Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.5.0-28-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 0x000070315bffb640 (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 0x0000703216a36b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py", line 85 in add_atom
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 949 in new_hydrogen
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 910 in add_altloc_hyds
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 909 in _attach_hydrogens
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/hbond.py", line 225 in add_hydrogens
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 184 in hbond_add_hydrogens
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/addh/cmd.py", line 77 in cmd_addh
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/coulombic.py", line 95 in assign_charges
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/coulombic/cmd.py", line 99 in cmd_coulombic
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 319 in execute
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
  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.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, chimerax.surface._surface, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 62)
===== 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: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/home/titsai1978/SynologyDrive/Job
> Application/Others/Next_Job/Prepare_Data/CD40L/PDB/ChimeraX_Cmd_v1.cxc"

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C,R,S smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> color /R,S lightpink

> hide atoms

> hide pbonds

> surface /R,S

> transparency 95 target s

> zoom factor 2

> label /A,B,C:194 size 48 height 3

> show /A,B,C:194 atoms

> select /A,B,C:194

18 atoms, 15 bonds, 3 residues, 1 model selected  

> style /A,B,C:194 sphere

Changed 18 atom styles  

> save /home/titsai1978/Downloads/CD40L_C194W.png format png width 2000 height
> 1500 supersample 3 transparentBackground true

executed ChimeraX_Cmd_v1.cxc  

> open "/home/titsai1978/SynologyDrive/Job
> Application/Others/Next_Job/Prepare_Data/CD40L/PDB/CD40L_template.cxs"

opened ChimeraX session  

> surface #1/A,B,C

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide all

> set bgColor linen

> set bgColor white

> lighting soft

> lighting fillIntensity .2

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide all

> set bgColor linen

> set bgColor white

> lighting soft

> lighting fillIntensity .2

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide all

> set bgColor linen

> set bgColor white

> lighting soft

> lighting fillIntensity .2

> show /A,B,C

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> hide all

> set bgColor linen

> set bgColor white

> lighting soft

> lighting fillIntensity .2

> show /A,B,C

> cartoon /A,B,C

> color /A deepskyblue

> color /B darkcyan

> color /C 50,40,65

> hide atoms

> set silhouettes true

> set silhouetteWidth 0.5

> lighting shadows true

> hide pbonds

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C,R,S smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> color /R,S lightpink

> hide atoms

> hide pbonds

> surface /R,S

> transparency 95 target s

> zoom factor 2

> label /A,B,C:194 size 48 height 3

> show /A,B,C:194 atoms

> select /A,B,C:194

18 atoms, 15 bonds, 3 residues, 1 model selected  

> style /A,B,C:194 sphere

Changed 18 atom styles  

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C,R,S smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /R,S

> transparency 95 target s

> zoom factor 2

> label /A,B,C:194 size 48 height 3

> show /A,B,C:194 atoms

> select /A,B,C:194

18 atoms, 15 bonds, 3 residues, 1 model selected  

> style /A,B,C:194 sphere

Changed 18 atom styles  

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /A,B,C

> transparency 95 target s

> zoom factor 2

> label /A,B,C:194 size 48 height 3

> show /A,B,C:194 atoms

> select /A,B,C:194

18 atoms, 15 bonds, 3 residues, 1 model selected  

> style /A,B,C:194 sphere

Changed 18 atom styles  

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /A,B,C

> transparency 95 target s

> zoom factor 2

> color bycharge #1/A,B,C

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color /A,B,C bycharge

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bycharge /A,B,C

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> color bycharge #1/A,B,C

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword  

> apbs A,B,C

Unknown command: apbs A,B,C  

> color electrostatic #1/A,B,C

Missing required "map" argument  

> show surfaces

> hide surfaces

Drag select of 405 residues  

> show sel surfaces

> color electrostatic A,B,C

Missing or invalid "surfaces" argument: invalid surfaces specifier  

> color electrostatic /A,B,C

Missing required "map" argument  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3qd6_A SES surface #1.2: minimum, -9.48, mean 0.49,
maximum 9.98  
Coulombic values for 3qd6_B SES surface #1.3: minimum, -10.59, mean 0.40,
maximum 12.25  
Coulombic values for 3qd6_C SES surface #1.4: minimum, -9.57, mean 0.52,
maximum 12.31  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic key true

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3qd6_A SES surface #1.2: minimum, -9.48, mean 0.49,
maximum 9.98  
Coulombic values for 3qd6_B SES surface #1.3: minimum, -10.59, mean 0.40,
maximum 12.25  
Coulombic values for 3qd6_C SES surface #1.4: minimum, -9.57, mean 0.52,
maximum 12.31  
Coulombic values for 3qd6_R SES surface #1.5: minimum, -18.09, mean -3.80,
maximum 6.63  
Coulombic values for 3qd6_S SES surface #1.6: minimum, -13.01, mean -3.77,
maximum 6.69  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> key pos 0.663928,0.506008 size 0.147872,0.185581

> key pos 0.8118,0.506008 size 0,0

> key pos 0.769231,0.134846 size 0.0463032,0.11749

> key pos 0.811053,0.324433 size 0.0313667,0.0226969

> key pos 0.890217,0.0547397 size 0.0261389,0.40721

> select clear

> select /A:133@CD

1 atom, 1 residue, 1 model selected  

> select /A:212@CD2

1 atom, 1 residue, 1 model selected  

> select up

10 atoms, 10 bonds, 1 residue, 2 models selected  

> select up

68 atoms, 69 bonds, 10 residues, 2 models selected  

> select up

1047 atoms, 1071 bonds, 136 residues, 2 models selected  

> select up

4948 atoms, 5068 bonds, 641 residues, 2 models selected  

> select up

4948 atoms, 5068 bonds, 5 pseudobonds, 641 residues, 7 models selected  

> select clear

> select /S:94@NZ

1 atom, 1 residue, 1 model selected  

> select up

9 atoms, 8 bonds, 1 residue, 2 models selected  

> select up

57 atoms, 56 bonds, 8 residues, 2 models selected  

> select up

921 atoms, 946 bonds, 119 residues, 2 models selected  

> show sel surfaces

> select clear

> close

> ui mousemode right translate

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /A,B,C

> transparency 95 target s

> zoom factor 2

> coulombic /A

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3qd6_A SES surface #1.2: minimum, -9.48, mean 0.49,
maximum 9.98  

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /A,B,C

> transparency 95 target s

> zoom factor 2

> coulombic /A

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3qd6_A SES surface #1.2: minimum, -9.48, mean 0.49,
maximum 9.98  

> coulombic key true

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3qd6_A SES surface #1.2: minimum, -9.48, mean 0.49,
maximum 9.98  
Coulombic values for 3qd6_B SES surface #1.3: minimum, -10.59, mean 0.40,
maximum 12.25  
Coulombic values for 3qd6_C SES surface #1.4: minimum, -9.57, mean 0.52,
maximum 12.31  
Coulombic values for 3qd6_R SES surface #1.5: minimum, -18.09, mean -3.80,
maximum 6.63  
Coulombic values for 3qd6_S SES surface #1.6: minimum, -13.01, mean -3.77,
maximum 6.69  

> key red-white-blue :-10 :0 :10 showTool true

> ui mousemode right "color key"

> close

> ui mousemode right translate

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /A,B,C

> transparency 95 target s

> zoom factor 2

> coulombic /A


===== 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  

> close

> open 3QD6

3qd6 title:  
Crystal structure of the CD40 and CD154 (CD40L) complex [more info...]  
  
Chain information for 3qd6 #1  
---  
Chain | Description | UniProt  
A B C D E F | CD40 ligand | CD40L_HUMAN 116-261  
R S T U | Tumor necrosis factor receptor superfamily member 5 | TNR5_HUMAN
21-190  
  
Non-standard residues in 3qd6 #1  
---  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine;
2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE)  
  
3qd6 mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /D,E,F,T,U

> hide all

> graphics silhouettes true width 1

> set bgColor linen

> lighting soft

> lighting fillIntensity .2

> show /A,B,C,R,S

> cartoon /A,B,C smooth 0

> color /A cornflower blue

> color /B darkcyan

> color /C tan

> hide atoms

> hide pbonds

> surface /A,B,C

> transparency 95 target s

> zoom factor 2

> coulombic /A

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 3qd6_A SES surface #1.2: minimum, -9.48, mean 0.49,
maximum 9.98  




OpenGL version: 3.3.0 NVIDIA 535.171.04
OpenGL renderer: NVIDIA GeForce RTX 2070/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=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B450 AORUS M
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 AMD Ryzen 5 3600 6-Core Processor
Cache Size: 512 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       2.8Gi        24Gi        98Mi       4.1Gi        27Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	07:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU106 [GeForce RTX 2070 Rev. A] [10de:1f07] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. TU106 [GeForce RTX 2070 Rev. A] [1043:8784]	
	Kernel driver in use: nvidia

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