothing selected  

> select #3

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #3

Nothing selected  

> select #3

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #3

Nothing selected  

> select #4

2 models selected  

> ~select #4

Nothing selected  

> select #2

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> color #2 cyan

> ~select #2

Nothing selected  

> select #3

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #3

Nothing selected  

> color #3 green

> color #3 lime

> color #3 spring green

> color #3 green

> color #3 lime green

> select #6

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #6

Nothing selected  

> select #6

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ~select #6

Nothing selected  

> color #6 lime green

> select #1

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> color #1 hotpink

> ~select #1

Nothing selected  

> select #5

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> color #5 purple

> color #5 dark orchid

> ~select #5

Nothing selected  

> surface dust #4 size 15

> lighting flat

> lighting flat

> lighting soft

> graphics silhouettes false

> graphics silhouettes true

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5.cxs" includeMaps
true

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5A.tif" width 1104
height 858

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5.cxs" includeMaps
true

> open /Users/cijilim/Downloads/W33_seg_masks/postprocess_masked.mrc

Opened postprocess_masked.mrc, grid size 400,400,400, pixel 1.08, shown at
level 0.0114, step 2, values float32  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> select #8

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> lighting flat

> lighting flat

> graphics silhouettes false

> graphics silhouettes true

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #8 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#8) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.00593, steps = 268  
shifted from previous position = 9.97  
rotated from previous position = 19.6 degrees  
atoms outside contour = 9979, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#8) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.80205326 -0.46307018 0.37719567 202.91658389  
-0.53555678 -0.83716979 0.11102114 77.03552641  
0.26436624 -0.29105456 -0.91945513 195.90970250  
Axis -0.94862515 0.26620071 -0.17101905  
Axis point 0.00000000 76.07082627 72.22173577  
Rotation angle (degrees) 167.76478512  
Shift along axis -205.48915418  
  

> hide #!7 models

> show #!7 models

> ui mousemode rightMode "translate selected models"

> fitmap #8 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#8) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.02296, steps = 296  
shifted from previous position = 2.38  
rotated from previous position = 39.3 degrees  
atoms outside contour = 5986, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#8) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.99998809 0.00339856 -0.00350310 227.62171352  
0.00334649 -0.99988541 -0.01476410 97.29903748  
-0.00355288 0.01475220 -0.99988487 193.35026091  
Axis 0.99999702 0.00168636 -0.00176409  
Axis point 0.00000000 47.74269549 97.23349905  
Rotation angle (degrees) 179.15438714  
Shift along axis 227.44402880  
  

> ~select #8

Nothing selected  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> hide atoms

> show cartoons

> select #9

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> fitmap #9 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#9) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.02299, steps = 220  
shifted from previous position = 11.3  
rotated from previous position = 14.5 degrees  
atoms outside contour = 5977, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#9) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.80692613 -0.59062038 -0.00614998 136.33325160  
0.59064298 -0.80681072 -0.01404867 126.97745938  
0.00333556 -0.01496868 0.99988241 237.82028893  
Axis -0.00077881 -0.00802973 0.99996746  
Axis point 47.19464272 86.75683324 0.00000000  
Rotation angle (degrees) 143.79678885  
Shift along axis 236.68677700  
  

> ~select #9

Nothing selected  

> hide #!4 models

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #10  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> select #10

11050 atoms, 11316 bonds, 11 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 "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #10 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#10) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.008568, steps = 240  
shifted from previous position = 5.39  
rotated from previous position = 24.5 degrees  
atoms outside contour = 9478, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#10) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.34385035 0.93863993 0.02687020 332.88982129  
0.93902420 -0.34373085 -0.00909166 184.69036832  
0.00070232 0.02835794 -0.99959759 190.47241544  
Axis 0.81968432 0.57275377 0.00841064  
Axis point 0.00000000 -25.26303010 93.29770825  
Rotation angle (degrees) 178.69102597  
Shift along axis 380.24866557  
  

> ui mousemode rightMode "translate selected models"

> fitmap #10 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#10) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.008513, steps = 60  
shifted from previous position = 0.603  
rotated from previous position = 1.94 degrees  
atoms outside contour = 9495, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#10) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.33200278 0.94327300 -0.00319378 331.87984156  
0.94327805 -0.33200370 0.00025186 190.01786328  
-0.00082277 -0.00309624 -0.99999487 187.49941116  
Axis -0.81608873 -0.57792531 0.00123097  
Axis point 0.00000000 -22.38576067 94.01875815  
Rotation angle (degrees) 179.88246836  
Shift along axis -380.42872566  
  

> fitmap #10 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#10) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.02295, steps = 120  
shifted from previous position = 2.92  
rotated from previous position = 1.89 degrees  
atoms outside contour = 5965, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#10) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
0.30578042 0.95201333 0.01299830 331.82375976  
0.95209585 -0.30570061 -0.00778654 190.48384055  
-0.00343930 0.01475660 -0.99988520 193.35622045  
Axis 0.80800579 0.58916712 0.00295782  
Axis point 0.00000000 -26.56444881 95.92427715  
Rotation angle (degrees) 179.20070585  
Shift along axis 380.91424705  
  

> ~select #10

Nothing selected  

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5_10merDock.cxs"
includeMaps true

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #11  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show atoms

> hide atoms

> show cartoons

> ui mousemode rightMode "translate selected models"

> select #11

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #11 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#11) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.02294, steps = 168  
shifted from previous position = 7.21  
rotated from previous position = 11.4 degrees  
atoms outside contour = 5983, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#11) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.81104616 0.58487066 0.01142078 275.39401646  
-0.58497197 -0.81099266 -0.00993471 112.84086007  
0.00345165 -0.01473834 0.99988543 237.83378393  
Axis -0.00410609 0.00681192 -0.99996837  
Axis point 155.69393063 12.91379897 0.00000000  
Rotation angle (degrees) 144.20126121  
Shift along axis -238.18839058  
  

> ~select #11

Nothing selected  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb"

Summary of feedback from opening /Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb  
---  
warnings | Ignored bad PDB record found on line 123  
ALLOWED : 12.56 %  
  
Ignored bad PDB record found on line 124  
CIS-PROLINE : 1.08695652174  
  
Ignored bad PDB record found on line 125  
CIS-GENERAL : 0.0776397515528  
  
Ignored bad PDB record found on line 126  
FAVORED : 87.37 %  
  
Ignored bad PDB record found on line 127  
OUTLIERS : 0.07 %  
  
16 messages similar to the above omitted  
  
Chain information for CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb #12  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
  

> show cartoons

> hide atoms

> select #12

11050 atoms, 11316 bonds, 11 pseudobonds, 2 models selected  

> ui mousemode rightMode "rotate selected models"

> ui mousemode rightMode "translate selected models"

> fitmap #12 inMap #7

Fit molecule CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#12) to map postprocess_masked.mrc (#7) using
11050 atoms  
average map value = 0.02294, steps = 156  
shifted from previous position = 5.25  
rotated from previous position = 12.7 degrees  
atoms outside contour = 5986, contour level = 0.019669  
  
Position of CTC1_143-1205-PolyA-STN1-TEN1-DNA-Zn-coot-
refine3-manual7-annotated.pdb (#12) relative to postprocess_masked.mrc (#7)
coordinates:  
Matrix rotation and translation  
-0.81105436 0.58485906 0.01143289 275.39277853  
0.58496112 0.81099841 0.01010252 318.36829400  
-0.00336351 0.01488149 -0.99988361 193.38730451  
Axis 0.30734206 0.95157647 0.00656392  
Axis point 86.67257830 0.00000000 95.27720853  
Rotation angle (degrees) 179.55453936  
Shift along axis 388.86093853  
  

> ~select #12

Nothing selected  

> hide #!7 models

> color /A medium purple

> color /A medium orchid

> color /B medium orchid

> color /C steel blue

> color /D cyan

> color /E coral

> color /F gold

> select /F

850 atoms, 950 bonds, 10 models selected  

> hide sel cartoons

> hide sel cartoons

> show sel atoms

> select clear

> lighting soft

> graphics silhouettes false

> lighting full

> lighting soft

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting simple

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> color /A medium orchid

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5_10merDock.cxs"
includeMaps true

> color /A orchid

> color /B orchid

> color /C light steel blue

> color /C deep sky blue

> color /E orange

> color /E orange red

> color /E dark orange

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5B.tif" width 1104
height 858

> turn z 90

> turn z 90

> turn x 90

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5C.tif" width 1104
height 858

> color /F yellow

> color /F yellow

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5C.tif" width 1104
height 858

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5_10merDock.cxs"
includeMaps true

> open /Users/cijilim/Downloads/TTAGGGX3_BDNA.pdb

Chain information for TTAGGGX3_BDNA.pdb #13  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> select #13

738 atoms, 826 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 "rotate selected models"

> ui mousemode rightMode "translate selected models"

> ui mousemode rightMode "rotate selected models"

> ~select #13

Nothing selected  

> save image "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5C.tif" width 1104
height 858

> save session "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5_10merDock.cxs"
includeMaps true

> close session

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 653, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 601, in restore_snapshot  
inst._finalize_init(data['alignment'])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 787, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1601, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2243, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2193, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2133, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2071, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2071, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 653, in restore  
obj = sm.restore_snapshot(self, data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 601, in restore_snapshot  
inst._finalize_init(data['alignment'])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 174, in _finalize_init  
self.seq_canvas = SeqCanvas(parent, self, self.alignment)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 184, in __init__  
self.layout_alignment()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 787, in layout_alignment  
self.label_width, self.font_pixels, self.numbering_widths, self.letter_gaps())  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 1601, in __init__  
self.layout_lines(alignment.seqs, self.normal_label_color)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2243, in layout_lines  
self._layout_line(line, label_color, bli, end)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2193, in _layout_line  
font=self._label_font(line))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2133, in _label_font  
if self.has_associated_structures(line):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2071, in
has_associated_structures  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/seq_canvas.py", line 2071, in <listcomp>  
and [chain for chain in line.match_maps.keys() if not
chain.structure.deleted]:  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 39, in _getattr_  
return look_in_class._attr_registration.get_attr(attr_name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/atomic/attr_registration.py", line 67, in get_attr  
raise AttributeError("'%s' object has no attribute '%s'" %
(self.class_.__name__, attr_name)) from None  
AttributeError: 'Sequence' object has no attribute 'structure'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 599, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 649, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 489, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 445, in open_data  
models, status = open_func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 883, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 659, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5_10merDock.cxs"

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 622, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 622, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 599, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]))  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 649, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 489, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 445, in open_data  
models, status = open_func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 883, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 659, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  

> open "/Users/cijilim/Desktop/Telomere_work/PPT/CST
collaborations/Manuscript/SCIENCE_submission/Figures/Figure5_10merDock.cxs"
format session

Unable to restore session, resetting.  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 622, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 622, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 571, in customEvent  
func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 338, in defer  
cxcmd(session, topic)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 459, in cxcmd  
run(session, cmd)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 68, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 649, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 489, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 445, in open_data  
models, status = open_func(*args, **kw)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 883, in open  
session.restore(stream, path=path, resize_window=resize_window)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 659, in restore  
self.reset()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/session.py", line 466, in reset  
sm.reset_state(container, self)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/manager.py", line 263, in reset_state  
alignment._destroy()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 494, in _destroy  
self._notify_observers("destroyed", None)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seqalign/alignment.py", line 531, in _notify_observers  
recipient.alignment_notification(note_name, note_data)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 460, in alignment_notification  
self.delete()  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
AttributeError: 'SequenceViewer' object has no attribute 'region_browser'  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/seq-view/tool.py", line 490, in delete  
self.region_browser.destroy()  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.11.20
OpenGL renderer: AMD Radeon Pro Vega 20 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[pett]

Tom, when done dealing with the framebuffer error to whatever extent you intend to, please reassign this ticket to me so I can deal with the sequence error.

--Eric

[Tom Goddard]

The warning about an offscreen Framebuffer not being deleted was probably caused by closing side view. I have fixed the bug so that offscreen Framebuffer is properly deleted. This is not related to the session save error.

[pett]

Sequence-to-chain information wasn't being saved in the session. Now it is. Fix available in next daily build.

[ciji.lim@…]

Thanks so much!! Greatly appreciate this!

Have a good weekend!

Best,
CJ

On 10/18/19, 2:55 PM, "ChimeraX" <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote:

    #2505: Session save failed: AttributeError: 'Sequence' object has no attribute
    'structure'
    ---------------------------------+----------------------------
              Reporter:  ciji.lim@…  |      Owner:  Eric Pettersen
                  Type:  defect      |     Status:  closed
              Priority:  normal      |  Milestone:
             Component:  Sequence    |    Version:
            Resolution:  fixed       |   Keywords:
            Blocked By:              |   Blocking:
    Notify when closed:              |   Platform:  all
               Project:  ChimeraX    |
    ---------------------------------+----------------------------
    Changes (by Eric Pettersen):
    
     * status:  assigned => closed
     * resolution:   => fixed
    
    
    Comment:
    
     Sequence-to-chain information wasn't being saved in the session.  Now it
     is.  Fix available in next daily build.
    
    --
    Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2505#comment:3>
    ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
    ChimeraX Issue Tracker