Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.15.0-152-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x00007f91e91c0b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 907 in atomspec_atoms
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 627 in _add_model_parts
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 476 in _check
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 490 in _check
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 470 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 612 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 455 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1004 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1001 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py", line 1091 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/args.py", line 36 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/args.py", line 71 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2499 in _parse_arg
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2640 in _process_positional_arguments
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2864 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/match_maker/tool.py", line 303 in run_matchmaker
  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.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 57)
===== Log before crash start =====
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/Clover_505.0_515.0_111000.0_0.76_84.36_6.2_model_0_0001.pdb
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/Citrine_516.0_529.0_77000.0_0.76_58.52_5.7_model_0_0001.pdb
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/Citrine2_509.0_522.0_98000.0_0.7_68.6_5.9_model_0_0001.pdb
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/AzamiGreen_492.0_505.0_72300.0_0.67_48.44_5.0_model_0_0001.pdb
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb

Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 3443  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3444  
#BEGIN_POSE_ENERGIES_TABLE
CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb  
  
Ignored bad PDB record found on line 3445  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 3446  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 3447  
pose -1274.01 148.648 734.15 2.3877 42.3432 -16.4858 -405.259 0.57911 -34.8478
-118.259 -28.2071 -46.5261 0 17.6041 251.97 -58.8328 1.34601 51.0031 0.57619
-731.824  
  
221 messages similar to the above omitted  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/Clover_505.0_515.0_111000.0_0.76_84.36_6.2_model_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 3739  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3740  
#BEGIN_POSE_ENERGIES_TABLE
Clover_505.0_515.0_111000.0_0.76_84.36_6.2_model_0_0001.pdb  
  
Ignored bad PDB record found on line 3741  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 3742  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 3743  
pose -1356.44 154.899 792.538 2.58245 47.5456 -17.666 -475.066 0.63949
-37.8417 -121.954 -43.9327 -47.8563 0 25.1145 286.657 -55.7194 0.24965 45.2584
3.67557 -797.32  
  
241 messages similar to the above omitted  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/Citrine_516.0_529.0_77000.0_0.76_58.52_5.7_model_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 3770  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3771  
#BEGIN_POSE_ENERGIES_TABLE
Citrine_516.0_529.0_77000.0_0.76_58.52_5.7_model_0_0001.pdb  
  
Ignored bad PDB record found on line 3772  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 3773  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 3774  
pose -1373.88 160.452 774.748 2.53954 46.3584 -20.6295 -463.733 0.63598
-34.2387 -121.35 -42.5708 -46.3768 0 29.009 294.828 -54.0691 0.37394 50.6613
5.59196 -791.65  
  
241 messages similar to the above omitted  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/Citrine2_509.0_522.0_98000.0_0.7_68.6_5.9_model_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 3759  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3760  
#BEGIN_POSE_ENERGIES_TABLE
Citrine2_509.0_522.0_98000.0_0.7_68.6_5.9_model_0_0001.pdb  
  
Ignored bad PDB record found on line 3761  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 3762  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 3763  
pose -1361.89 159.718 788.863 2.6172 47.4772 -20.5966 -463.968 0.59148
-34.5423 -122.537 -47.6699 -46.3832 0 24.8758 295.298 -56.3809 0.44307 48.9715
2.99041 -782.123  
  
241 messages similar to the above omitted  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/AzamiGreen_492.0_505.0_72300.0_0.67_48.44_5.0_model_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 3622  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3623  
#BEGIN_POSE_ENERGIES_TABLE
AzamiGreen_492.0_505.0_72300.0_0.67_48.44_5.0_model_0_0001.pdb  
  
Ignored bad PDB record found on line 3624  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 3625  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 3626  
pose -1305.03 151.827 729.315 2.48454 46.1341 -19.8624 -418.035 0.64176
-25.7968 -122.9 -41.2289 -39.5373 0 29.9795 272.652 -51.5938 0.54553 51.7083
-8.13084 -746.83  
  
227 messages similar to the above omitted  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/relax_pdbs/AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb  
---  
warnings | Ignored bad PDB record found on line 3600  
# All scores below are weighted scores, not raw scores.  
  
Ignored bad PDB record found on line 3601  
#BEGIN_POSE_ENERGIES_TABLE
AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb  
  
Ignored bad PDB record found on line 3602  
label fa_atr fa_rep fa_sol fa_intra_rep fa_intra_sol_xover4 lk_ball_wtd
fa_elec pro_close hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_fa13 omega
fa_dun p_aa_pp yhh_planarity ref rama_prepro total  
  
Ignored bad PDB record found on line 3603  
weights 1 0.55 1 0.005 1 1 1 1.25 1 1 1 1 1.25 0.4 0.7 0.6 0.625 1 0.45 NA  
  
Ignored bad PDB record found on line 3604  
pose -1311.11 154.286 741.409 2.50031 41.52 -17.0527 -426.724 0.69898 -33.3725
-120.014 -41.5807 -42.4307 0 18.4568 265.935 -58.7206 0.5466 81.1576 1.77696
-742.718  
  
234 messages similar to the above omitted  
  
Chain information for
CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb #1  
---  
Chain | Description  
A | No description available  
  
Chain information for
Clover_505.0_515.0_111000.0_0.76_84.36_6.2_model_0_0001.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for
Citrine_516.0_529.0_77000.0_0.76_58.52_5.7_model_0_0001.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for
Citrine2_509.0_522.0_98000.0_0.7_68.6_5.9_model_0_0001.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for
AzamiGreen_492.0_505.0_72300.0_0.67_48.44_5.0_model_0_0001.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for
AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb #6  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-6 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 CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb, chain
A (#1) with Clover_505.0_515.0_111000.0_0.76_84.36_6.2_model_0_0001.pdb, chain
A (#2), sequence alignment score = 289.7  
RMSD between 146 pruned atom pairs is 0.976 angstroms; (across all 215 pairs:
3.733)  
  
Matchmaker CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb, chain
A (#1) with Citrine_516.0_529.0_77000.0_0.76_58.52_5.7_model_0_0001.pdb, chain
A (#3), sequence alignment score = 289.8  
RMSD between 143 pruned atom pairs is 1.016 angstroms; (across all 215 pairs:
3.405)  
  
Matchmaker CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb, chain
A (#1) with Citrine2_509.0_522.0_98000.0_0.7_68.6_5.9_model_0_0001.pdb, chain
A (#4), sequence alignment score = 293.3  
RMSD between 152 pruned atom pairs is 0.926 angstroms; (across all 214 pairs:
3.746)  
  
Matchmaker CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb, chain
A (#1) with AzamiGreen_492.0_505.0_72300.0_0.67_48.44_5.0_model_0_0001.pdb,
chain A (#5), sequence alignment score = 369.4  
RMSD between 165 pruned atom pairs is 0.912 angstroms; (across all 214 pairs:
3.591)  
  
Matchmaker CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb, chain
A (#1) with AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb,
chain A (#6), sequence alignment score = 289.1  
RMSD between 121 pruned atom pairs is 1.090 angstroms; (across all 208 pairs:
3.150)  
  

> color orange

> select ::name="TYR"

1512 atoms, 1512 bonds, 72 residues, 6 models selected  

> color sel cornflower blue

> color sel lime

> show sel atoms

> hide sel atoms

> select ::name="GLU"

1410 atoms, 1322 bonds, 94 residues, 6 models selected  

> show sel atoms

> color sel cornflower blue

> hide sel atoms

> select ::name="ASP"

1056 atoms, 971 bonds, 88 residues, 6 models selected  

> show sel atoms

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for
CpYGFP_508.0_518.0_101000.0_0.53_53.53_nan_model_0_0001.pdb_A SES surface
#1.1: minimum, -12.79, mean -0.61, maximum 12.38  
Coulombic values for
Clover_505.0_515.0_111000.0_0.76_84.36_6.2_model_0_0001.pdb_A SES surface
#2.1: minimum, -15.59, mean -1.80, maximum 8.83  
Coulombic values for
Citrine_516.0_529.0_77000.0_0.76_58.52_5.7_model_0_0001.pdb_A SES surface
#3.1: minimum, -21.22, mean -1.95, maximum 9.28  
Coulombic values for
Citrine2_509.0_522.0_98000.0_0.7_68.6_5.9_model_0_0001.pdb_A SES surface #4.1:
minimum, -15.96, mean -2.14, maximum 8.78  
Coulombic values for
AzamiGreen_492.0_505.0_72300.0_0.67_48.44_5.0_model_0_0001.pdb_A SES surface
#5.1: minimum, -9.62, mean 0.37, maximum 13.57  
Coulombic values for
AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb_A SES surface
#6.1: minimum, -11.80, mean -0.21, maximum 11.05  
To also show corresponding color key, enter the above coulombic command and
add key true  

> select #26

Nothing selected  

> select ~sel

21867 atoms, 22138 bonds, 1393 residues, 6 models selected  

> hide sel cartoons

> hide sel surfaces

> hide sel atoms

> select #6

3589 atoms, 3633 bonds, 232 residues, 1 model selected  

> show sel cartoons

> coulombic sel

Coulombic values for
AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb_A SES surface
#6.1: minimum, -11.80, mean -0.21, maximum 11.05  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> show sel atoms

> hide sel atoms

> select #6/A:66

21 atoms, 21 bonds, 1 residue, 1 model selected  

> hbonds sel reveal true

8 hydrogen bonds found  

> close #1-5

> select ::name="GLU"

210 atoms, 196 bonds, 14 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #6/A:66,220,146

53 atoms, 52 bonds, 1 pseudobond, 3 residues, 2 models selected  

> show sel atoms

> interfaces select & ~solvent

Missing or invalid "atoms" argument: invalid atoms specifier  

> select ::name="ARG"

168 atoms, 161 bonds, 7 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select #6/A:66,220,146,94

77 atoms, 75 bonds, 2 pseudobonds, 4 residues, 2 models selected  

> show sel atoms

> select ::name="HIS"

153 atoms, 154 bonds, 9 residues, 1 model selected  

> show sel atoms

> select ::name="ASP"

132 atoms, 121 bonds, 11 residues, 1 model selected  

> show sel atoms

> select ::name="HIS"

153 atoms, 154 bonds, 9 residues, 1 model selected  

> hide sel cartoons

> show sel cartoons

> hide sel atoms

> select ::name="ASP"

132 atoms, 121 bonds, 11 residues, 1 model selected  

> color (#!6 & sel) purple

> hide sel atoms

> color (#!6 & sel) orange

> select #6/A:66,220,146,94,65

91 atoms, 89 bonds, 2 pseudobonds, 5 residues, 2 models selected  

> show sel atoms

> open
> /home/pwoolley/work/NAD_sensor/boltz/fpbase/AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0.pdb

Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/fpbase/AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 1812  
  
Chain information for AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0.pdb
#1  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker

> matchmaker #!6 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 AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0.pdb, chain A
(#1) with AausFP1_504.0_510.0_170000.0_0.97_164.9_4.4_model_0_0001.pdb, chain
A (#6), sequence alignment score = 1233.9  
RMSD between 231 pruned atom pairs is 0.658 angstroms; (across all 232 pairs:
0.688)  
  

> select #*/A:66,220,146,94,65

140 atoms, 136 bonds, 2 pseudobonds, 10 residues, 3 models selected  

> show sel atoms

> hide #!6 models

> select #1

1810 atoms, 1854 bonds, 232 residues, 1 model selected  

> color byattribute bfactor

5399 atoms, 464 residues, 1 surfaces, atom bfactor range 0 to 98.8  

> open
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_0.76_1123429_model_0_7_NAD_4_NAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_0.76_1123429_model_0_7_NAD_4_noNAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.23_399416_model_4_8_NAD_8_NAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.04_448511_model_3_18_NAD_8_noNAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.04_448511_model_3_18_NAD_8_NAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.23_399416_model_4_8_NAD_8_noNAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.97_789971_model_1_10_NAD_6_NAD_model_0.pdb
> /home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.97_789971_model_1_10_NAD_6_noNAD_model_0.pdb

Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_0.76_1123429_model_0_7_NAD_4_NAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4558  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_0.76_1123429_model_0_7_NAD_4_noNAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4465  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.23_399416_model_4_8_NAD_8_NAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4556  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.04_448511_model_3_18_NAD_8_noNAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4489  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.04_448511_model_3_18_NAD_8_NAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4582  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.23_399416_model_4_8_NAD_8_noNAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4463  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.97_789971_model_1_10_NAD_6_NAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4549  
  
Summary of feedback from opening
/home/pwoolley/work/NAD_sensor/boltz/8-7-2025/partial_diffusion_1.97_789971_model_1_10_NAD_6_noNAD_model_0.pdb  
---  
warning | Ignored bad PDB record found on line 4456  
  
Chain information for
partial_diffusion_0.76_1123429_model_0_7_NAD_4_NAD_model_0.pdb #2  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_0.76_1123429_model_0_7_NAD_4_noNAD_model_0.pdb #3  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_1.23_399416_model_4_8_NAD_8_NAD_model_0.pdb #4  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_1.04_448511_model_3_18_NAD_8_noNAD_model_0.pdb #5  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_1.04_448511_model_3_18_NAD_8_NAD_model_0.pdb #8  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_1.23_399416_model_4_8_NAD_8_noNAD_model_0.pdb #9  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_1.97_789971_model_1_10_NAD_6_NAD_model_0.pdb #10  
---  
Chain | Description  
A | No description available  
  
Chain information for
partial_diffusion_1.97_789971_model_1_10_NAD_6_noNAD_model_0.pdb #11  
---  
Chain | Description  
A | No description available  
  

> ui tool show Matchmaker


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

Log:
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 550.163.01
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.2
Locale: en_US.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=cinnamon
XDG_SESSION_DESKTOP=cinnamon
XDG_CURRENT_DESKTOP=X-Cinnamon
DISPLAY=:0
Manufacturer: Micro-Star International Co., Ltd.
Model: MS-7D69
OS: Linux Mint 21.3 Virginia
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD Ryzen 9 7950X 16-Core Processor
Cache Size: 1024 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           124Gi       7.9Gi        59Gi       685Mi        57Gi       115Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102 [GeForce RTX 3090] [10de:2204] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. GA102 [GeForce RTX 3090] [1043:87b3]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    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: 2.10.5
    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: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    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: 1.1.3
    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: 1.2.2
    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: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 2.1.2
    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: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    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: 1.1.2
    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: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    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: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 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: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.9.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9