Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-25-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.dev202306232350 (2023-06-23 23:50:16 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f010e0eab80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 112 in save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 90 in provider_save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/cmd.py", line 75 in cmd_save
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2897 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 38 in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 51 in display
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 127 in show_save_file_dialog
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/save_command/dialog.py", line 116 in 
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 893 in init
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1044 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, psutil._psutil_linux, psutil._psutil_posix, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.dssp._dssp, chimerax.mmcif.mmcif_write (total: 53)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.dev202306232350 (2023-06-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/dell/Desktop/cage58/cryosparc_P20_J563_map_sharp (1).mrc"

Opened cryosparc_P20_J563_map_sharp (1).mrc as #1, grid size 440,440,440,
pixel 0.93, shown at level 0.000704, step 2, values float32  

> open /home/dell/Desktop/cage58/30_012345.pdb

Summary of feedback from opening /home/dell/Desktop/cage58/30_012345.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 1 1 GLU3b 2
GLU3b 36 1 35  
Start residue of secondary structure not found: HELIX 2 2 ALA3b 64 GLU3b 67 1
4  
Start residue of secondary structure not found: HELIX 3 3 PRO3b 69 SER3b 83 1
15  
Start residue of secondary structure not found: HELIX 4 4 GLU3a 2 GLU3a 36 1
35  
Start residue of secondary structure not found: HELIX 5 5 ALA3a 64 GLU3a 67 1
4  
205 messages similar to the above omitted  
  
Chain information for 30_012345.pdb  
---  
Chain | Description  
2.4/0a 2.4/0b 2.4/0c 2.4/0d 2.4/0e 2.6/1a 2.6/1b 2.6/1c 2.6/1d 2.6/1e 2.5/2a
2.5/2b 2.5/2c 2.5/2d 2.5/2e 2.1/3a 2.1/3b 2.1/3c 2.1/3d 2.1/3e 2.3/4a 2.3/4b
2.3/4c 2.3/4d 2.3/4e 2.2/5a 2.2/5b 2.2/5c 2.2/5d 2.2/5e | No description
available  
  

> volume #1 step 1

> volume #1 level 0.1594

> transparency 50

> hide atoms

> show cartoons

> color bypolymer

> ui tool show "Fit in Map"

> fitmap #2.6 inMap #1

Fit molecule 30_012345.pdb (#2.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3671, steps = 48  
shifted from previous position = 0.00781  
rotated from previous position = 0.0232 degrees  
atoms outside contour = 1392, contour level = 0.15943  
  
Position of 30_012345.pdb (#2.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999994 0.00002258 -0.00033899 0.05974135  
-0.00002250 0.99999998 0.00021972 -0.03493768  
0.00033899 -0.00021971 0.99999992 -0.01841819  
Axis -0.54305041 -0.83785016 -0.05570788  
Axis point 54.72617967 0.00000000 172.79109197  
Rotation angle (degrees) 0.02318154  
Shift along axis -0.00214399  
  

> fitmap #2.5 inMap #1

Fit molecule 30_012345.pdb (#2.5) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3606, steps = 48  
shifted from previous position = 0.0056  
rotated from previous position = 0.0225 degrees  
atoms outside contour = 1407, contour level = 0.15943  
  
Position of 30_012345.pdb (#2.5) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999993 0.00037788 0.00008102 -0.11303525  
-0.00037789 0.99999993 0.00007198 0.06178273  
-0.00008099 -0.00007201 0.99999999 0.03048225  
Axis -0.18313464 0.20605844 -0.96125003  
Axis point 161.18380669 297.15740200 0.00000000  
Rotation angle (degrees) 0.02252410  
Shift along axis 0.00413046  
  

> fitmap #2.4 inMap #1

Fit molecule 30_012345.pdb (#2.4) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3727, steps = 48  
shifted from previous position = 0.00394  
rotated from previous position = 0.0184 degrees  
atoms outside contour = 1382, contour level = 0.15943  
  
Position of 30_012345.pdb (#2.4) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999999 -0.00017182 0.00000482 0.03220426  
0.00017183 0.99999995 -0.00027028 0.01648358  
-0.00000477 0.00027028 0.99999996 -0.05505578  
Axis 0.84381152 0.01496104 0.53643106  
Axis point 0.00000000 199.51264064 61.06584874  
Rotation angle (degrees) 0.01835244  
Shift along axis -0.00211270  
  

> select add #2.2

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models #2.2,1,0,0,0.60827,0,1,0,0.3224,0,0,1,3.1275

> fitmap #2.2 inMap #1

Fit molecule 30_012345.pdb (#2.2) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1487, steps = 64  
shifted from previous position = 1.84  
rotated from previous position = 3.65 degrees  
atoms outside contour = 2917, contour level = 0.15943  
  
Position of 30_012345.pdb (#2.2) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99797766 -0.01144788 0.06252626 -9.29053548  
0.01119885 0.99992791 0.00433186 -2.48032264  
-0.06257134 -0.00362288 0.99803392 20.70445730  
Axis -0.06244908 0.98208507 0.17778925  
Axis point 320.76963715 0.00000000 157.13797685  
Rotation angle (degrees) 3.65162839  
Shift along axis 1.82532751  
  

> view matrix models
> #2.2,0.99798,-0.011448,0.062526,-10.665,0.011199,0.99993,0.0043319,-3.2786,-0.062571,-0.0036229,0.99803,18.211

> view matrix models
> #2.2,0.99798,-0.011448,0.062526,-8.0753,0.011199,0.99993,0.0043319,-2.0687,-0.062571,-0.0036229,0.99803,19.441

> fitmap #2.2 inMap #1

Fit molecule 30_012345.pdb (#2.2) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3655, steps = 80  
shifted from previous position = 0.913  
rotated from previous position = 4.19 degrees  
atoms outside contour = 1382, contour level = 0.15943  
  
Position of 30_012345.pdb (#2.2) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99374301 0.01704887 0.11038192 -19.88877626  
-0.02253522 0.99856173 0.04864809 -2.17605494  
-0.10939377 -0.05083118 0.99269794 38.00380358  
Axis -0.40692223 0.89899740 -0.16191963  
Axis point 334.08375905 0.00000000 199.18033788  
Rotation angle (degrees) 7.02103757  
Shift along axis -0.01664460  
  

> select subtract #2.2

Nothing selected  

> info

9 models  
#1, cryosparc_P20_J563_map_sharp (1).mrc, shown size 440,440,440, step 1,
voxel size 0.93, level 0.1594, value range -0.002022 - 1.6352, value type
float32, 0 symmetry operators  
#1.1, surface, shown, 981732 triangles  
#2, 30_012345.pdb group, shown  
#2.1, 30_012345.pdb, shown  
4185 atoms, 4280 bonds, 495 residues, 5 chains (3b,3a,3c,3d,3e)  
#2.2, 30_012345.pdb, shown  
4185 atoms, 4280 bonds, 495 residues, 5 chains (5b,5a,5c,5d,5e)  
#2.3, 30_012345.pdb, shown  
4185 atoms, 4280 bonds, 495 residues, 5 chains (4b,4a,4c,4d,4e)  
#2.4, 30_012345.pdb, shown  
4185 atoms, 4280 bonds, 495 residues, 5 chains (0b,0a,0c,0d,0e)  
#2.5, 30_012345.pdb, shown  
4185 atoms, 4280 bonds, 495 residues, 5 chains (2b,2a,2c,2d,2e)  
#2.6, 30_012345.pdb, shown  
4185 atoms, 4280 bonds, 495 residues, 5 chains (1b,1a,1c,1d,1e)  

> dssp

> save /home/dell/Desktop/cage58/30_0.12345.cif relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> close #2

> open /home/dell/Desktop/cage58/30_0.12345.cif

Summary of feedback from opening /home/dell/Desktop/cage58/30_0.12345.cif  
---  
warnings | Unknown polymer entity '1' near line 5651  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 14252  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 22853  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 31454  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 40055  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 30_0.12345.cif  
---  
Chain | Description  
2.4/0a 2.4/0b 2.4/0c 2.4/0d 2.4/0e 2.6/1a 2.6/1b 2.6/1c 2.6/1d 2.6/1e 2.5/2a
2.5/2b 2.5/2c 2.5/2d 2.5/2e 2.1/3a 2.1/3b 2.1/3c 2.1/3d 2.1/3e 2.3/4a 2.3/4b
2.3/4c 2.3/4d 2.3/4e 2.2/5a 2.2/5b 2.2/5c 2.2/5d 2.2/5e | No description
available  
  

> open /home/dell/Desktop/cage58/30_0.12345.cif

Summary of feedback from opening /home/dell/Desktop/cage58/30_0.12345.cif  
---  
warnings | Unknown polymer entity '1' near line 5651  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 14252  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 22853  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 31454  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 40055  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 30_0.12345.cif  
---  
Chain | Description  
3.4/0a 3.4/0b 3.4/0c 3.4/0d 3.4/0e 3.6/1a 3.6/1b 3.6/1c 3.6/1d 3.6/1e 3.5/2a
3.5/2b 3.5/2c 3.5/2d 3.5/2e 3.1/3a 3.1/3b 3.1/3c 3.1/3d 3.1/3e 3.3/4a 3.3/4b
3.3/4c 3.3/4d 3.3/4e 3.2/5a 3.2/5b 3.2/5c 3.2/5d 3.2/5e | No description
available  
  

> color bypolymer

> select add #3

25110 atoms, 25680 bonds, 2970 residues, 7 models selected  

> hide sel atoms

> show sel cartoons

> select add #2

50220 atoms, 51360 bonds, 5940 residues, 14 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #2

25110 atoms, 25680 bonds, 2970 residues, 7 models selected  

> ui mousemode right "translate selected models"

> view matrix models #3,1,0,0,-57.369,0,1,0,-35.316,0,0,1,29.85

> view matrix models #3,1,0,0,-74.673,0,1,0,-16.177,0,0,1,16.704

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.57373,0.46732,-0.67264,327.72,-0.80522,-0.47206,0.35885,397.81,-0.14983,0.74751,0.64714,-31.354

> view matrix models
> #3,-0.73631,0.40088,-0.54511,354.33,-0.67501,-0.49117,0.55056,331.18,-0.047027,0.77334,0.63225,-57.85

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.73631,0.40088,-0.54511,314.52,-0.67501,-0.49117,0.55056,384.13,-0.047027,0.77334,0.63225,-21.814

> view matrix models
> #3,-0.73631,0.40088,-0.54511,352.78,-0.67501,-0.49117,0.55056,329.14,-0.047027,0.77334,0.63225,-26.391

> view matrix models
> #3,-0.73631,0.40088,-0.54511,352.94,-0.67501,-0.49117,0.55056,329.45,-0.047027,0.77334,0.63225,-25.973

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.79357,0.4173,-0.44285,342.22,-0.58144,-0.73461,0.34969,399.38,-0.17939,0.53499,0.82559,16.072

> view matrix models
> #3,-0.66309,0.74219,0.097309,136.27,-0.6313,-0.62433,0.46008,367.39,0.40222,0.24364,0.88253,-74.511

> view matrix models
> #3,-0.66162,0.74962,0.018022,149.41,-0.56697,-0.51584,0.64223,295.68,0.49072,0.41469,0.7663,-108.18

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.66162,0.74962,0.018022,210.84,-0.56697,-0.51584,0.64223,342.4,0.49072,0.41469,0.7663,-127.06

> view matrix models
> #3,-0.66162,0.74962,0.018022,167.76,-0.56697,-0.51584,0.64223,288.2,0.49072,0.41469,0.7663,-140.83

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.99519,-0.086005,-0.046891,434.1,0.090726,-0.98977,-0.11015,387.88,-0.036937,-0.11387,0.99281,46.316

> ui mousemode right "translate selected models"

> view matrix models
> #3,-0.99519,-0.086005,-0.046891,433.96,0.090726,-0.98977,-0.11015,389.73,-0.036937,-0.11387,0.99281,49.635

> view matrix models
> #3,-0.99519,-0.086005,-0.046891,415.9,0.090726,-0.98977,-0.11015,415.26,-0.036937,-0.11387,0.99281,29.853

> view matrix models
> #3,-0.99519,-0.086005,-0.046891,431.02,0.090726,-0.98977,-0.11015,408.81,-0.036937,-0.11387,0.99281,29.853

> view matrix models
> #3,-0.99519,-0.086005,-0.046891,426.54,0.090726,-0.98977,-0.11015,407.08,-0.036937,-0.11387,0.99281,24.96

> ui mousemode right "rotate selected models"

> view matrix models
> #3,-0.9967,-0.062373,-0.051855,423.1,0.064324,-0.99725,-0.036841,399.51,-0.049414,-0.040055,0.99797,11.738

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1111, steps = 96  
shifted from previous position = 2.5  
rotated from previous position = 3.56 degrees  
atoms outside contour = 3251, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99952518 -0.01812743 -0.02491590 5.67582439  
0.01675779 0.99839374 -0.05412126 5.47265603  
0.02585696 0.05367803 0.99822347 -11.78355617  
Axis 0.86823326 -0.40893292 0.28097132  
Axis point 0.00000000 219.24912474 89.92027727  
Rotation angle (degrees) 3.55919261  
Shift along axis -0.62085101  
  

> fitmap #3.2 inMap #1

Fit molecule 30_0.12345.cif (#3.2) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1109, steps = 120  
shifted from previous position = 4.72  
rotated from previous position = 6.6 degrees  
atoms outside contour = 3215, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.2) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99499183 -0.08446041 -0.05345752 19.39799859  
0.08128778 0.99494427 -0.05897619 -6.99348074  
0.05816841 0.05433539 0.99682702 -19.82210108  
Axis 0.49325465 -0.48591689 0.72151551  
Axis point 108.38695567 231.04250798 0.00000000  
Rotation angle (degrees) 6.59561579  
Shift along axis -1.33554986  
  

> fitmap #3.3 inMap #1

Fit molecule 30_0.12345.cif (#3.3) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3752, steps = 156  
shifted from previous position = 12.3  
rotated from previous position = 5.15 degrees  
atoms outside contour = 1362, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.3) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670613 -0.06435534 -0.04934866 14.98512895  
0.06240967 0.99724855 -0.04000461 -8.41127883  
0.05178739 0.03679301 0.99798013 -11.31597645  
Axis 0.42800468 -0.56364640 0.70648052  
Axis point 115.31330918 205.93054961 0.00000000  
Rotation angle (degrees) 5.14726091  
Shift along axis 3.16017549  
  

> fitmap #3.4 inMap #1

Fit molecule 30_0.12345.cif (#3.4) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.09011, steps = 84  
shifted from previous position = 6.52  
rotated from previous position = 4.24 degrees  
atoms outside contour = 3407, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.4) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99797210 -0.05364400 -0.03426383 13.54379293  
0.05231436 0.99788476 -0.03859039 -5.43005013  
0.03626149 0.03671964 0.99866750 -16.39301167  
Axis 0.50921670 -0.47686442 0.71644866  
Axis point 135.25333635 268.80255614 0.00000000  
Rotation angle (degrees) 4.24071790  
Shift along axis -2.25862787  
  

> fitmap #3.5 inMap #1

Fit molecule 30_0.12345.cif (#3.5) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.08747, steps = 148  
shifted from previous position = 8.35  
rotated from previous position = 0.784 degrees  
atoms outside contour = 3433, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.5) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999893 -0.00101477 0.00105526 -6.95244225  
0.00102903 0.99990693 -0.01360382 0.43675924  
-0.00104136 0.01360489 0.99990691 0.45308631  
Axis 0.99425972 0.07661473 0.07468461  
Axis point 0.00000000 -70.39359243 71.13854635  
Rotation angle (degrees) 0.78399697  
Shift along axis -6.84523252  
  

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.09863, steps = 168  
shifted from previous position = 12.1  
rotated from previous position = 6.16 degrees  
atoms outside contour = 3326, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99576275 -0.08354503 0.03842881 6.13196208  
0.08555223 0.99487214 -0.05394665 -13.46131928  
-0.03372478 0.05700574 0.99780408 -1.28982876  
Axis 0.51669822 0.33601468 0.78747514  
Axis point 152.84910206 80.30583913 0.00000000  
Rotation angle (degrees) 6.16354117  
Shift along axis -2.37053508  
  

> select subtract #3

Nothing selected  

> color #2 #ffa348ff models

> color #2 #8ff0a4ff models

> select add #3.1

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> ui mousemode right "translate selected models"

> view matrix models
> #3.1,0.99953,-0.018127,-0.024916,6.9472,0.016758,0.99839,-0.054121,2.0563,0.025857,0.053678,0.99822,-9.4524

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.15, steps = 60  
shifted from previous position = 1.74  
rotated from previous position = 2.47 degrees  
atoms outside contour = 2918, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99798115 0.00081270 -0.06350559 8.52315821  
-0.00429463 0.99849296 -0.05471157 6.68867481  
0.06336542 0.05487385 0.99648065 -15.68530394  
Axis 0.65336802 -0.75642778 -0.03045084  
Axis point 253.50566681 0.00000000 115.99871292  
Rotation angle (degrees) 4.81058527  
Shift along axis 0.98689020  
  

> view matrix models
> #3.1,0.99798,0.0008127,-0.063506,9.3116,-0.0042946,0.99849,-0.054712,5.3074,0.063365,0.054874,0.99648,-14.726

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3664, steps = 68  
shifted from previous position = 4.13  
rotated from previous position = 3.97 degrees  
atoms outside contour = 1403, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670111 -0.06438797 -0.04940745 15.00068814  
0.06244354 0.99724905 -0.03993920 -8.43755438  
0.05184313 0.03672227 0.99797984 -11.32956354  
Axis 0.42711892 -0.56411697 0.70664098  
Axis point 115.64603242 206.08040870 0.00000000  
Rotation angle (degrees) 5.14879571  
Shift along axis 3.16091148  
  

> select subtract #3.1

Nothing selected  

> select add #3.2

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> view matrix models
> #3.2,0.99499,-0.08446,-0.053458,19.825,0.081288,0.99494,-0.058976,-5.8303,0.058168,0.054335,0.99683,-13.129

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3664, steps = 40  
shifted from previous position = 0.01  
rotated from previous position = 0.00123 degrees  
atoms outside contour = 1406, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670270 -0.06437641 -0.04939039 15.00289899  
0.06243295 0.99724998 -0.03993254 -8.44206911  
0.05182528 0.03671728 0.99798095 -11.32043207  
Axis 0.42714997 -0.56404920 0.70667631  
Axis point 115.65348834 206.09008609 0.00000000  
Rotation angle (degrees) 5.14763603  
Shift along axis 3.17034913  
  

> view matrix models
> #3.2,0.99499,-0.08446,-0.053458,17.821,0.081288,0.99494,-0.058976,-7.4245,0.058168,0.054335,0.99683,-14.799

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3664, steps = 40  
shifted from previous position = 0.00815  
rotated from previous position = 0.000967 degrees  
atoms outside contour = 1405, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670151 -0.06438408 -0.04940429 15.00129787  
0.06243981 0.99724931 -0.03993846 -8.43813615  
0.05183980 0.03672193 0.99798003 -11.32868577  
Axis 0.42713552 -0.56411072 0.70663593  
Axis point 115.64903027 206.09238270 0.00000000  
Rotation angle (degrees) 5.14852230  
Shift along axis 3.16237378  
  

> select subtract #3.2

Nothing selected  

> select add #3.3

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> view matrix models
> #3.3,0.99671,-0.064355,-0.049349,14.56,0.06241,0.99725,-0.040005,-8.464,0.051787,0.036793,0.99798,-12.092

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3663, steps = 48  
shifted from previous position = 0.0137  
rotated from previous position = 0.00596 degrees  
atoms outside contour = 1402, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670713 -0.06428211 -0.04942371 14.99515902  
0.06233758 0.99725611 -0.03992850 -8.42733074  
0.05185478 0.03671607 0.99797946 -11.32385782  
Axis 0.42736067 -0.56471637 0.70601578  
Axis point 115.52722225 206.26130463 0.00000000  
Rotation angle (degrees) 5.14473748  
Shift along axis 3.17257059  
  

> select subtract #3.3

Nothing selected  

> select add #3.4

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> view matrix models
> #3.4,0.99797,-0.053644,-0.034264,9.0809,0.052314,0.99788,-0.03859,-5.8791,0.036261,0.03672,0.99867,-8.6336

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3664, steps = 40  
shifted from previous position = 0.0162  
rotated from previous position = 0.00722 degrees  
atoms outside contour = 1402, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670067 -0.06440448 -0.04939467 15.00183889  
0.06246065 0.99724807 -0.03993690 -8.44016143  
0.05183085 0.03671991 0.99798057 -11.32694535  
Axis 0.42707478 -0.56395338 0.70679821  
Axis point 115.66619301 206.04589311 0.00000000  
Rotation angle (degrees) 5.14901506  
Shift along axis 3.16089994  
  

> view matrix models
> #3.4,0.99797,-0.053644,-0.034264,7.7922,0.052314,0.99788,-0.03859,-7.7813,0.036261,0.03672,0.99867,-8.173

> fitmap #3.1 inMap #1

Fit molecule 30_0.12345.cif (#3.1) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3664, steps = 48  
shifted from previous position = 0.0166  
rotated from previous position = 0.00619 degrees  
atoms outside contour = 1403, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.1) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670648 -0.06429857 -0.04941547 14.99679279  
0.06235424 0.99725498 -0.03993071 -8.43063521  
0.05184731 0.03671793 0.99797978 -11.32234114  
Axis 0.42734459 -0.56457763 0.70613646  
Axis point 115.55084525 206.22659838 0.00000000  
Rotation angle (degrees) 5.14520537  
Shift along axis 3.17342849  
  

> fitmap #3.4 inMap #1

Fit molecule 30_0.12345.cif (#3.4) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3718, steps = 56  
shifted from previous position = 2.07  
rotated from previous position = 1.07 degrees  
atoms outside contour = 1373, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.4) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99670122 -0.06426099 -0.04957009 15.00333299  
0.06230094 0.99725060 -0.04012264 -8.35229731  
0.05201213 0.03690202 0.99796442 -11.41651635  
Axis 0.42877804 -0.56548418 0.70454030  
Axis point 114.93644729 206.80486409 0.00000000  
Rotation angle (degrees) 5.15318298  
Shift along axis 3.11279589  
  

> select subtract #3.4

Nothing selected  

> select add #3.5

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> view matrix models
> #3.5,1,-0.0010148,0.0010553,-14.655,0.001029,0.99991,-0.013604,-3.7539,-0.0010414,0.013605,0.99991,1.6025

> fitmap #3.5 inMap #1

Fit molecule 30_0.12345.cif (#3.5) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.358, steps = 84  
shifted from previous position = 3.05  
rotated from previous position = 4.87 degrees  
atoms outside contour = 1415, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.5) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99669266 -0.06467517 -0.04920224 15.01542591  
0.06273797 0.99723019 -0.03994858 -8.50806530  
0.05164964 0.03672961 0.99798960 -11.28996593  
Axis 0.42674959 -0.56128732 0.70911306  
Axis point 116.24750096 205.25631143 0.00000000  
Rotation angle (degrees) 5.15439074  
Shift along axis 3.17743367  
  

> select subtract #3.5

Nothing selected  

> select add #3.6

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.09862, steps = 60  
shifted from previous position = 0.00267  
rotated from previous position = 0.00251 degrees  
atoms outside contour = 3328, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99576539 -0.08352125 0.03841213 6.12705353  
0.08552645 0.99487607 -0.05391501 -13.46479270  
-0.03371226 0.05697195 0.99780643 -1.28494650  
Axis 0.51659231 0.33600802 0.78754746  
Axis point 152.92817847 80.27090541 0.00000000  
Rotation angle (degrees) 6.16115976  
Shift along axis -2.37104590  
  

> view matrix models
> #3.6,0.99577,-0.083521,0.038412,0.75574,0.085526,0.99488,-0.053915,-13.018,-0.033712,0.056972,0.99781,1.4661

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1377, steps = 88  
shifted from previous position = 3.75  
rotated from previous position = 3.41 degrees  
atoms outside contour = 3018, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99570860 -0.06328455 0.06752368 -9.20375679  
0.07000767 0.99228179 -0.10235125 3.52600908  
-0.06052526 0.10663920 0.99245391 -1.56194255  
Axis 0.74907282 0.45895868 0.47775186  
Axis point 0.00000000 -7.94191746 62.05349616  
Rotation angle (degrees) 8.01888113  
Shift along axis -6.02221257  
  

> view matrix models
> #3.6,0.99571,-0.063285,0.067524,-12.13,0.070008,0.99228,-0.10235,6.1525,-0.060525,0.10664,0.99245,-5.3175

> view matrix models
> #3.6,0.99571,-0.063285,0.067524,-7.9621,0.070008,0.99228,-0.10235,2.4521,-0.060525,0.10664,0.99245,3.9533

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.129, steps = 132  
shifted from previous position = 1.42  
rotated from previous position = 1.55 degrees  
atoms outside contour = 3100, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99536410 -0.07954327 0.05406650 -0.40766847  
0.08548722 0.98928210 -0.11837596 1.90346270  
-0.04407100 0.12244918 0.99149581 -5.24576528  
Axis 0.78190483 0.31863029 0.53581673  
Axis point 0.00000000 33.17978337 19.86684941  
Rotation angle (degrees) 8.85874683  
Shift along axis -2.52302588  
  

> view matrix models
> #3.6,0.99536,-0.079543,0.054066,-0.6938,0.085487,0.98928,-0.11838,2.155,-0.044071,0.12245,0.9915,-6.0461

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1291, steps = 164  
shifted from previous position = 0.886  
rotated from previous position = 0.0113 degrees  
atoms outside contour = 3102, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99537308 -0.07955862 0.05387825 -0.36575421  
0.08547700 0.98928938 -0.11832249 1.89354315  
-0.04388761 0.12238037 0.99151244 -5.27680827  
Axis 0.78204382 0.31764138 0.53620091  
Axis point 0.00000000 33.47101375 19.72234886  
Rotation angle (degrees) 8.85262619  
Shift along axis -2.51399757  
  

> ui mousemode right "rotate selected models"

> view matrix models
> #3.6,0.99909,-0.042249,-0.0061915,0.77375,0.040495,0.98347,-0.17648,26.276,0.013545,0.17607,0.98428,-32.448

> view matrix models
> #3.6,0.99687,0.079004,0.0016871,-33.07,-0.078026,0.98746,-0.13724,46.383,-0.012509,0.13668,0.99054,-16.657

> ui mousemode right "translate selected models"

> view matrix models
> #3.6,0.99687,0.079004,0.0016871,-35.443,-0.078026,0.98746,-0.13724,49.971,-0.012509,0.13668,0.99054,-17.378

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1377, steps = 108  
shifted from previous position = 4.18  
rotated from previous position = 9.16 degrees  
atoms outside contour = 3016, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99570697 -0.06334485 0.06749113 -9.17534790  
0.07006323 0.99227964 -0.10233405 3.50857625  
-0.06048774 0.10662338 0.99245790 -1.56979536  
Axis 0.74895851 0.45870998 0.47816975  
Axis point 0.00000000 -7.87037908 61.83315040  
Rotation angle (degrees) 8.01883753  
Shift along axis -6.01316462  
  

> view matrix models
> #3.6,0.99571,-0.063345,0.067491,-10.594,0.070063,0.99228,-0.10233,3.501,-0.060488,0.10662,0.99246,-0.54747

> view matrix models
> #3.6,0.99571,-0.063345,0.067491,-10.546,0.070063,0.99228,-0.10233,3.4964,-0.060488,0.10662,0.99246,-0.53331

> view matrix models
> #3.6,0.99571,-0.063345,0.067491,-6.4183,0.070063,0.99228,-0.10233,3.6256,-0.060488,0.10662,0.99246,-4.5934

> view matrix models
> #3.6,0.99571,-0.063345,0.067491,-9.9564,0.070063,0.99228,-0.10233,4.0061,-0.060488,0.10662,0.99246,-6.0953

> view matrix models
> #3.6,0.99571,-0.063345,0.067491,-11.268,0.070063,0.99228,-0.10233,3.7983,-0.060488,0.10662,0.99246,1.0312

> ui mousemode right "rotate selected models"

> view matrix models
> #3.6,0.99821,-0.059884,-0.0002531,0.87678,0.059748,0.9962,-0.063354,-2.608,0.004046,0.063225,0.99799,-4.2042

> ui mousemode right "translate selected models"

> view matrix models
> #3.6,0.99821,-0.059884,-0.0002531,3.4318,0.059748,0.9962,-0.063354,-4.0587,0.004046,0.063225,0.99799,-4.5543

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.1551, steps = 72  
shifted from previous position = 0.727  
rotated from previous position = 1.64 degrees  
atoms outside contour = 2903, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99673606 -0.07884546 0.01733812 5.57742360  
0.07963726 0.99551466 -0.05107319 -10.66667948  
-0.01323346 0.05228725 0.99854440 2.84795151  
Axis 0.53928168 0.15950679 0.82688140  
Axis point 143.51322822 39.75532308 0.00000000  
Rotation angle (degrees) 5.49918481  
Shift along axis 3.66131274  
  

> select subtract #3.6

Nothing selected  

> select add #3.6

4185 atoms, 4280 bonds, 495 residues, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #3.6,0.99623,-0.084814,-0.018026,14.464,0.084561,0.99632,-0.014335,-19.52,0.019175,0.012757,0.99973,5.3368

> ui mousemode right "translate selected models"

> view matrix models
> #3.6,0.99623,-0.084814,-0.018026,14.123,0.084561,0.99632,-0.014335,-19.496,0.019175,0.012757,0.99973,2.9156

> fitmap #3.6 inMap #1

Fit molecule 30_0.12345.cif (#3.6) to map cryosparc_P20_J563_map_sharp (1).mrc
(#1) using 4185 atoms  
average map value = 0.3733, steps = 72  
shifted from previous position = 0.645  
rotated from previous position = 2.62 degrees  
atoms outside contour = 1368, contour level = 0.15943  
  
Position of 30_0.12345.cif (#3.6) relative to cryosparc_P20_J563_map_sharp
(1).mrc (#1) coordinates:  
Matrix rotation and translation  
0.99671492 -0.06428226 -0.04926619 14.93822642  
0.06234295 0.99725532 -0.03993987 -8.43463203  
0.05169839 0.03673726 0.99798680 -11.29960149  
Axis 0.42792221 -0.56346638 0.70667406  
Axis point 115.77871326 205.43294852 0.00000000  
Rotation angle (degrees) 5.14015691  
Shift along axis 3.15989524  
  

> select subtract #3.6

Nothing selected  

> close #2

> select add #3

25110 atoms, 25680 bonds, 2970 residues, 7 models selected  

> ui tool show "Change Chain IDs"

> changechains sel
> 0a,0b,0c,0d,0e,1a,1b,1c,1d,1e,2a,2b,2c,2d,2e,3a,3b,3c,3d,3e,4a,4b,4c,4d,4e,5a,5b,5c,5d,5e
> 6a,6b,6c,6d,6e,7a,7b,7c,7d,7e,8a,8b,8c,8d,8e,9a,9b,9c,9d,9e,aa,ab,ac,ad,ae,ba,bb,bc,bd,be

Chain IDs of 2970 residues changed  
No model chosen to save relative to  

> save /home/dell/Desktop/cage58/30_6789ab.cif relModel #1

Not saving entity_poly_seq for non-authoritative sequences  

> open /home/dell/Desktop/cage58/30_6789ab.cif
> /home/dell/Desktop/cage58/30_0.12345.cif

Summary of feedback from opening /home/dell/Desktop/cage58/30_6789ab.cif  
---  
warnings | Unknown polymer entity '1' near line 5653  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 14255  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 22857  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 31459  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 40061  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Summary of feedback from opening /home/dell/Desktop/cage58/30_0.12345.cif  
---  
warnings | Unknown polymer entity '1' near line 5651  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 14252  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 22853  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 31454  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 40055  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 30_6789ab.cif  
---  
Chain | Description  
2.4/6a 2.4/6b 2.4/6c 2.4/6d 2.4/6e 2.6/7a 2.6/7b 2.6/7c 2.6/7d 2.6/7e 2.5/8a
2.5/8b 2.5/8c 2.5/8d 2.5/8e 2.1/9a 2.1/9b 2.1/9c 2.1/9d 2.1/9e 2.3/aa 2.3/ab
2.3/ac 2.3/ad 2.3/ae 2.2/ba 2.2/bb 2.2/bc 2.2/bd 2.2/be | No description
available  
  
Chain information for 30_0.12345.cif  
---  
Chain | Description  
4.4/0a 4.4/0b 4.4/0c 4.4/0d 4.4/0e 4.6/1a 4.6/1b 4.6/1c 4.6/1d 4.6/1e 4.5/2a
4.5/2b 4.5/2c 4.5/2d 4.5/2e 4.1/3a 4.1/3b 4.1/3c 4.1/3d 4.1/3e 4.3/4a 4.3/4b
4.3/4c 4.3/4d 4.3/4e 4.2/5a 4.2/5b 4.2/5c 4.2/5d 4.2/5e | No description
available  
  

> close #3

> close #4

> open /home/dell/Desktop/cage58/30_0.12345.cif

Summary of feedback from opening /home/dell/Desktop/cage58/30_0.12345.cif  
---  
warnings | Unknown polymer entity '1' near line 5651  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 14252  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 22853  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 31454  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
Unknown polymer entity '1' near line 40055  
Missing or incomplete entity_poly_seq table. Inferred polymer connectivity.  
  
Chain information for 30_0.12345.cif  
---  
Chain | Description  
3.4/0a 3.4/0b 3.4/0c 3.4/0d 3.4/0e 3.6/1a 3.6/1b 3.6/1c 3.6/1d 3.6/1e 3.5/2a
3.5/2b 3.5/2c 3.5/2d 3.5/2e 3.1/3a 3.1/3b 3.1/3c 3.1/3d 3.1/3e 3.3/4a 3.3/4b
3.3/4c 3.3/4d 3.3/4e 3.2/5a 3.2/5b 3.2/5c 3.2/5d 3.2/5e | No description
available  
  

> color bypolymer

> hide atoms

> show cartoons

> combine #2 #3

> hide #!2 models

> hide #!3 models

> info #4

1 models  
#4, combination, shown  
50220 atoms, 51360 bonds, 5940 residues, 60 chains
(9a,9b,9c,9d,9e,ba,bb,bc,bd,be,aa,ab,ac,ad,ae,6a,6b,6c,6d,6e,8a,8b,8c,8d,8e,7a,7b,7c,7d,7e,3a,3b,3c,3d,3e,5a,5b,5c,5d,5e,4a,4b,4c,4d,4e,0a,0b,0c,0d,0e,2a,2b,2c,2d,2e,1a,1b,1c,1d,1e)  

> save /home/dell/Desktop/cage58/60_1.cif models #4 relModel #1


===== Log before crash end =====

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.dev202306232350 (2023-06-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/dell/Desktop/cage58/cryosparc_P20_J563_map_sharp (1).mrc"

Opened cryosparc_P20_J563_map_sharp (1).mrc as #1, grid size 440,440,440,
pixel 0.93, shown at level 0.000704, step 2, values float32  

> volume #1 step 1




OpenGL version: 3.3.0 NVIDIA 530.30.02
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision 3660
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900K
Cache Size: 36864 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi       5.4Gi       116Gi        40Mi       3.4Gi       118Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2684] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:5108]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46
    ChimeraX-AtomicLibrary: 10.0.7
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.3
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202306232350
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.7
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.30
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.40.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2023.3.16
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.8.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.6
    PyOpenGL-accelerate: 3.1.6
    pyparsing: 3.1.0
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.6.3
    tzdata: 2023.3
    urllib3: 2.0.3
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7