Volume Viewer: wrapped C/C++ object of type QScrollArea has been deleted

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_chopped_fitting_J99_zflip.cxs"

Opened P598_J99_009_sharp_zflip.mrc as #1, grid size 384,384,384, pixel 0.833,
shown at level 0.075, step 1, values float32  
Log from Wed Jun 14 15:16:48 2023 Startup Messages  
---  
warning | Custom presets folder 'ui tool show "Model Panel"' does not exist  
note | Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database.json  
  

> set bgColor white

> ~display atoms

> display cart

UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/P598_J99_009_sharp_zflip.mrc"

Opened P598_J99_009_sharp_zflip.mrc as #1, grid size 384,384,384, pixel 0.833,
shown at level 0.0294, step 2, values float32  

> surface dust #1 size 8.33

> transparency 50

> volume #1 step 1

> volume #1 level 0.05756

> volume #1 level 0.07823

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_P.pdb"

Chain information for 6pzk_P.pdb #2  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> ui tool show "Model Panel"

> fitmap #2 inMap #1

Fit molecule 6pzk_P.pdb (#2) to map P598_J99_009_sharp_zflip.mrc (#1) using
2047 atoms  
average map value = 0.09362, steps = 96  
shifted from previous position = 2.07  
rotated from previous position = 3.59 degrees  
atoms outside contour = 973, contour level = 0.078232  
  
Position of 6pzk_P.pdb (#2) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99846252 -0.01995447 0.05171466 -8.22910664  
0.01844648 0.99939530 0.02947489 -9.51881104  
-0.05227154 -0.02847562 0.99822684 13.85662991  
Axis -0.46329247 0.83133049 0.30700115  
Axis point 258.57746175 0.00000000 165.44019588  
Rotation angle (degrees) 3.58573502  
Shift along axis 0.15320667  
  

> volume #1 level 0.08462

> select add #2

2047 atoms, 2050 bonds, 1 pseudobond, 263 residues, 2 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #2,0.98262,-0.12038,0.14129,-5.2203,0.11152,0.99136,0.069066,-30.117,-0.14838,-0.052109,0.98756,34.972

> fitmap #2 inMap #1

Fit molecule 6pzk_P.pdb (#2) to map P598_J99_009_sharp_zflip.mrc (#1) using
2047 atoms  
average map value = 0.09362, steps = 104  
shifted from previous position = 0.824  
rotated from previous position = 7.96 degrees  
atoms outside contour = 1047, contour level = 0.084616  
  
Position of 6pzk_P.pdb (#2) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99846374 -0.01992833 0.05170133 -8.23237541  
0.01841684 0.99939367 0.02954857 -9.52545793  
-0.05225884 -0.02855100 0.99822535 13.86627719  
Axis -0.46437131 0.83092051 0.30648067  
Axis point 258.79312816 0.00000000 165.50261969  
Rotation angle (degrees) 3.58660720  
Shift along axis 0.15772657  
  

> view matrix models
> #2,0.98977,-0.07966,0.1184,-9.073,0.070307,0.99422,0.081183,-26.433,-0.12418,-0.072028,0.98964,34.23

> fitmap #2 inMap #1

Fit molecule 6pzk_P.pdb (#2) to map P598_J99_009_sharp_zflip.mrc (#1) using
2047 atoms  
average map value = 0.09362, steps = 84  
shifted from previous position = 0.848  
rotated from previous position = 5.82 degrees  
atoms outside contour = 1050, contour level = 0.084616  
  
Position of 6pzk_P.pdb (#2) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99846479 -0.02009669 0.05161567 -8.19402584  
0.01860094 0.99939766 0.02929728 -9.50265915  
-0.05217336 -0.02829220 0.99823719 13.79629889  
Axis -0.46128871 0.83134459 0.30996598  
Axis point 257.92800331 0.00000000 165.02625161  
Rotation angle (degrees) 3.57886596  
Shift along axis 0.15621061  
  

> view matrix models
> #2,0.99872,-0.05063,0.00085048,6.5543,0.050623,0.99869,0.0072363,-10.254,-0.0012157,-0.007184,0.99997,1.8567

> fitmap #2 inMap #1

Fit molecule 6pzk_P.pdb (#2) to map P598_J99_009_sharp_zflip.mrc (#1) using
2047 atoms  
average map value = 0.09362, steps = 76  
shifted from previous position = 0.719  
rotated from previous position = 3.65 degrees  
atoms outside contour = 1049, contour level = 0.084616  
  
Position of 6pzk_P.pdb (#2) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99846619 -0.01987640 0.05167403 -8.23701579  
0.01836885 0.99939636 0.02948722 -9.50683402  
-0.05222894 -0.02849280 0.99822858 13.85079298  
Axis -0.46391130 0.83135123 0.30600887  
Axis point 258.65947012 0.00000000 165.67880841  
Rotation angle (degrees) 3.58277167  
Shift along axis 0.15619200  
  

> volume #1 level 0.07504

> fitmap #2 inMap #1

Fit molecule 6pzk_P.pdb (#2) to map P598_J99_009_sharp_zflip.mrc (#1) using
2047 atoms  
average map value = 0.09362, steps = 36  
shifted from previous position = 0.00939  
rotated from previous position = 0.0121 degrees  
atoms outside contour = 923, contour level = 0.07504  
  
Position of 6pzk_P.pdb (#2) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99845769 -0.02005674 0.05176841 -8.22378020  
0.01854900 0.99939435 0.02944253 -9.51998387  
-0.05232758 -0.02843687 0.99822501 13.85066377  
Axis -0.46227546 0.83140145 0.30833915  
Axis point 258.16208841 0.00000000 165.14264741  
Rotation angle (degrees) 3.58921879  
Shift along axis 0.15742535  
  

> view matrix models
> #2,0.9935,0.019496,0.11215,-25.596,-0.026018,0.99804,0.056988,-7.4788,-0.11082,-0.059536,0.99206,29.525

> fitmap #2 inMap #1

Fit molecule 6pzk_P.pdb (#2) to map P598_J99_009_sharp_zflip.mrc (#1) using
2047 atoms  
average map value = 0.09361, steps = 76  
shifted from previous position = 0.889  
rotated from previous position = 4.51 degrees  
atoms outside contour = 926, contour level = 0.07504  
  
Position of 6pzk_P.pdb (#2) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99845612 -0.01998843 0.05182503 -8.24794109  
0.01847868 0.99939546 0.02944909 -9.51325237  
-0.05238234 -0.02844597 0.99822188 13.87231962  
Axis -0.46218932 0.83191091 0.30709163  
Axis point 258.28618412 -0.00000000 165.43503483  
Rotation angle (degrees) 3.59086075  
Shift along axis 0.15800510  
  

> select subtract #2

Nothing selected  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_1-446.pdb"

Chain information for 6pzk_1-446.pdb #3  
---  
Chain | Description  
A | No description available  
  

> select add #3

3187 atoms, 3247 bonds, 1 pseudobond, 390 residues, 2 models selected  

> view matrix models
> #3,0.96689,0.16938,0.19089,-51.516,-0.17603,0.98421,0.018329,27.077,-0.18477,-0.051324,0.98144,39.836

> fitmap #3 inMap #1

Fit molecule 6pzk_1-446.pdb (#3) to map P598_J99_009_sharp_zflip.mrc (#1)
using 3187 atoms  
average map value = 0.09712, steps = 412  
shifted from previous position = 1.83  
rotated from previous position = 14.5 degrees  
atoms outside contour = 1480, contour level = 0.07504  
  
Position of 6pzk_1-446.pdb (#3) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99944866 -0.01900994 0.02722137 -1.86102815  
0.01861999 0.99972137 0.01450795 -5.35906770  
-0.02748958 -0.01399309 0.99952414 6.42703477  
Axis -0.39441965 0.75713284 0.52075234  
Axis point 232.09681902 0.00000000 72.72837968  
Rotation angle (degrees) 2.07056737  
Shift along axis 0.02339329  
  

> volume #1 level 0.08781

> fitmap #3 inMap #1

Fit molecule 6pzk_1-446.pdb (#3) to map P598_J99_009_sharp_zflip.mrc (#1)
using 3187 atoms  
average map value = 0.09713, steps = 40  
shifted from previous position = 0.0528  
rotated from previous position = 0.0829 degrees  
atoms outside contour = 1637, contour level = 0.087808  
  
Position of 6pzk_1-446.pdb (#3) relative to P598_J99_009_sharp_zflip.mrc (#1)
coordinates:  
Matrix rotation and translation  
0.99940952 -0.02036612 0.02767362 -1.72235022  
0.01996309 0.99969172 0.01476268 -5.62695941  
-0.02796574 -0.01420151 0.99950800 6.53991222  
Axis -0.38840142 0.74610760 0.54080291  
Axis point 232.52993397 0.00000000 67.09497681  
Rotation angle (degrees) 2.13684970  
Shift along axis 0.00744964  
  

> select subtract #3

Nothing selected  

> volume #1 color #b2b2b264

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_447_826.pdb"

Chain information for 6pzk_447_826.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select add #4

2752 atoms, 2820 bonds, 2 pseudobonds, 333 residues, 2 models selected  

> view matrix models
> #4,0.99069,-0.11625,0.070886,8.7768,0.11827,0.99266,-0.025081,-12.714,-0.067451,0.033231,0.99717,5.3173

> fitmap #4 inMap #1

Fit molecule 6pzk_447_826.pdb (#4) to map P598_J99_009_sharp_zflip.mrc (#1)
using 2752 atoms  
average map value = 0.07821, steps = 56  
shifted from previous position = 1.1  
rotated from previous position = 3.66 degrees  
atoms outside contour = 1623, contour level = 0.087808  
  
Position of 6pzk_447_826.pdb (#4) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99169992 -0.10226938 0.07792465 5.53956895  
0.09975154 0.99437688 0.03555638 -19.79073689  
-0.08112279 -0.02748815 0.99632499 17.99991790  
Axis -0.23814452 0.60078609 0.76311419  
Axis point 203.76335024 38.85585839 0.00000000  
Rotation angle (degrees) 7.60634249  
Shift along axis 0.52677531  
  

> select subtract #4

Nothing selected  

> volume #1 level 0.09738

> volume #1 level 0.091

> volume #1 level 0.08142

> fitmap #4 inMap #1

Fit molecule 6pzk_447_826.pdb (#4) to map P598_J99_009_sharp_zflip.mrc (#1)
using 2752 atoms  
average map value = 0.0782, steps = 36  
shifted from previous position = 0.0155  
rotated from previous position = 0.022 degrees  
atoms outside contour = 1542, contour level = 0.081424  
  
Position of 6pzk_447_826.pdb (#4) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99173842 -0.10212078 0.07762896 5.57474980  
0.09959622 0.99438604 0.03573514 -19.80432760  
-0.08084245 -0.02770836 0.99634168 17.98617770  
Axis -0.24008898 0.59970280 0.76335695  
Axis point 204.15981354 39.28335626 0.00000000  
Rotation angle (degrees) 7.59240264  
Shift along axis 0.51472696  
  

> select add #4

2752 atoms, 2820 bonds, 2 pseudobonds, 333 residues, 2 models selected  

> view matrix models
> #4,0.99203,-0.11594,0.049307,12.975,0.11392,0.9926,0.042062,-22.865,-0.053819,-0.03611,0.9979,14.935

> fitmap #4 inMap #1

Fit molecule 6pzk_447_826.pdb (#4) to map P598_J99_009_sharp_zflip.mrc (#1)
using 2752 atoms  
average map value = 0.07822, steps = 52  
shifted from previous position = 0.221  
rotated from previous position = 1.8 degrees  
atoms outside contour = 1546, contour level = 0.081424  
  
Position of 6pzk_447_826.pdb (#4) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99165162 -0.10314500 0.07738327 5.81763513  
0.10067395 0.99429688 0.03519193 -19.84252373  
-0.08057182 -0.02710766 0.99638013 17.83543021  
Axis -0.23484508 0.59542893 0.76831776  
Axis point 202.51949719 41.19993040 0.00000000  
Rotation angle (degrees) 7.62216025  
Shift along axis 0.52222224  
  

> volume #1 level 0.07185

> graphics silhouettes true

> select subtract #4

Nothing selected  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_823-901.pdb"

Chain information for 6pzk_823-901.pdb #5  
---  
Chain | Description  
A | No description available  
  

> volume #1 level 0.08302

> volume #1 level 0.07664

> volume #1 level 0.07504

> select add #5

653 atoms, 667 bonds, 81 residues, 1 model selected  

> view matrix models
> #5,0.99457,0.085906,0.058776,-23.032,-0.08787,0.99563,0.031673,8.0472,-0.055798,-0.036666,0.99777,14.363

> ui mousemode right "translate selected models"

> view matrix models
> #5,0.99457,0.085906,0.058776,-23.273,-0.08787,0.99563,0.031673,7.7941,-0.055798,-0.036666,0.99777,12.874

> fitmap #5 inMap #1

Fit molecule 6pzk_823-901.pdb (#5) to map P598_J99_009_sharp_zflip.mrc (#1)
using 653 atoms  
average map value = 0.1004, steps = 72  
shifted from previous position = 4.87  
rotated from previous position = 2.65 degrees  
atoms outside contour = 273, contour level = 0.07504  
  
Position of 6pzk_823-901.pdb (#5) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99723266 0.04060431 0.06227617 -12.85094157  
-0.04231537 0.99875528 0.02640660 4.07800710  
-0.06112643 -0.02896876 0.99770956 14.41506688  
Axis -0.34903766 0.77782172 -0.52265292  
Axis point 228.79122981 0.00000000 215.82947084  
Rotation angle (degrees) 4.54981150  
Shift along axis 0.12334828  
  

> fitmap #5 inMap #1

Fit molecule 6pzk_823-901.pdb (#5) to map P598_J99_009_sharp_zflip.mrc (#1)
using 653 atoms  
average map value = 0.1004, steps = 28  
shifted from previous position = 0.0141  
rotated from previous position = 0.0301 degrees  
atoms outside contour = 272, contour level = 0.07504  
  
Position of 6pzk_823-901.pdb (#5) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99724023 0.04091346 0.06195175 -12.85761474  
-0.04263109 0.99873508 0.02666158 4.09541563  
-0.06078257 -0.02922907 0.99772298 14.40295666  
Axis -0.35230750 0.77365768 -0.52662437  
Axis point 229.80634238 0.00000000 217.13507978  
Rotation angle (degrees) 4.54952770  
Shift along axis 0.11333596  
  

> view matrix models
> #5,0.99724,0.040913,0.061952,-12.749,-0.042631,0.99874,0.026662,4.2563,-0.060783,-0.029229,0.99772,14.516

> fitmap #5 inMap #1

Fit molecule 6pzk_823-901.pdb (#5) to map P598_J99_009_sharp_zflip.mrc (#1)
using 653 atoms  
average map value = 0.1004, steps = 48  
shifted from previous position = 0.224  
rotated from previous position = 0.0138 degrees  
atoms outside contour = 272, contour level = 0.07504  
  
Position of 6pzk_823-901.pdb (#5) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99723671 0.04074174 0.06212134 -12.86084378  
-0.04246458 0.99874196 0.02666953 4.07586333  
-0.06095663 -0.02923379 0.99771222 14.42669230  
Axis -0.35218121 0.77536971 -0.52418528  
Axis point 229.64059960 0.00000000 216.52050313  
Rotation angle (degrees) 4.55219787  
Shift along axis 0.12738871  
  

> select subtract #5

Nothing selected  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_902-1131.pdb"

Chain information for 6pzk_902-1131.pdb #6  
---  
Chain | Description  
A | No description available  
  

> select add #6

1867 atoms, 1907 bonds, 229 residues, 1 model selected  

> view matrix models #6,1,0,0,0.65125,0,1,0,-0.29488,0,0,1,-0.30814

> view matrix models #6,1,0,0,2.2232,0,1,0,-1.6061,0,0,1,0.82454

> fitmap #5 inMap #1

Fit molecule 6pzk_823-901.pdb (#5) to map P598_J99_009_sharp_zflip.mrc (#1)
using 653 atoms  
average map value = 0.1004, steps = 28  
shifted from previous position = 0.0222  
rotated from previous position = 0.0312 degrees  
atoms outside contour = 273, contour level = 0.07504  
  
Position of 6pzk_823-901.pdb (#5) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99722649 0.04042198 0.06249309 -12.85642294  
-0.04214182 0.99876143 0.02645132 4.04469875  
-0.06134648 -0.02901153 0.99769481 14.45539511  
Axis -0.34918121 0.77966519 -0.51980254  
Axis point 228.64177769 0.00000000 215.15329451  
Rotation angle (degrees) 4.55513783  
Shift along axis 0.12878097  
  

> fitmap #6 inMap #1

Fit molecule 6pzk_902-1131.pdb (#6) to map P598_J99_009_sharp_zflip.mrc (#1)
using 1867 atoms  
average map value = 0.0988, steps = 72  
shifted from previous position = 3.61  
rotated from previous position = 0.217 degrees  
atoms outside contour = 791, contour level = 0.07504  
  
Position of 6pzk_902-1131.pdb (#6) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99999323 0.00260320 -0.00260218 3.89097387  
-0.00260551 0.99999621 -0.00088507 2.09879729  
0.00259987 0.00089184 0.99999622 -0.26110127  
Axis 0.23463972 -0.68692616 -0.68780568  
Axis point 715.68450468 -1524.29675129 0.00000000  
Rotation angle (degrees) 0.21694937  
Shift along axis -0.34915480  
  

> select subtract #6

Nothing selected  

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_823-901.pdb"

Chain information for 6pzk_823-901.pdb #7  
---  
Chain | Description  
A | No description available  
  

> close #7

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_1132-1456.pdb"

Chain information for 6pzk_1132-1456.pdb #7  
---  
Chain | Description  
A | No description available  
  

> select add #7

2647 atoms, 2695 bonds, 328 residues, 1 model selected  

> view matrix models #7,1,0,0,3.1718,0,1,0,-2.3531,0,0,1,0.19095

> ui mousemode right "rotate selected models"

> view matrix models
> #7,0.99758,0.030818,0.062272,-10.876,-0.034163,0.99799,0.053391,-5.4729,-0.060501,-0.05539,0.99663,17.812

> fitmap #7 inMap #1

Fit molecule 6pzk_1132-1456.pdb (#7) to map P598_J99_009_sharp_zflip.mrc (#1)
using 2647 atoms  
average map value = 0.08445, steps = 92  
shifted from previous position = 5.19  
rotated from previous position = 4.02 degrees  
atoms outside contour = 1339, contour level = 0.07504  
  
Position of 6pzk_1132-1456.pdb (#7) relative to P598_J99_009_sharp_zflip.mrc
(#1) coordinates:  
Matrix rotation and translation  
0.99883643 0.04584026 0.01498194 -3.09679288  
-0.04589414 0.99894095 0.00327263 8.86071398  
-0.01481605 -0.00395640 0.99988241 3.53918113  
Axis -0.07473934 0.30807490 -0.94842179  
Axis point 194.03541147 73.12612186 0.00000000  
Rotation angle (degrees) 2.77199714  
Shift along axis -0.39542068  
  

> select subtract #7

Nothing selected  

> volume #1 level 0.06387

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_P.pdb"

Chain information for 6pzk_P.pdb #8  
---  
Chain | Description  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> close #8

> hide #!1 models

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk.pdb"

Chain information for 6pzk.pdb #8  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide atoms

> show cartoons

> color #8 #6367fa transparency 0

> hide #!8 models

> show #!1 models

> show #!8 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/zhouling95/Desktop/movie37.mp4

Movie saved to /Users/zhouling95/Desktop/movie37.mp4  
  

> show #!1 models

> hide #!8 models

> volume #1 level 0.06546

> volume #1 level 0.06706

> volume #1 level 0.07344

> volume #1 level 0.07504

> volume #1 color #e4e4e464

> set bgColor black

> volume #1 color #e4e4e463

> set bgColor white

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/zhouling95/Desktop/movie38.mp4

Movie saved to /Users/zhouling95/Desktop/movie38.mp4  
  

Populating font family aliases took 422 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_chopped_fitting_J99_zflip.cxs" includeMaps true

> hide #!1 models

> show #!1 models

> hide #!1 models

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_P_docked.pdb" models #2 relModel #1

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_1-446_docked.pdb" models #3 relModel #1

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_447_826_docked.pdb" models #4 relModel #1

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_823-901_docked.pdb" models #5 relModel #1

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_902-1131_docked.pdb" models #6 relModel #1

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_1132-1456_docked.pdb" models #7 relModel #1

> hide #!2 models

> hide #!3 models

> hide #!4 models

> hide #5 models

> hide #6 models

> hide #7 models

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_J99_docked.pdb"

Chain information for 6pzk_J99_docked.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide #!9 atoms

> show #!9 cartoons

> show #!1 models

> show #!8 models

> hide #!1 models

> movie record supersample 3

> wait 100

> morph #8,9

Computed 51 frame morph #10  

> coordset #10 1,51

> wait 100

> movie encode LingMorph.mp4 quality high

Movie saved to LingMorph.mp4  
  

> hide #!10 models

> show #!9 models

> show #!8 models

> hide #!8 models

> hide #!9 models

> show #!9 models

> close #9

> open "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_J99_docked-coot_merge.pdb"

Chain information for 6pzk_J99_docked-coot_merge.pdb #9  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
  

> hide #!9 atoms

> show #!9 cartoons

> show #!10 models

> hide #!10 models

> close #10

> show #!8 models

> color #9 #f2c456 transparency 0

> movie record supersample 3

> wait 100

> morph #10,9

Require at least 2 structures for morph  

> wait 100

> movie encode LingMorph.mp4 quality high

Movie saved to LingMorph.mp4  
  

> hide #!9 models

> show #!9 models

> movie record supersample 3

> wait 100

> morph #9,8

Computed 51 frame morph #10  

> coordset #10 1,51

> wait 100

> movie encode LingMorph.mp4 quality high

Movie saved to LingMorph.mp4  
  

> movie record supersample 3

> wait 100

> morph #8,9

Computed 51 frame morph #11  

> coordset #11 1,51

> wait 100

> movie encode LingMorph.mp4 quality high

Movie saved to LingMorph.mp4  
  

> hide #!10 models

> hide #!11 models

> show #!11 models

> show #!10 models

> hide #!10 models

> hide #!11 models

> show #!11 models

> movie record supersample 3

> wait 100

> morph #8,9

Computed 51 frame morph #12  

> coordset #12 1,51

> wait 100

> movie encode LingMorph.mp4 quality high

Movie saved to LingMorph.mp4  
  

> hide #!12 models

> hide #!11 models

> movie record supersample 3

> wait 50

> morph #8,9

Computed 51 frame morph #13  

> coordset #13 1,51

> wait 50

> movie encode LingMorph.mp4 quality high

Movie saved to LingMorph.mp4  
  

> movie record supersample 3

> wait 50

> morph #8,9

Computed 51 frame morph #14  

> coordset #14 1,51

> wait 100

> movie encode LingMorph2.mp4 quality high

Movie saved to LingMorph2.mp4  
  

> close #10-14

> show #!9 models

> save "/Users/zhouling95/Documents/00 Academic/03 McLellan Lab/2023/02 RSV
> Polymerase/6pzk_chopped_fitting_J99_zflip.cxs" includeMaps true

——— End of log from Wed Jun 14 15:16:48 2023 ———

opened ChimeraX session  
Traceback (most recent call last):  
File
"/Users/zhouling95/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in <lambda>  
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))  
RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted  
  

Populating font family aliases took 367 ms. Replace uses of missing font
family ".AppleSystemUIFont" with one that exists to avoid this cost.  

RuntimeError: wrapped C/C++ object of type QScrollArea has been deleted  
  
File
"/Users/zhouling95/Desktop/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/map/volume_viewer.py", line 1530, in  
QTimer.singleShot(200, lambda f=f: f.setMinimumHeight(50))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-20.5.7
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645
OpenGL vendor: Intel Inc.

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,3
      Processor Name: Quad-Core Intel Core i7
      Processor Speed: 1.7 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1968.100.17.0.0 (iBridge: 20.16.4252.0.0,0)
      OS Loader Version: 577~129

Software:

    System Software Overview:

      System Version: macOS 13.3 (22E252)
      Kernel Version: Darwin 22.4.0
      Time since boot: 41 days, 4 hours, 59 minutes

Graphics/Displays:

    Intel Iris Plus Graphics 645:

      Chipset Model: Intel Iris Plus Graphics 645
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea6
      Revision ID: 0x0001
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        LG ULTRAGEAR:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 202NTCZHP955
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7.59


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2021.10.8
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.0
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0