Crash in garbage collection

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-51-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.8rc202405160048 (2024-05-16 00:48:52 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x000074a8e2a00640 (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 0x000074a9f7a41b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molobject.py", line 1839 in new_bond
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py", line 173 in add_bond
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/struct_edit.py", line 108 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 102 in cmd_coulombic
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3209 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/shortcuts/shortcuts.py", line 535 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 592 in run_expanded_command
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 72 in func_plus_tip
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 338 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 419 in run_shortcut
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 401 in try_shortcut
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1386 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 285 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1006 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1169 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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 58)
===== Log before crash start =====
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405160048 (2024-05-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> close

> label delete

> set bgColor white

> graphics silhouettes true width 1.5

> cofr centerOfView

> alias cofron cofr centerofview showpivot 7,0.25

> alias cofroff cofr centerofview showpivot false

> alias lico show cartoon; cartoon style protein modeh default arrows f x
> round width 0.8 thick 0.8

> alias dc lighting depthCue false

> alias complex color bychain; color byhetero

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue

> alias cootmode2 set bgColor white; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues #26A269; color byhet ; disp; ~disp @H*; style ions ball;
> style solvent ball; size ballscale 0.2; size stickradius 0.07; transparency
> 70; cofr centerofview; clip near -10 far 10 position cofr; color
> ~##num_residues #6495ED

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias af_color color bfactor palette alphafold

> alias af_bar key red:low orange: yellow: cornflowerblue: blue:high

> alias resbetween sel ($1 & ($2: mousemode rightMode zoom

> mousemode wheelMode clip

> mousemode alt leftMode "contour level"

> mousemode alt rightMode "translate selected models"

> mousemode control rightMode "rotate selected models"

> lighting flat depthCue false

> color bychain

> color byhetero

> alias tape sel /TP, Tc

> alias zippers sel /ze, zB, zf, zC, zd, zD, zA, zE, zI, zF, zP, zG, zV, zH

> alias internal sel /TP, Tc /ze, zB, zf, zC, zd, zD, zA, zE, zI, zF, zP, zG,
> zV, zH

> alias pentons_c1 sel /k1,k2,k3,k4,k5

> alias pentons_c6 sel /l1,l2,l3,l4,l5

> alias hexons sel
> /A1,A2,A3,B1,B2,B3,C1,C2,C3,D1,D2,D3,E1,E2,E3,F1,F2,F3,G1,G2,G3,H1,H2,H3,I1,I2,I3,J1,J2,J3,K1,K2,K3,L1,L2,L3,M1,M2,M3,N1,N2,N3,O1,O2,O3,P1,P2,P3,Q1,Q2,Q3,R1,R2,R3,S1,S2,S3,T1,T2,T3,U1,U2,U3,V1,V2,V3,W1,W2,W3,X1,X2,X3,Y1,Y2,Y3,Z1,Z2,Z3,a1,a2,a3,b1,b2,b3,c1,c2,c3,d1,d2,d3,e1,e2,e3,f1,f2,f3,11,12,13,21,22,23,31,32,33,41,42,43,51,52,53

> alias hexons_cys sel
> /A1,A2,A3,B1,B2,B3,C1,C2,C3,D1,D2,D3,E1,E2,E3,F1,F2,F3,G1,G2,G3,H1,H2,H3,I1,I2,I3,J1,J2,J3,K1,K2,K3,L1,L2,L3,M1,M2,M3,N1,N2,N3,O1,O2,O3,P1,P2,P3,Q1,Q2,Q3,R1,R2,R3,S1,S2,S3,T1,T2,T3,U1,U2,U3,V1,V2,V3,W1,W2,W3,X1,X2,X3,Y1,Y2,Y3,Z1,Z2,Z3,a1,a2,a3,b1,b2,b3,c1,c2,c3,d1,d2,d3,e1,e2,e3,f1,f2,f3,11,12,13,21,22,23,31,32,33,41,42,43,51,52,53:165,316

> alias external_suture sel /uB,vC, wD, xE, xF, xG, xH, 76

> alias external_main sel /o*

> alias external sel /uB,vC, wD, xE, xF, xG, xH, 76 /o*

> alias channel sel /p4,CA,CB,CC

> alias internal_penta sel /p4,CA,CB,CC /o*

> alias internal_newtork sel /pW, pX, pZ, pY, tX, tY, tZ, t4, t2, j2, mO, n3,
> nO, mO, i1, m2, n2

> alias internal sel /p4,CA,CB,CC /TP, Tc /ze, zB, zf, zC, zd, zD, zA, zE, zI,
> zF, zP, zG, zV, zH /pW, pX, pZ, pY, tX, tY, tZ, t4, t2, j2, mO, n3, nO, mO,
> i1, m2, n2 /he, 57, gc, gd

> open fold_a7b1rgd_model_0.cif

Chain information for fold_a7b1rgd_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_1.cif

Chain information for fold_a7b1rgd_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_2.cif

Chain information for fold_a7b1rgd_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_3.cif

Chain information for fold_a7b1rgd_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_4.cif

Chain information for fold_a7b1rgd_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> mmaker #1-4 to #5

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 fold_a7b1rgd_model_4.cif, chain A (#5) with
fold_a7b1rgd_model_0.cif, chain A (#1), sequence alignment score = 2413.2  
RMSD between 429 pruned atom pairs is 0.264 angstroms; (across all 484 pairs:
8.618)  
  
Matchmaker fold_a7b1rgd_model_4.cif, chain A (#5) with
fold_a7b1rgd_model_1.cif, chain A (#2), sequence alignment score = 2421  
RMSD between 440 pruned atom pairs is 0.226 angstroms; (across all 484 pairs:
2.168)  
  
Matchmaker fold_a7b1rgd_model_4.cif, chain A (#5) with
fold_a7b1rgd_model_2.cif, chain A (#3), sequence alignment score = 2433  
RMSD between 436 pruned atom pairs is 0.220 angstroms; (across all 484 pairs:
2.333)  
  
Matchmaker fold_a7b1rgd_model_4.cif, chain A (#5) with
fold_a7b1rgd_model_3.cif, chain A (#4), sequence alignment score = 2419.2  
RMSD between 449 pruned atom pairs is 0.252 angstroms; (across all 484 pairs:
1.823)  
  

> color bychain

> color byhetero

> n

> hide #2-5 target m

> show #1 surfaces

> coulombic #!1

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for fold_a7b1rgd_model_0.cif_A SES surface #1.1: minimum,
-17.08, mean -4.29, maximum 7.13  
Coulombic values for fold_a7b1rgd_model_0.cif_B SES surface #1.2: minimum,
-22.63, mean -2.35, maximum 11.10  
Coulombic values for fold_a7b1rgd_model_0.cif_C SES surface #1.3: minimum,
-10.56, mean -0.96, maximum 9.01  
To also show corresponding color key, enter the above coulombic command and
add key true  

> split *

Expected a structures specifier or a keyword  

> split #1

Split fold_a7b1rgd_model_0.cif (#1) into 3 models  
Chain information for fold_a7b1rgd_model_0.cif A #1.1  
---  
Chain | Description  
A | No description available  
  
Chain information for fold_a7b1rgd_model_0.cif B #1.2  
---  
Chain | Description  
B | No description available  
  
Chain information for fold_a7b1rgd_model_0.cif C #1.3  
---  
Chain | Description  
C | No description available  
  

> show #1.1-3 surfaces

> coulombic #!1.1-3


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

Log:
Startup Messages  
---  
notes | available bundle cache has not been initialized yet  
Database-fetch provider 'redo' in bundle Map specified unknown data format
'MTZ'  
  
UCSF ChimeraX version: 1.8rc202405160048 (2024-05-16)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> close

> label delete

> set bgColor white

> graphics silhouettes true width 1.5

> cofr centerOfView

> alias cofron cofr centerofview showpivot 7,0.25

> alias cofroff cofr centerofview showpivot false

> alias lico show cartoon; cartoon style protein modeh default arrows f x
> round width 0.8 thick 0.8

> alias dc lighting depthCue false

> alias complex color bychain; color byhetero

> alias cootmode set bgColor black; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues gold; color byhet ; disp; ~disp @H*; style ions ball; style
> solvent ball; size ballscale 0.2; size stickradius 0.07; transparency 70;
> cofr centerofview; clip near -10 far 10 position cofr; color ~##num_residues
> cornflower blue

> alias cootmode2 set bgColor white; surface cap false; surface style solid;
> lighting flat; graphics silhouettes false; style stick; ~rib; color
> ##num_residues #26A269; color byhet ; disp; ~disp @H*; style ions ball;
> style solvent ball; size ballscale 0.2; size stickradius 0.07; transparency
> 70; cofr centerofview; clip near -10 far 10 position cofr; color
> ~##num_residues #6495ED

> alias cootmode_mesh surface cap false; surface style mesh; lighting flat;
> graphics silhouettes false; style stick; ~rib; color ##num_residues gold;
> color byhet ; disp; ~disp @H*; style solvent ball; style ions ball; size
> ballscale 0.2; size stickradius 0.07; cofr centerofview; clip near -10 far
> 10 position cofr; color ~##num_residues #3d60ffff; transparency 50

> alias ca_and_sidechains ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1;
> disp @P&nucleic&$1; style $1 stick; disp sidechain&$1; disp
> ~backbone&nucleic&$1; size stickradius 0.1; size pseudobondradius 0.1

> alias ca_trace ~rib $1; ~surf $1; ~disp $1; disp @CA&protein&$1; disp
> @P&nucleic&$1; style $1 stick; size stickradius 0.1; size pseudobondradius
> 0.1

> alias af_color color bfactor palette alphafold

> alias af_bar key red:low orange: yellow: cornflowerblue: blue:high

> alias resbetween sel ($1 & ($2:<5)) | ($2 & ($1:<5)); show sel atoms; color sel byhetero; style sel stick; select clear;

> mousemode rightMode zoom

> mousemode wheelMode clip

> mousemode alt leftMode "contour level"

> mousemode alt rightMode "translate selected models"

> mousemode control rightMode "rotate selected models"

> lighting flat depthCue false

> color bychain

> color byhetero

> alias tape sel /TP, Tc

> alias zippers sel /ze, zB, zf, zC, zd, zD, zA, zE, zI, zF, zP, zG, zV, zH

> alias internal sel /TP, Tc /ze, zB, zf, zC, zd, zD, zA, zE, zI, zF, zP, zG,
> zV, zH

> alias pentons_c1 sel /k1,k2,k3,k4,k5

> alias pentons_c6 sel /l1,l2,l3,l4,l5

> alias hexons sel
> /A1,A2,A3,B1,B2,B3,C1,C2,C3,D1,D2,D3,E1,E2,E3,F1,F2,F3,G1,G2,G3,H1,H2,H3,I1,I2,I3,J1,J2,J3,K1,K2,K3,L1,L2,L3,M1,M2,M3,N1,N2,N3,O1,O2,O3,P1,P2,P3,Q1,Q2,Q3,R1,R2,R3,S1,S2,S3,T1,T2,T3,U1,U2,U3,V1,V2,V3,W1,W2,W3,X1,X2,X3,Y1,Y2,Y3,Z1,Z2,Z3,a1,a2,a3,b1,b2,b3,c1,c2,c3,d1,d2,d3,e1,e2,e3,f1,f2,f3,11,12,13,21,22,23,31,32,33,41,42,43,51,52,53

> alias hexons_cys sel
> /A1,A2,A3,B1,B2,B3,C1,C2,C3,D1,D2,D3,E1,E2,E3,F1,F2,F3,G1,G2,G3,H1,H2,H3,I1,I2,I3,J1,J2,J3,K1,K2,K3,L1,L2,L3,M1,M2,M3,N1,N2,N3,O1,O2,O3,P1,P2,P3,Q1,Q2,Q3,R1,R2,R3,S1,S2,S3,T1,T2,T3,U1,U2,U3,V1,V2,V3,W1,W2,W3,X1,X2,X3,Y1,Y2,Y3,Z1,Z2,Z3,a1,a2,a3,b1,b2,b3,c1,c2,c3,d1,d2,d3,e1,e2,e3,f1,f2,f3,11,12,13,21,22,23,31,32,33,41,42,43,51,52,53:165,316

> alias external_suture sel /uB,vC, wD, xE, xF, xG, xH, 76

> alias external_main sel /o*

> alias external sel /uB,vC, wD, xE, xF, xG, xH, 76 /o*

> alias channel sel /p4,CA,CB,CC

> alias internal_penta sel /p4,CA,CB,CC /o*

> alias internal_newtork sel /pW, pX, pZ, pY, tX, tY, tZ, t4, t2, j2, mO, n3,
> nO, mO, i1, m2, n2

> alias internal sel /p4,CA,CB,CC /TP, Tc /ze, zB, zf, zC, zd, zD, zA, zE, zI,
> zF, zP, zG, zV, zH /pW, pX, pZ, pY, tX, tY, tZ, t4, t2, j2, mO, n3, nO, mO,
> i1, m2, n2 /he, 57, gc, gd

> open fold_a7b1rgd_model_0.cif

Chain information for fold_a7b1rgd_model_0.cif #1  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_1.cif

Chain information for fold_a7b1rgd_model_1.cif #2  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_2.cif

Chain information for fold_a7b1rgd_model_2.cif #3  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_3.cif

Chain information for fold_a7b1rgd_model_3.cif #4  
---  
Chain | Description  
A | .  
B | .  
C | .  
  

> open fold_a7b1rgd_model_4.cif

Chain information for fold_a7b1rgd_model_4.cif #5  
---  
Chain | Description  
A | .  
B | .  
C | .  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: Mesa Intel(R) Graphics (RPL-P)
OpenGL vendor: Intel

Python: 3.11.4
Locale: en_GB.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Micro-Star International Co., Ltd.
Model: Katana 17 B13VGK
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 20 13th Gen Intel(R) Core(TM) i7-13700H
Cache Size: 24576 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       4.6Gi        18Gi       710Mi       8.3Gi        25Gi
	Swap:           18Gi          0B        18Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation Device [8086:a7a0] (rev 04)	
	DeviceName: Onboard - Video	
	Subsystem: Micro-Star International Co., Ltd. [MSI] Device [1462:13c7]

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.2.2
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57
    ChimeraX-AtomicLibrary: 14.0.4
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.4
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8rc202405160048
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.1
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    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: 1.1.10
    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: 1.2
    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-maskChains: 1.4
    ChimeraX-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.16
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 1.3.4
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    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: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.0
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10