Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-26-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 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 0x000078387efcfb80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/ctypes/__init__.py", line 512 in cast
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/numpy/core/_internal.py", line 282 in data_as
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 208 in get_prop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1887 in _update_graphics_if_needed
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 149 in invoke
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 248 in _activate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 217 in activate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/triggerset.py", line 393 in activate_trigger
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 294 in check_for_drawing_change
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 76 in draw_new_frame
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/updateloop.py", line 150 in _redraw_timer_callback
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, openmm._openmm, openmm.app.internal.compiled, lxml._elementpath, lxml.etree, chimerax.pdb_lib._load_libs, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 59)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> alias sethel setattr $1 residue ss_type 1 type int; setattr $1 residue ss_id
> 100 type int

> alias setstr setattr $1 residue ss_type 2 type int; setattr $1 residue ss_id
> 100 type int

> alias setloop setattr $1 residue ss_type 0 type int; setattr $1 residue
> ss_id 100 type int

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/xiyosong/Desktop/Fascin-actin/PDB/3llp_A_2010.pdb

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/3llp_A_2010.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 12 12 ALA B
28 PHE B 31 1 4  
Start residue of secondary structure not found: HELIX 13 13 LYS B 41 ILE B 45
1 5  
Start residue of secondary structure not found: HELIX 14 14 GLY B 86 CYS B 89
1 4  
Start residue of secondary structure not found: HELIX 15 15 SER B 127 LYS B
131 1 5  
Start residue of secondary structure not found: HELIX 16 16 GLY B 172 LEU B
176 1 5  
54 messages similar to the above omitted  
Cannot find LINK/SSBOND residue THR (275 )  
Cannot find LINK/SSBOND residue GLY (278 )  
Cannot find LINK/SSBOND residue K (497 )  
Cannot find LINK/SSBOND residue ARG (276 )  
  
Chain information for 3llp_A_2010.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/0603_sim/actin_fascin_actin0603_sim.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/0603_sim/actin_fascin_actin0603_sim.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 851  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "22" near line 118  
Bad residue range for struct_conf "44" near line 140  
Bad residue range for struct_conf "66" near line 162  
Bad residue range for struct_conf "88" near line 184  
Bad residue range for struct_conf "110" near line 206  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "108 1" near line 840  
Invalid sheet range for struct_sheet_range "109 1" near line 841  
Invalid sheet range for struct_sheet_range "110 1" near line 842  
Invalid sheet range for struct_sheet_range "111 1" near line 843  
Invalid sheet range for struct_sheet_range "112 1" near line 844  
5 messages similar to the above omitted  
Atom HN is not in the residue template for GLU /A:49  
Atom H1 is not in the residue template for ALA /A:55  
Atom HN is not in the residue template for ALA /A:157  
Atom H1 is not in the residue template for ALA /A:160  
Atom HN is not in the residue template for ARG /A:217  
Atom H1 is not in the residue template for LYS /A:220  
Atom HN is not in the residue template for LYS /A:244  
Atom H1 is not in the residue template for VAL /A:248  
Atom HN is not in the residue template for ARG /A:276  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin_fascin_actin0603_sim.cif #2  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> select add #2

41164 atoms, 41608 bonds, 341 pseudobonds, 2662 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> select add #1

44871 atoms, 45377 bonds, 351 pseudobonds, 3144 residues, 6 models selected  

> hide sel atoms

> show sel cartoons

> mmaker #1 to #2

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker actin_fascin_actin0603_sim.cif, chain A (#2) with 3llp_A_2010.pdb,
chain A (#1), sequence alignment score = 2281.1  
RMSD between 366 pruned atom pairs is 1.276 angstroms; (across all 472 pairs:
1.756)  
  

> view

> select clear

> select add #2

41164 atoms, 41608 bonds, 341 pseudobonds, 2662 residues, 3 models selected  

> color (#!2 & sel) orange

> select subtract #2

Nothing selected  

> select add #1

3707 atoms, 3769 bonds, 10 pseudobonds, 482 residues, 3 models selected  

> color (#!1 & sel) hot pink

> select clear

> close #2

> close

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/0603_sim/actin_fascin_actin0603_sim.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/0603_sim/actin_fascin_actin0603_sim.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 851  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "22" near line 118  
Bad residue range for struct_conf "44" near line 140  
Bad residue range for struct_conf "66" near line 162  
Bad residue range for struct_conf "88" near line 184  
Bad residue range for struct_conf "110" near line 206  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "108 1" near line 840  
Invalid sheet range for struct_sheet_range "109 1" near line 841  
Invalid sheet range for struct_sheet_range "110 1" near line 842  
Invalid sheet range for struct_sheet_range "111 1" near line 843  
Invalid sheet range for struct_sheet_range "112 1" near line 844  
5 messages similar to the above omitted  
Atom HN is not in the residue template for GLU /A:49  
Atom H1 is not in the residue template for ALA /A:55  
Atom HN is not in the residue template for ALA /A:157  
Atom H1 is not in the residue template for ALA /A:160  
Atom HN is not in the residue template for ARG /A:217  
Atom H1 is not in the residue template for LYS /A:220  
Atom HN is not in the residue template for LYS /A:244  
Atom H1 is not in the residue template for VAL /A:248  
Atom HN is not in the residue template for ARG /A:276  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin_fascin_actin0603_sim.cif #1  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> open /home/xiyosong/Desktop/Fascin-actin/PDB/0603_before/actin-
> fascin_actin_0603_before.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/0603_before/actin-fascin_actin_0603_before.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 861  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "18" near line 114  
Bad residue range for struct_conf "36" near line 132  
Bad residue range for struct_conf "54" near line 150  
Bad residue range for struct_conf "72" near line 168  
Bad residue range for struct_conf "90" near line 186  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "107 1" near line 851  
Invalid sheet range for struct_sheet_range "108 1" near line 852  
Invalid sheet range for struct_sheet_range "109 1" near line 853  
Invalid sheet range for struct_sheet_range "110 1" near line 854  
Invalid sheet range for struct_sheet_range "111 1" near line 855  
4 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin-fascin_actin_0603_before.cif #2  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> select add #1

41164 atoms, 41608 bonds, 341 pseudobonds, 2662 residues, 3 models selected  

> select add #2

61896 atoms, 62784 bonds, 720 pseudobonds, 5324 residues, 6 models selected  

> hide sel atoms

> show sel cartoons

> select subtract #1

20732 atoms, 21176 bonds, 379 pseudobonds, 2662 residues, 3 models selected  

> color (#!2 & sel) orange

> close #1

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/structure_3parameters_simulation_correct/actin-
> fascin_actin_3llp_3parameters_simulation.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/structure_3parameters_simulation_correct/actin-
fascin_actin_3llp_3parameters_simulation.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 851  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "22" near line 118  
Bad residue range for struct_conf "44" near line 140  
Bad residue range for struct_conf "66" near line 162  
Bad residue range for struct_conf "88" near line 184  
Bad residue range for struct_conf "110" near line 206  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "108 1" near line 840  
Invalid sheet range for struct_sheet_range "109 1" near line 841  
Invalid sheet range for struct_sheet_range "110 1" near line 842  
Invalid sheet range for struct_sheet_range "111 1" near line 843  
Invalid sheet range for struct_sheet_range "112 1" near line 844  
5 messages similar to the above omitted  
Atom HN is not in the residue template for GLU /A:49  
Atom H1 is not in the residue template for ALA /A:55  
Atom HN is not in the residue template for ALA /A:157  
Atom H1 is not in the residue template for ALA /A:160  
Atom HN is not in the residue template for ARG /A:217  
Atom H1 is not in the residue template for LYS /A:220  
Atom HN is not in the residue template for LYS /A:244  
Atom H1 is not in the residue template for VAL /A:248  
Atom HN is not in the residue template for ARG /A:276  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin-fascin_actin_3llp_3parameters_simulation.cif #1  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> select add #1

61896 atoms, 62784 bonds, 720 pseudobonds, 5324 residues, 6 models selected  

> select subtract #2

41164 atoms, 41608 bonds, 341 pseudobonds, 2662 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> color (#!1 & sel) hot pink

> close #1

> select add #2

20732 atoms, 21176 bonds, 379 pseudobonds, 2662 residues, 3 models selected  

> show sel atoms

> save /home/xiyosong/Desktop/Fascin-
> actin/PDB/0603_before/actin_fascin_actin_before0603.pdb displayedOnly true
> relModel #2

> hide #!2 models

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/0603_before/actin_fascin_actin_before0603.pdb

Chain information for actin_fascin_actin_before0603.pdb #1  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> select subtract #2

Nothing selected  

> select add #1

20732 atoms, 21176 bonds, 6 pseudobonds, 2662 residues, 2 models selected  

> hide sel atoms

> show sel cartoons

> close

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/0603_before/actin_fascin_actin_before0603.pdb

Chain information for actin_fascin_actin_before0603.pdb #1  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> open /home/xiyosong/Desktop/Fascin-actin/PDB/3llp_A_2010.pdb

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/3llp_A_2010.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 12 12 ALA B
28 PHE B 31 1 4  
Start residue of secondary structure not found: HELIX 13 13 LYS B 41 ILE B 45
1 5  
Start residue of secondary structure not found: HELIX 14 14 GLY B 86 CYS B 89
1 4  
Start residue of secondary structure not found: HELIX 15 15 SER B 127 LYS B
131 1 5  
Start residue of secondary structure not found: HELIX 16 16 GLY B 172 LEU B
176 1 5  
54 messages similar to the above omitted  
Cannot find LINK/SSBOND residue THR (275 )  
Cannot find LINK/SSBOND residue GLY (278 )  
Cannot find LINK/SSBOND residue K (497 )  
Cannot find LINK/SSBOND residue ARG (276 )  
  
Chain information for 3llp_A_2010.pdb #2  
---  
Chain | Description  
A | No description available  
  

> hide atoms

> show ribbons

> select add #1

20732 atoms, 21176 bonds, 6 pseudobonds, 2662 residues, 2 models selected  

> color (#!1 & sel) cyan

> select subtract #1

Nothing selected  

> select add #2

3707 atoms, 3769 bonds, 10 pseudobonds, 482 residues, 3 models selected  

> color (#!2 & sel) hot pink

> mmaker #2 to #1

Parameters  
---  
Chain pairing | bb  
Alignment algorithm | Needleman-Wunsch  
Similarity matrix | BLOSUM-62  
SS fraction | 0.3  
Gap open (HH/SS/other) | 18/18/6  
Gap extend | 1  
SS matrix |  |  | H | S | O  
---|---|---|---  
H | 6 | -9 | -6  
S |  | 6 | -6  
O |  |  | 4  
Iteration cutoff | 2  
  
Matchmaker actin_fascin_actin_before0603.pdb, chain A (#1) with
3llp_A_2010.pdb, chain A (#2), sequence alignment score = 2267.9  
RMSD between 465 pruned atom pairs is 0.962 angstroms; (across all 472 pairs:
0.992)  
  

> ui tool show "Show Sequence Viewer"

> sequence chain #2/A

Alignment identifier is 2/A  

> select clear

> select #1/B

2842 atoms, 2904 bonds, 365 residues, 1 model selected  

> select /B,C,D,E,F,G

17052 atoms, 17424 bonds, 2190 residues, 1 model selected  

> hide sel cartoons

> select clear

> select #2/A:7-60

364 atoms, 368 bonds, 1 pseudobond, 49 residues, 2 models selected  

> select #2/A:118

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:111-118

66 atoms, 67 bonds, 8 residues, 1 model selected  

> select #2/A:136-137

13 atoms, 12 bonds, 2 residues, 1 model selected  

> select #2/A:136-240

806 atoms, 824 bonds, 2 pseudobonds, 101 residues, 2 models selected  

> select #2/A:136

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #2/A:136-150

122 atoms, 124 bonds, 15 residues, 1 model selected  

> select #2/A:151

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select #2/A:151-180

215 atoms, 218 bonds, 1 pseudobond, 28 residues, 2 models selected  

> hide #!2 models

> hide #!1 models

> open /home/xiyosong/Desktop/Fascin-actin/PDB/actin_fascin_actin0603.pdb
> /home/xiyosong/Desktop/Fascin-actin/PDB/3llp_A_2010.pdb

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/3llp_A_2010.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 12 12 ALA B
28 PHE B 31 1 4  
Start residue of secondary structure not found: HELIX 13 13 LYS B 41 ILE B 45
1 5  
Start residue of secondary structure not found: HELIX 14 14 GLY B 86 CYS B 89
1 4  
Start residue of secondary structure not found: HELIX 15 15 SER B 127 LYS B
131 1 5  
Start residue of secondary structure not found: HELIX 16 16 GLY B 172 LEU B
176 1 5  
54 messages similar to the above omitted  
Cannot find LINK/SSBOND residue THR (275 )  
Cannot find LINK/SSBOND residue GLY (278 )  
Cannot find LINK/SSBOND residue K (497 )  
Cannot find LINK/SSBOND residue ARG (276 )  
  
Chain information for actin_fascin_actin0603.pdb #3  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  
Chain information for 3llp_A_2010.pdb #4  
---  
Chain | Description  
A | No description available  
  

> select clear

> select add #4

3707 atoms, 3769 bonds, 10 pseudobonds, 482 residues, 3 models selected  

> select add #3

44871 atoms, 45377 bonds, 16 pseudobonds, 3144 residues, 5 models selected  

> hide sel atoms

> show sel cartoons

> close

> open
> /home/ad/home/x/xiyosong/Desktop/fascin_check/job174/postprocess_submit.mrc

Opened postprocess_submit.mrc as #1, grid size 256,256,256, pixel 1.54, shown
at level 1.86, step 1, values float32  

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/structure_3parameters_simulation_correct/actin-
> fascin_actin_3llp_3parameters_simulation.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/structure_3parameters_simulation_correct/actin-
fascin_actin_3llp_3parameters_simulation.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 851  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "22" near line 118  
Bad residue range for struct_conf "44" near line 140  
Bad residue range for struct_conf "66" near line 162  
Bad residue range for struct_conf "88" near line 184  
Bad residue range for struct_conf "110" near line 206  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "108 1" near line 840  
Invalid sheet range for struct_sheet_range "109 1" near line 841  
Invalid sheet range for struct_sheet_range "110 1" near line 842  
Invalid sheet range for struct_sheet_range "111 1" near line 843  
Invalid sheet range for struct_sheet_range "112 1" near line 844  
5 messages similar to the above omitted  
Atom HN is not in the residue template for GLU /A:49  
Atom H1 is not in the residue template for ALA /A:55  
Atom HN is not in the residue template for ALA /A:157  
Atom H1 is not in the residue template for ALA /A:160  
Atom HN is not in the residue template for ARG /A:217  
Atom H1 is not in the residue template for LYS /A:220  
Atom HN is not in the residue template for LYS /A:244  
Atom H1 is not in the residue template for VAL /A:248  
Atom HN is not in the residue template for ARG /A:276  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin-fascin_actin_3llp_3parameters_simulation.cif #2  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> select add #2

41164 atoms, 41608 bonds, 341 pseudobonds, 2662 residues, 3 models selected  

> hide sel atoms

> show sel cartoons

> volume #1 level 1.35

> set bgColor white

> set bgColor #ffffff00

> camera ortho

> lighting full

> lighting soft

> lighting simple

> lighting soft

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule actin-fascin_actin_3llp_3parameters_simulation.cif (#2) to map
postprocess_submit.mrc (#1) using 41164 atoms  
average map value = 1.803, steps = 40  
shifted from previous position = 0.0534  
rotated from previous position = 0.0362 degrees  
atoms outside contour = 6426, contour level = 1.35  
  
Position of actin-fascin_actin_3llp_3parameters_simulation.cif (#2) relative
to postprocess_submit.mrc (#1) coordinates:  
Matrix rotation and translation  
0.99999988 -0.00015866 -0.00045501 0.13157464  
0.00015885 0.99999990 0.00040837 -0.14817159  
0.00045495 -0.00040845 0.99999981 -0.04566153  
Axis -0.64655221 -0.72028053 0.25132886  
Axis point 106.11425780 0.00000000 303.60316056  
Rotation angle (degrees) 0.03619219  
Shift along axis 0.01017917  
  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 2/A  

> select /A:138

17 atoms, 16 bonds, 1 residue, 1 model selected  

> select /A:7-138

1943 atoms, 1963 bonds, 1 pseudobond, 127 residues, 2 models selected  

> color (#!2 & sel) orange

> hide #!1 models

> select /A:259

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /A:139-259

1755 atoms, 1773 bonds, 3 pseudobonds, 114 residues, 2 models selected  

> color (#!2 & sel) lime

> select /A:383

24 atoms, 23 bonds, 1 residue, 1 model selected  

> select /A:260-383

1898 atoms, 1908 bonds, 1 pseudobond, 123 residues, 2 models selected  

> color (#!2 & sel) cyan

> select /A:384

14 atoms, 14 bonds, 1 residue, 1 model selected  

> select /A:384-493

1626 atoms, 1647 bonds, 1 pseudobond, 108 residues, 2 models selected  

> color (#!2 & sel) cornflower blue

> select clear

> select /B,C,D,E,F,G

33942 atoms, 34314 bonds, 335 pseudobonds, 2190 residues, 2 models selected  

> hide sel cartoons

> show #!1 models

> ui tool show "Color Zone"

> color zone #1 near #2 distance 9.26

> select /B,C,D,E,F,G

33942 atoms, 34314 bonds, 335 pseudobonds, 2190 residues, 2 models selected  

> color (#!2 & sel) light gray

> color zone #1 near #2 distance 9.26

> color (#!2 & sel) gray

> color zone #1 near #2 distance 9.26

> color (#!2 & sel) dark gray

> color zone #1 near #2 distance 9.26

> color zone #1 near #2 distance 10.82

> hide #!2 models

> camera ortho

> turn y 90

> save /home/xiyosong/Desktop/Fascin-actin/Figs/Fig1/1.png width 2201 height
> 1471 supersample 3

> turn y 180

> save /home/xiyosong/Desktop/Fascin-actin/Figs/Fig1/2.png width 2201 height
> 1471 supersample 3

> camera ortho

> close

> open /home/xiyosong/Desktop/Fascin-actin/PDB/0528_before/actin-
> fascin_actin_bef.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/0528_before/actin-fascin_actin_bef.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 861  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "18" near line 114  
Bad residue range for struct_conf "36" near line 132  
Bad residue range for struct_conf "54" near line 150  
Bad residue range for struct_conf "72" near line 168  
Bad residue range for struct_conf "90" near line 186  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "107 1" near line 851  
Invalid sheet range for struct_sheet_range "108 1" near line 852  
Invalid sheet range for struct_sheet_range "109 1" near line 853  
Invalid sheet range for struct_sheet_range "110 1" near line 854  
Invalid sheet range for struct_sheet_range "111 1" near line 855  
4 messages similar to the above omitted  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin-fascin_actin_bef.cif #1  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/0603_before/actin_fascin_actin_before0603.pdb

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/0603_before/actin_fascin_actin_before0603.pdb  
---  
warnings | Ignored bad PDB record found on line 288  
  
  
Ignored bad PDB record found on line 398  
  
Chain information for actin_fascin_actin_before0603.pdb #2  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  

> open /home/xiyosong/Desktop/Fascin-
> actin/PDB/structure_3parameters_simulation_correct/actin-
> fascin_actin_3llp_3parameters_simulation.cif

Summary of feedback from opening /home/xiyosong/Desktop/Fascin-
actin/PDB/structure_3parameters_simulation_correct/actin-
fascin_actin_3llp_3parameters_simulation.cif  
---  
warnings | Skipping chem_comp category: Missing column 'type' near line 851  
Missing entity information. Treating each chain as a separate entity.  
Bad residue range for struct_conf "22" near line 118  
Bad residue range for struct_conf "44" near line 140  
Bad residue range for struct_conf "66" near line 162  
Bad residue range for struct_conf "88" near line 184  
Bad residue range for struct_conf "110" near line 206  
2 messages similar to the above omitted  
Invalid sheet range for struct_sheet_range "108 1" near line 840  
Invalid sheet range for struct_sheet_range "109 1" near line 841  
Invalid sheet range for struct_sheet_range "110 1" near line 842  
Invalid sheet range for struct_sheet_range "111 1" near line 843  
Invalid sheet range for struct_sheet_range "112 1" near line 844  
5 messages similar to the above omitted  
Atom HN is not in the residue template for GLU /A:49  
Atom H1 is not in the residue template for ALA /A:55  
Atom HN is not in the residue template for ALA /A:157  
Atom H1 is not in the residue template for ALA /A:160  
Atom HN is not in the residue template for ARG /A:217  
Atom H1 is not in the residue template for LYS /A:220  
Atom HN is not in the residue template for LYS /A:244  
Atom H1 is not in the residue template for VAL /A:248  
Atom HN is not in the residue template for ARG /A:276  
Too many hydrogens missing from residue template(s) to warn about  
Missing or incomplete sequence information. Inferred polymer connectivity.  
  
  
Chain information for actin-fascin_actin_3llp_3parameters_simulation.cif #3  
---  
Chain | Description  
A | No description available  
B C D E F G | No description available  
  


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  

> alias sethel setattr $1 residue ss_type 1 type int; setattr $1 residue ss_id
> 100 type int

> alias setstr setattr $1 residue ss_type 2 type int; setattr $1 residue ss_id
> 100 type int

> alias setloop setattr $1 residue ss_type 0 type int; setattr $1 residue
> ss_id 100 type int

UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: NVIDIA RTX A4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_GB.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 30GUS48Q00
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 13th Gen Intel(R) Core(TM) i7-13700K
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi        10Gi        25Gi       1.2Gi        25Gi        49Gi
	Swap:           31Gi       0.0Ki        31Gi

Graphics:
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	Subsystem: Lenovo GA104GL [RTX A4000] [17aa:14ad]	
	Kernel driver in use: nvidia

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