ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-13.3.1-arm64-arm-64bit
ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.11 (2025-12-17)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/aashvin/Desktop/PEPC_MDH_FUSIONS/PEPC.pdb

PEPC.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for PEPC.pdb #1  
---  
Chain | Description  
A | No description available  
B C D | No description available  
  
Non-standard residues in PEPC.pdb #1  
---  
GLY — (GLY)  
  
Computing secondary structure  

> select /A

8178 atoms, 8350 bonds, 1005 residues, 1 model selected  

> delete sel

> select /C

8166 atoms, 8337 bonds, 1004 residues, 1 model selected  

> delete sel

> select /B

8166 atoms, 8337 bonds, 1004 residues, 1 model selected  

> delete sel

> ui mousemode right select

Drag select of 5 atoms, 4 bonds  

> delete sel

> open /Users/aashvin/Desktop/PEPC_MDH_FUSIONS/MDH.pdb

MDH.pdb title:  
SWISS-MODEL SERVER (https://swissmodel.expasy.org) Untitled Project [more
info...]  
  
Chain information for MDH.pdb #2  
---  
Chain | Description  
A B C D | No description available  
  
Computing secondary structure  

> ui mousemode right "translate selected models"

> select add #2

9212 atoms, 9344 bonds, 1240 residues, 1 model selected  

> view matrix models #2,1,0,0,0.94243,0,1,0,-6.8136,0,0,1,32.088

> select #2/C

2303 atoms, 2336 bonds, 310 residues, 1 model selected  

> delete sel

> select #2/B

2303 atoms, 2336 bonds, 310 residues, 1 model selected  

> delete sel

> select #2/A

2303 atoms, 2336 bonds, 310 residues, 1 model selected  

> select add #2

4606 atoms, 4672 bonds, 620 residues, 1 model selected  

> select subtract #2

Nothing selected  

> ui mousemode right select

> select add #2/D:140

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select add #2/D:319

10 atoms, 8 bonds, 2 residues, 1 model selected  

> select add #2/D:149

19 atoms, 16 bonds, 3 residues, 1 model selected  

> select add #2/D:139

27 atoms, 23 bonds, 4 residues, 1 model selected  

> select add #2/D:320

35 atoms, 30 bonds, 5 residues, 1 model selected  

> select add #2/D:141

49 atoms, 45 bonds, 6 residues, 1 model selected  

> select add #2/D:111

54 atoms, 49 bonds, 7 residues, 1 model selected  

> select add #2/D:112

63 atoms, 57 bonds, 8 residues, 1 model selected  

> select add #2/D:113

67 atoms, 60 bonds, 9 residues, 1 model selected  

> select add #2/D:108

75 atoms, 67 bonds, 10 residues, 1 model selected  

> select add #2/D:126

83 atoms, 74 bonds, 11 residues, 1 model selected  

> select add #2/D:104

87 atoms, 77 bonds, 12 residues, 1 model selected  

> select add #2/D:135

94 atoms, 83 bonds, 13 residues, 1 model selected  

> select add #2/D:316

101 atoms, 89 bonds, 14 residues, 1 model selected  

> select add #2/D:312

109 atoms, 96 bonds, 15 residues, 1 model selected  

> select add #2/D:309

114 atoms, 100 bonds, 16 residues, 1 model selected  

> select add #2/D:305

122 atoms, 107 bonds, 17 residues, 1 model selected  

> select add #2/D:302

127 atoms, 111 bonds, 18 residues, 1 model selected  

> select add #2/D:298

136 atoms, 119 bonds, 19 residues, 1 model selected  

> select add #2/D:301

141 atoms, 123 bonds, 20 residues, 1 model selected  

> select add #2/D:300

150 atoms, 131 bonds, 21 residues, 1 model selected  

> select add #2/D:269

162 atoms, 143 bonds, 22 residues, 1 model selected  

> delete sel

> select add #2/D:200

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select add #2/D:176

12 atoms, 10 bonds, 2 residues, 1 model selected  

> select add #2/D:168

17 atoms, 14 bonds, 3 residues, 1 model selected  

> select add #2/D:170

26 atoms, 22 bonds, 4 residues, 1 model selected  

> select add #2/D:175

33 atoms, 29 bonds, 5 residues, 1 model selected  

> select add #2/D:171

41 atoms, 36 bonds, 6 residues, 1 model selected  

> select add #2/D:173

46 atoms, 40 bonds, 7 residues, 1 model selected  

> select add #2/D:174

52 atoms, 45 bonds, 8 residues, 1 model selected  

> select add #2/D:172

56 atoms, 48 bonds, 9 residues, 1 model selected  

> select add #2/D:169

64 atoms, 55 bonds, 10 residues, 1 model selected  

> select add #2/D:167

72 atoms, 62 bonds, 11 residues, 1 model selected  

> select add #2/D:165

77 atoms, 66 bonds, 12 residues, 1 model selected  

> select add #2/D:164

86 atoms, 74 bonds, 13 residues, 1 model selected  

> select add #2/D:163

94 atoms, 81 bonds, 14 residues, 1 model selected  

> select add #2/D:161

99 atoms, 85 bonds, 15 residues, 1 model selected  

> select add #2/D:162

110 atoms, 95 bonds, 16 residues, 1 model selected  

> select add #2/D:160

116 atoms, 100 bonds, 17 residues, 1 model selected  

> delete sel

Drag select of 211 residues, 13 pseudobonds  

> delete sel

Drag select of 7 residues, 1 pseudobonds  

> select clear

Drag select of 20 residues, 5 pseudobonds  

> delete sel

Drag select of 7 residues, 1 pseudobonds  

> delete sel

> select clear

> delete sel

Drag select of 2 residues, 3 pseudobonds  

> select #2/D:293

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select clear

> select #2/D:293

7 atoms, 6 bonds, 1 residue, 1 model selected  

> delete sel

> select clear

> ui mousemode right translate

> ui mousemode right select

> select #2/D:208

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

> select #2/D:207

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

> select add #2/D:208

16 atoms, 14 bonds, 2 residues, 1 model selected  

> select add #2/D:205

23 atoms, 20 bonds, 3 residues, 1 model selected  

> select add #2/D:206

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select add #2/D:204

40 atoms, 35 bonds, 5 residues, 1 model selected  

> select add #2/D:194

47 atoms, 42 bonds, 6 residues, 1 model selected  

> select add #2/D:195

58 atoms, 52 bonds, 7 residues, 1 model selected  

> select add #2/D:196

70 atoms, 64 bonds, 8 residues, 1 model selected  

> select add #2/D:197

76 atoms, 69 bonds, 9 residues, 1 model selected  

> delete sel

> select add #2/D:198

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #2/D:202

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

> select add #2/D:199

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

> select add #2/D:203

28 atoms, 25 bonds, 4 residues, 1 model selected  

> delete sel

> select add #2/D:35

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

> select add #2/D:36

17 atoms, 15 bonds, 2 residues, 1 model selected  

> delete sel

> select add #2/D:180

7 atoms, 6 bonds, 1 residue, 1 model selected  

> select add #2/D:179

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

> select add #2/D:178

23 atoms, 20 bonds, 3 residues, 1 model selected  

> select add #2/D:177

31 atoms, 27 bonds, 4 residues, 1 model selected  

> select add #2/D:181

39 atoms, 34 bonds, 5 residues, 1 model selected  

> delete sel

> select add #2/D:257

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

> select add #2/D:258

19 atoms, 17 bonds, 2 residues, 1 model selected  

> select add #2/D:255

28 atoms, 25 bonds, 3 residues, 1 model selected  

> delete sel

> select add #2

2366 atoms, 2391 bonds, 8 pseudobonds, 319 residues, 2 models selected  

> ui tool show "Minimize Structure"

> minimize #2 logEnergy true

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to MDH.pdb #2  
---  
notes | No usable SEQRES records for MDH.pdb (#2) chain A; guessing termini instead  
No usable SEQRES records for MDH.pdb (#2) chain D; guessing termini instead  
Chain-initial residues that are actual N termini: MDH.pdb #2/A GLN 12  
Chain-initial residues that are not actual N termini: MDH.pdb #2/D PHE 166,
MDH.pdb #2/D GLY 201, MDH.pdb #2/D GLY 223, MDH.pdb #2/D ALA 239, MDH.pdb #2/D
VAL 246, MDH.pdb #2/D SER 256, MDH.pdb #2/D GLN 294, MDH.pdb #2/D GLU 299,
MDH.pdb #2/D VAL 321  
Chain-final residues that are actual C termini: MDH.pdb #2/A VAL 321, MDH.pdb
#2/D VAL 321  
Chain-final residues that are not actual C termini: MDH.pdb #2/D PHE 166,
MDH.pdb #2/D GLY 201, MDH.pdb #2/D GLY 223, MDH.pdb #2/D ALA 239, MDH.pdb #2/D
VAL 246, MDH.pdb #2/D SER 256, MDH.pdb #2/D GLN 294, MDH.pdb #2/D GLU 299  
286 hydrogen bonds  
Adding 'H' to MDH.pdb #2/D PHE 166  
Adding 'H' to MDH.pdb #2/D GLY 201  
Adding 'H' to MDH.pdb #2/D GLY 223  
Adding 'H' to MDH.pdb #2/D ALA 239  
Adding 'H' to MDH.pdb #2/D VAL 246  
4 messages similar to the above omitted  
MDH.pdb #2/D PHE 166 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D GLY 223 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D ALA 239 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D VAL 246 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D SER 256 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
2438 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 107, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 157, in _minimize  
if cx_atom.num_bonds == 0:  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 157, in _minimize  
if cx_atom.num_bonds == 0:  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> ui tool show "Minimize Structure"

> minimize #2 logEnergy true

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Summary of feedback from adding hydrogens to MDH.pdb #2  
---  
notes | No usable SEQRES records for MDH.pdb (#2) chain A; guessing termini instead  
No usable SEQRES records for MDH.pdb (#2) chain D; guessing termini instead  
Chain-initial residues that are actual N termini: MDH.pdb #2/A GLN 12  
Chain-initial residues that are not actual N termini: MDH.pdb #2/D PHE 166,
MDH.pdb #2/D GLY 201, MDH.pdb #2/D GLY 223, MDH.pdb #2/D ALA 239, MDH.pdb #2/D
VAL 246, MDH.pdb #2/D SER 256, MDH.pdb #2/D GLN 294, MDH.pdb #2/D GLU 299,
MDH.pdb #2/D VAL 321  
Chain-final residues that are actual C termini: MDH.pdb #2/A VAL 321, MDH.pdb
#2/D VAL 321  
Chain-final residues that are not actual C termini: MDH.pdb #2/D PHE 166,
MDH.pdb #2/D GLY 201, MDH.pdb #2/D GLY 223, MDH.pdb #2/D ALA 239, MDH.pdb #2/D
VAL 246, MDH.pdb #2/D SER 256, MDH.pdb #2/D GLN 294, MDH.pdb #2/D GLU 299  
276 hydrogen bonds  
MDH.pdb #2/D PHE 166 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D GLY 223 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D ALA 239 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D VAL 246 is not terminus, removing H atom from 'C'  
MDH.pdb #2/D SER 256 is not terminus, removing H atom from 'C'  
1 messages similar to the above omitted  
0 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 101, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 41, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 146, in dock_prep_caller  
run_steps(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 107, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/addh/dock_prep.py", line 56, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 161, in run_steps  
step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'],
state['memorize_name'],  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/add_charge/dock_prep.py", line 58, in run_for_dock_prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/cmd.py", line 156, in run_steps  
callback()  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 106, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 157, in _minimize  
if cx_atom.num_bonds == 0:  
^^^^^^^^^^^^^^^^^  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
AttributeError: 'NoneType' object has no attribute 'num_bonds'  
  
File
"/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 157, in _minimize  
if cx_atom.num_bonds == 0:  
^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 83.1
OpenGL renderer: Apple M1
OpenGL vendor: Apple

Python: 3.11.9
Locale: UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGN73HN/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 8422.100.650
      OS Loader Version: 8422.100.650

Software:

    System Software Overview:

      System Version: macOS 13.3.1 (a) (22E772610a)
      Kernel Version: Darwin 22.4.0
      Time since boot: 4 days, 15 hours, 17 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal


Installed Packages:
    aiohappyeyeballs: 2.6.1
    aiohttp: 3.13.1
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.12.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 25.4.0
    babel: 2.17.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 3.12.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.4
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.1.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Animations: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.61.4
    ChimeraX-AtomicLibrary: 14.2.1
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.3
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-Boltz: 1.1
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.2
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.6.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.0
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.11
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.5
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.4
    ChimeraX-Dicom: 1.2.7
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.4
    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: 1.4.1
    ChimeraX-Hbonds: 2.5.3
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.4
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.7.3
    ChimeraX-Label: 1.2
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.2
    ChimeraX-Map: 1.3
    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: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.1.0
    ChimeraX-MDcrds: 2.17.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.6
    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: 1.0.1
    ChimeraX-MutationScores: 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: 1.15.2
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.11
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.5
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.4
    ChimeraX-ProfileGrids: 1.4.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.5
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.3
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.2
    ChimeraX-Scenes: 0.3.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.10
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.3
    ChimeraX-Shape: 1.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.1
    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: 2.5.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.49.1
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.5.2
    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: 1.1.5
    ChimeraX-Zone: 1.0.1
    click: 8.3.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.13.0
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.4
    debugpy: 1.8.19
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.61.1
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.15.1
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.11
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.3.0
    ipykernel: 6.30.1
    ipython: 9.5.0
    ipython_pygments_lexers: 1.1.1
    ipywidgets: 8.1.8
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.25.1
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.6.3
    jupyter_core: 5.9.1
    jupyterlab_widgets: 3.0.16
    kiwisolver: 1.4.9
    line_profiler: 5.0.0
    lxml: 6.0.2
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.3
    matplotlib: 3.10.7
    matplotlib-inline: 0.2.1
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.0
    ndindex: 1.10.1
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.14.1
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.5
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 11.3.0
    pip: 25.2
    pkginfo: 1.12.1.2
    platformdirs: 4.5.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.4.1
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pybind11: 3.0.1
    pycollada: 0.8
    pydantic: 2.12.5
    pydantic-settings: 2.12.0
    pydantic_core: 2.41.5
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.3.6
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.2.5
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.2
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.2
    PyQt6_sip: 13.10.2
    pytest: 9.0.2
    pytest-cov: 7.0.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.1
    python-multipart: 0.0.21
    pytz: 2025.2
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.0.0
    roman-numerals-py: 4.0.0
    rpds-py: 0.30.0
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.0.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.2.0
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    sse-starlette: 3.0.4
    stack-data: 0.6.3
    starlette: 0.50.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.4
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    tzdata: 2025.3
    urllib3: 2.6.2
    uvicorn: 0.38.0
    wcwidth: 0.2.14
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.15
    yarl: 1.22.0