Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-21-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

Thread 0x00007f404cffa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 324 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 622 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1392 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007f419d419b80 (most recent call first):
  Garbage-collecting
  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/label/label3d.py", line 888 in location
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/label/label3d.py", line 832 in _label_rectangle
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/label/label3d.py", line 611 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/label/label3d.py", line 611 in _label_vertices
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/label/label3d.py", line 604 in _reposition_label_graphics
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/label/label3d.py", line 517 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, chimerax.surface._surface, 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.pdb_lib._load_libs, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 54)
===== Log before crash start =====
> open
> /home/ng/Documents/Class_IIA_hdacs/2A/5/hdac5_mef2a_500_1/hdac5_mef2a_run1/25_run1_500ns.pdb

Chain information for 25_run1_500ns.pdb #2  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> open
> /home/ng/Documents/Class_IIA_hdacs/2A/9/hdac9_mef2a/hdac9_mef2a_run1/mef2a_hdac9_run1_500ns_protein.pdb

Chain information for mef2a_hdac9_run1_500ns_protein.pdb #3  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> ui tool show Matchmaker

> matchmaker #2-3 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 24_500_run1.pdb, chain A (#1) with 25_run1_500ns.pdb, chain B (#2),
sequence alignment score = 442.8  
RMSD between 76 pruned atom pairs is 0.854 angstroms; (across all 90 pairs:
3.468)  
  
Matchmaker 24_500_run1.pdb, chain A (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain A (#3), sequence alignment score =
453  
RMSD between 76 pruned atom pairs is 0.745 angstroms; (across all 90 pairs:
4.747)  
  

> matchmaker #2-3 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 24_500_run1.pdb, chain A (#1) with 25_run1_500ns.pdb, chain B (#2),
sequence alignment score = 442.8  
RMSD between 76 pruned atom pairs is 0.854 angstroms; (across all 90 pairs:
3.468)  
  
Matchmaker 24_500_run1.pdb, chain A (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain A (#3), sequence alignment score =
453  
RMSD between 76 pruned atom pairs is 0.745 angstroms; (across all 90 pairs:
4.747)  
  

> matchmaker #2-3 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 24_500_run1.pdb, chain B (#1) with 25_run1_500ns.pdb, chain B (#2),
sequence alignment score = 430.2  
RMSD between 78 pruned atom pairs is 0.819 angstroms; (across all 90 pairs:
2.455)  
  
Matchmaker 24_500_run1.pdb, chain B (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain B (#3), sequence alignment score =
441.6  
RMSD between 74 pruned atom pairs is 0.795 angstroms; (across all 90 pairs:
3.854)  
  

> matchmaker #2-3 to #1/C pairing bs

Parameters  
---  
Chain pairing | bs  
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 24_500_run1.pdb, chain C (#1) with 25_run1_500ns.pdb, chain C (#2),
sequence alignment score = 98.2  
RMSD between 13 pruned atom pairs is 0.291 angstroms; (across all 24 pairs:
5.869)  
  
Matchmaker 24_500_run1.pdb, chain C (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain C (#3), sequence alignment score =
91  
RMSD between 18 pruned atom pairs is 0.742 angstroms; (across all 24 pairs:
5.646)  
  

> matchmaker #2-3 to #1/A pairing bs

Parameters  
---  
Chain pairing | bs  
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 24_500_run1.pdb, chain A (#1) with 25_run1_500ns.pdb, chain B (#2),
sequence alignment score = 442.8  
RMSD between 76 pruned atom pairs is 0.854 angstroms; (across all 90 pairs:
3.468)  
  
Matchmaker 24_500_run1.pdb, chain A (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain A (#3), sequence alignment score =
453  
RMSD between 76 pruned atom pairs is 0.745 angstroms; (across all 90 pairs:
4.747)  
  

> ui tool show Matchmaker

> matchmaker #2-3 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 24_500_run1.pdb, chain B (#1) with 25_run1_500ns.pdb, chain B (#2),
sequence alignment score = 430.2  
RMSD between 78 pruned atom pairs is 0.819 angstroms; (across all 90 pairs:
2.455)  
  
Matchmaker 24_500_run1.pdb, chain B (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain B (#3), sequence alignment score =
441.6  
RMSD between 74 pruned atom pairs is 0.795 angstroms; (across all 90 pairs:
3.854)  
  

> matchmaker #2-3 to #1/B pairing bs

Parameters  
---  
Chain pairing | bs  
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 24_500_run1.pdb, chain B (#1) with 25_run1_500ns.pdb, chain B (#2),
sequence alignment score = 430.2  
RMSD between 78 pruned atom pairs is 0.819 angstroms; (across all 90 pairs:
2.455)  
  
Matchmaker 24_500_run1.pdb, chain B (#1) with
mef2a_hdac9_run1_500ns_protein.pdb, chain B (#3), sequence alignment score =
441.6  
RMSD between 74 pruned atom pairs is 0.795 angstroms; (across all 90 pairs:
3.854)  
  

> ui tool show Matchmaker

> matchmaker #2/A to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 24_500_run1.pdb, chain B (#1) with 25_run1_500ns.pdb, chain A (#2),
sequence alignment score = 428.4  
RMSD between 73 pruned atom pairs is 0.876 angstroms; (across all 90 pairs:
5.074)  
  

> matchmaker #2/A to #1/B pairing ss

Parameters  
---  
Chain pairing | ss  
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 24_500_run1.pdb, chain B (#1) with 25_run1_500ns.pdb, chain A (#2),
sequence alignment score = 428.4  
RMSD between 73 pruned atom pairs is 0.876 angstroms; (across all 90 pairs:
5.074)  
  

> ui tool show Matchmaker

> close #1

> ui tool show Matchmaker

No reference and/or match structure/chain chosen  

> matchmaker #3/A to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 25_run1_500ns.pdb, chain A (#2) with
mef2a_hdac9_run1_500ns_protein.pdb, chain A (#3), sequence alignment score =
444.6  
RMSD between 78 pruned atom pairs is 0.721 angstroms; (across all 90 pairs:
2.555)  
  

> matchmaker #3/A to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 25_run1_500ns.pdb, chain A (#2) with
mef2a_hdac9_run1_500ns_protein.pdb, chain A (#3), sequence alignment score =
444.6  
RMSD between 78 pruned atom pairs is 0.721 angstroms; (across all 90 pairs:
2.555)  
  

> open
> /home/ng/Documents/Class_IIA_hdacs/2A/4/hdac4_mef2a_500_1/hdac4_mef2a_run1/24_500_run1.pdb

Chain information for 24_500_run1.pdb #1  
---  
Chain | Description  
A B | No description available  
C | No description available  
  

> ui tool show Matchmaker

> matchmaker #1/A to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 25_run1_500ns.pdb, chain A (#2) with 24_500_run1.pdb, chain A (#1),
sequence alignment score = 441  
RMSD between 77 pruned atom pairs is 0.781 angstroms; (across all 90 pairs:
5.997)  
  

> matchmaker #1/A to #2/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 25_run1_500ns.pdb, chain A (#2) with 24_500_run1.pdb, chain A (#1),
sequence alignment score = 441  
RMSD between 77 pruned atom pairs is 0.781 angstroms; (across all 90 pairs:
5.997)  
  

> open /home/ng/Desktop/hdac4_mef2a_crys_alphafold/7XUZ_CHAIN_A_G_H.pdb

7XUZ_CHAIN_A_G_H.pdb title:  
Crystal structure of A HDAC4-MEF2A-DNA ternary complex [more info...]  
  
Chain information for 7XUZ_CHAIN_A_G_H.pdb #4  
---  
Chain | Description | UniProt  
A | HD4 | HDAC4_HUMAN 62-192  
G H | myocyte-specific enhancer factor 2A isoform X4 |  
  

> ui tool show Matchmaker

> matchmaker #1/A to #4/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 7XUZ_CHAIN_A_G_H.pdb, chain A (#4) with 24_500_run1.pdb, chain A
(#1), sequence alignment score = 40.4  
RMSD between 21 pruned atom pairs is 0.820 angstroms; (across all 65 pairs:
20.699)  
  

> matchmaker #1/A to #4/A pairing ss

Parameters  
---  
Chain pairing | ss  
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 7XUZ_CHAIN_A_G_H.pdb, chain A (#4) with 24_500_run1.pdb, chain A
(#1), sequence alignment score = 40.4  
RMSD between 21 pruned atom pairs is 0.820 angstroms; (across all 65 pairs:
20.699)  
  

> ui tool show Matchmaker

> matchmaker #1-3 to #4

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 7XUZ_CHAIN_A_G_H.pdb, chain H (#4) with 24_500_run1.pdb, chain B
(#1), sequence alignment score = 438  
RMSD between 75 pruned atom pairs is 0.756 angstroms; (across all 90 pairs:
4.881)  
  
Matchmaker 7XUZ_CHAIN_A_G_H.pdb, chain H (#4) with 25_run1_500ns.pdb, chain B
(#2), sequence alignment score = 444  
RMSD between 80 pruned atom pairs is 0.828 angstroms; (across all 90 pairs:
4.880)  
  
Matchmaker 7XUZ_CHAIN_A_G_H.pdb, chain H (#4) with
mef2a_hdac9_run1_500ns_protein.pdb, chain B (#3), sequence alignment score =
442.2  
RMSD between 79 pruned atom pairs is 1.026 angstroms; (across all 90 pairs:
3.321)  
  

> matchmaker #1-3 to #4

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 7XUZ_CHAIN_A_G_H.pdb, chain H (#4) with 24_500_run1.pdb, chain B
(#1), sequence alignment score = 438  
RMSD between 75 pruned atom pairs is 0.756 angstroms; (across all 90 pairs:
4.881)  
  
Matchmaker 7XUZ_CHAIN_A_G_H.pdb, chain H (#4) with 25_run1_500ns.pdb, chain B
(#2), sequence alignment score = 444  
RMSD between 80 pruned atom pairs is 0.828 angstroms; (across all 90 pairs:
4.880)  
  
Matchmaker 7XUZ_CHAIN_A_G_H.pdb, chain H (#4) with
mef2a_hdac9_run1_500ns_protein.pdb, chain B (#3), sequence alignment score =
442.2  
RMSD between 79 pruned atom pairs is 1.026 angstroms; (across all 90 pairs:
3.321)  
  

> hide #3 models

> hide #2 models

> show #3 models

> show #2 models

> hide #3 models

> hide #2 models

> show #3 models

> show #2 models

> measure buriedarea /C: ALA, LEU, ILE, MET, PRO, PHE, GLY, VAL, TYR
> withAtoms2 /A,B: ALA, LEU, ILE, MET, PRO, PHE, GLY, VAL, TYR probeRadius 1.4
> listResidues true cutoffArea 1 select true

Buried area between /C:ALA,LEU,ILE,MET,PRO,PHE,GLY,VAL,TYR and
/A,B:ALA,LEU,ILE,MET,PRO,PHE,GLY,VAL,TYR = 1081  
area /C:ALA,LEU,ILE,MET,PRO,PHE,GLY,VAL,TYR = 2905.3, area
/A,B:ALA,LEU,ILE,MET,PRO,PHE,GLY,VAL,TYR = 15848, area both = 16591  
60 contacting residues  
24_500_run1.pdb #1/C GLY 161 47.915  
25_run1_500ns.pdb #2/C LEU 187 5.5955  
25_run1_500ns.pdb #2/C LEU 192 20.843  
25_run1_500ns.pdb #2/C LEU 185 11.411  
25_run1_500ns.pdb #2/C VAL 183 2.5351  
25_run1_500ns.pdb #2/C PHE 190 47.329  
25_run1_500ns.pdb #2/C ALA 179 5.4573  
25_run1_500ns.pdb #2/C LEU 191 21.226  
25_run1_500ns.pdb #2/C ILE 178 29.149  
25_run1_500ns.pdb #2/C ALA 177 86.425  
24_500_run1.pdb #1/C PHE 178 75.892  
mef2a_hdac9_run1_500ns_protein.pdb #3/C ALA 139 38.939  
mef2a_hdac9_run1_500ns_protein.pdb #3/C LEU 152 81.543  
mef2a_hdac9_run1_500ns_protein.pdb #3/C VAL 143 26.472  
mef2a_hdac9_run1_500ns_protein.pdb #3/C LEU 147 24.366  
mef2a_hdac9_run1_500ns_protein.pdb #3/C PHE 150 17.606  
mef2a_hdac9_run1_500ns_protein.pdb #3/C LEU 151 34.699  
mef2a_hdac9_run1_500ns_protein.pdb #3/C ALA 156 16.906  
24_500_run1.pdb #1/C LEU 180 88.359  
24_500_run1.pdb #1/C ALA 165 79.268  
24_500_run1.pdb #1/C VAL 171 65.26  
24_500_run1.pdb #1/C ALA 167 74.618  
24_500_run1.pdb #1/C VAL 179 56.965  
24_500_run1.pdb #1/C LEU 175 65.614  
24_500_run1.pdb #1/C MET 173 29.103  
24_500_run1.pdb #1/C VAL 166 53.21  
7XUZ_CHAIN_A_G_H.pdb #4/A LEU 155 41.623  
7XUZ_CHAIN_A_G_H.pdb #4/A LEU 152 86.288  
25_run1_500ns.pdb #2/B LEU 66 8.0567  
25_run1_500ns.pdb #2/B TYR 72 3.2789  
25_run1_500ns.pdb #2/B LEU 67 18.199  
25_run1_500ns.pdb #2/B MET 62 6.0847  
25_run1_500ns.pdb #2/B TYR 69 4.3863  
25_run1_500ns.pdb #2/A TYR 69 1.8639  
24_500_run1.pdb #1/B LEU 54 9.8505  
24_500_run1.pdb #1/B MET 62 16.508  
24_500_run1.pdb #1/A LEU 66 1.72  
24_500_run1.pdb #1/B LEU 67 1.2937  
24_500_run1.pdb #1/B TYR 69 39.001  
24_500_run1.pdb #1/B PRO 75 24.133  
7XUZ_CHAIN_A_G_H.pdb #4/A VAL 179 52.633  
7XUZ_CHAIN_A_G_H.pdb #4/A PHE 178 76.074  
7XUZ_CHAIN_A_G_H.pdb #4/A LEU 180 99.258  
7XUZ_CHAIN_A_G_H.pdb #4/A ALA 167 70.296  
25_run1_500ns.pdb #2/A MET 62 6.4399  
25_run1_500ns.pdb #2/A TYR 72 9.0887  
25_run1_500ns.pdb #2/A LEU 66 3.8741  
24_500_run1.pdb #1/A TYR 69 4.914  
7XUZ_CHAIN_A_G_H.pdb #4/A VAL 171 75.867  
mef2a_hdac9_run1_500ns_protein.pdb #3/A TYR 72 3.1777  
mef2a_hdac9_run1_500ns_protein.pdb #3/A LEU 67 10.629  
7XUZ_CHAIN_A_G_H.pdb #4/A LEU 175 40.782  
mef2a_hdac9_run1_500ns_protein.pdb #3/B TYR 72 6.2572  
mef2a_hdac9_run1_500ns_protein.pdb #3/B MET 62 3.1029  
mef2a_hdac9_run1_500ns_protein.pdb #3/A TYR 69 20.369  
mef2a_hdac9_run1_500ns_protein.pdb #3/B TYR 69 3.4436  
7XUZ_CHAIN_A_G_H.pdb #4/A MET 173 168.7  
24_500_run1.pdb #1/A TYR 72 5.6051  
7XUZ_CHAIN_A_G_H.pdb #4/A GLY 161 62.036  
7XUZ_CHAIN_A_G_H.pdb #4/A VAL 166 69.52  

> show sel atoms

> hide #!4 models

> close #4

> show sel surfaces

> surface style mesh

> transparency (#!1-3 & sel) 50

> label (#!1-3 & sel) text "{0.label_one_letter_code}
> {0.number}{0.insertion_code}"

> ui tool show "Color Actions"

> color sel bychain target acspfl

> select clear

> hide #!2 models

> hide #!1 models

> color byhetero target acspfl

> color bychain target acspfl

> color bychain target l

> ui tool show "Color Actions"

> color white target sl

> ui tool show "Color Actions"

> color white target s

> color dark green target l

> ui tool show "Color Actions"

> color bychain target l

No target buttons for the coloring action are checked  

> color bychain target l

> hide #!3 surfaces

> color #!3 byhetero


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




OpenGL version: 4.3 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: NV138
OpenGL vendor: Mesa

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=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Inspiron 3501
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.5Gi       2.4Gi       728Mi       702Mi       4.4Gi       4.1Gi
	Swap:          2.0Gi       0.0Ki       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	Subsystem: Dell TigerLake-LP GT2 [Iris Xe Graphics] [1028:0a25]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.16
    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: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.5
    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-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: 1.7.1
    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: 2.6.1
    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: 1.5.14
    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: 1.0.4
    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: 1.12.4
    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: 1.33.3
    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: 0.2.1
    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: 4.47.2
    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: 5.7.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.4
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.6.0
    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: 10.2.0
    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: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    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: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9