ChimeraX bug report submission

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.7.7-arm64-arm-64bit
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
UCSF ChimeraX version: 1.12 (2026-06-12)  
© 2016-2026 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> ui tool show Registration

> open 7B6w fromDatabase ccd format ccd

Unknown CCD ligand name  

> open 7b6w fromDatabase pdbe_bio format mmcif

Summary of feedback from opening 7b6w fetched from pdbe_bio  
---  
warnings | Missing or incorrect sequence information. Inferred polymer connectivity.  
Atom H is not in the residue template for PRO /A:38  
notes | Fetching compressed 7b6w bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/7b6w-assembly-1.cif.gz  
Fetching CCD T0B from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/T0B/T0B.cif  
  
7b6w bioassembly 1 title:  
Crystal structure of the human alpha1B adrenergic receptor in complex with
inverse agonist (+)-cyclazosin [more info...]  
  
Chain information for 7b6w bioassembly 1 #1  
---  
Chain | Description  
A | Alpha-1B adrenergic receptor,alpha1B adrenergic receptor,Alpha-1B adrenergic receptor,alpha1B adrenergic receptor,Alpha-1B adrenergic receptor,alpha1B adrenergic receptor,Alpha-1B adrenergic receptor,alpha1B adrenergic receptor  
  
Non-standard residues in 7b6w bioassembly 1 #1  
---  
T0B — (T0B)  
  
118 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  
Opened 1 biological assemblies for 7b6w  

> select ::name="T0B"

118 atoms, 126 bonds, 2 residues, 1 model selected  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui tool show "Dock Prep"

Populating font family aliases took 183 ms. Replace uses of missing font
family "Times" with one that exists to avoid this cost.  

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A GLN 39: phi -74.5, psi -29.3 trans  
/A LEU 40: phi -68.2, psi -25.3 trans  
/A ASP 41: phi -48.6, psi -35.4 trans  
/A ILE 42: phi -71.6, psi -51.6 trans  
/A ARG 44: phi -63.5, psi -35.1 trans  
/A ARG 74: phi -66.4, psi -30.2 trans  
/A ARG 115: phi -41.4, psi -34.1 trans  
/A ILE 145: phi -58.6, psi -37.2 trans  
/A ARG 148: phi -57.0, psi -52.3 trans  
/A TYR 150: phi -59.1, psi -49.8 trans  
/A LEU 151: phi -96.9, psi -6.0 trans  
/A GLN 152: phi -93.7, psi -34.4 trans  
/A THR 158: phi -112.9, psi -176.3 trans  
/A ARG 159: phi -62.7, psi -38.3 trans  
/A ARG 160: phi -61.1, psi -52.1 trans  
/A LYS 185: phi -79.6, psi -58.5 trans  
/A GLU 186: phi -88.7, psi 139.6 trans  
/A LYS 193: phi -137.8, psi 54.3 trans  
/A VAL 194: phi -52.1, psi -53.8 trans  
/A VAL 197: phi -66.6, psi -33.6 trans  
/A THR 198: phi -56.9, psi 163.3 trans  
/A GLU 199: phi 179.5, psi -175.5 trans  
/A PHE 206: phi -54.1, psi -41.1 trans  
/A TYR 227: phi -55.8, psi -47.1 trans  
/A LYS 231: phi -73.3, psi -44.2 trans  
/A ARG 232: phi -64.1, psi -36.6 trans  
/A THR 234: phi -69.9, psi -43.0 trans  
/A LYS 235: phi -63.2, psi -49.6 trans  
/A LEU 237: phi -84.9, psi none trans  
/A SER 248: phi none, psi 133.7 trans  
/A LYS 285: phi -47.7, psi -44.9 trans  
/A ARG 288: phi -93.8, psi -24.4 trans  
/A LYS 291: phi -65.5, psi -48.2 trans  
/A LYS 294: phi -71.7, psi -47.7 trans  
/A LYS 324: phi none, psi -57.4 trans  
/A VAL 329: phi -70.5, psi -44.8 trans  
/A GLU 352: phi -97.6, psi 106.4 trans  
/A LEU 354: phi -57.0, psi -41.0 trans  
/A GLU 356: phi -72.2, psi -45.6 trans  
/A LYS 360: phi -76.9, psi -24.6 trans  
/A GLU 391: phi -59.9, psi -27.0 trans  
/A LYS 414: phi -60.0, psi -28.5 trans  
/A GLU 473: phi -59.7, psi -39.1 trans  
/A LYS 490: phi -66.1, psi -29.5 trans  
/A GLU 505: phi -65.5, psi -47.9 trans  
/A LYS 513: phi -59.5, psi -48.1 trans  
/A ARG 517: phi -60.2, psi -42.5 trans  
/A GLU 518: phi -64.9, psi -22.4 trans  
/A GLN 524: phi -127.3, psi none trans  
Applying GLN rotamer (chi angles: 65.0 -86.1 56.2) to /A GLN 39  
Applying LEU rotamer (chi angles: -67.8 174.1) to /A LEU 40  
Applying ASP rotamer (chi angles: -71.6 -14.7) to /A ASP 41  
Applying ILE rotamer (chi angles: -66.5 168.5) to /A ILE 42  
Applying ARG rotamer (chi angles: -68.6 -73.6 -68.1 108.8) to /A ARG 44  
Applying ARG rotamer (chi angles: 178.9 65.5 -178.1 84.0) to /A ARG 74  
Applying ARG rotamer (chi angles: -178.9 75.0 -85.4 170.0) to /A ARG 115  
Applying ILE rotamer (chi angles: -68.1 168.5) to /A ILE 145  
Applying ARG rotamer (chi angles: -178.5 178.6 178.4 85.5) to /A ARG 148  
Applying TYR rotamer (chi angles: 74.5 111.2) to /A TYR 150  
Applying LEU rotamer (chi angles: -61.2 176.5) to /A LEU 151  
Applying GLN rotamer (chi angles: -174.7 64.2 73.5) to /A GLN 152  
Applying THR rotamer (chi angles: 65.5) to /A THR 158  
Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to /A ARG 159  
Applying ARG rotamer (chi angles: 179.8 76.0 -84.5 167.6) to /A ARG 160  
Applying LYS rotamer (chi angles: -178.2 178.5 -70.6 78.8) to /A LYS 185  
Applying GLU rotamer (chi angles: -64.4 83.2 -6.6) to /A GLU 186  
Applying LYS rotamer (chi angles: -61.1 -66.1 -174.5 -67.0) to /A LYS 193  
Applying VAL rotamer (chi angles: 170.9) to /A VAL 194  
Applying VAL rotamer (chi angles: 173.2) to /A VAL 197  
Applying THR rotamer (chi angles: 60.9) to /A THR 198  
Applying GLU rotamer (chi angles: -66.3 179.3 54.2) to /A GLU 199  
Applying PHE rotamer (chi angles: 179.8 79.4) to /A PHE 206  
Applying TYR rotamer (chi angles: 177.2 79.4) to /A TYR 227  
Applying LYS rotamer (chi angles: -70.5 -177.0 175.0 65.8) to /A LYS 231  
Applying ARG rotamer (chi angles: 178.6 66.1 -178.0 85.6) to /A ARG 232  
Applying THR rotamer (chi angles: -60.5) to /A THR 234  
Applying LYS rotamer (chi angles: -179.0 178.1 178.3 180.0) to /A LYS 235  
Applying LEU rotamer (chi angles: -64.7 174.5) to /A LEU 237  
Applying SER rotamer (chi angles: 179.0) to /A SER 248  
Applying LYS rotamer (chi angles: -63.9 -64.8 -87.6 70.8) to /A LYS 285  
Applying ARG rotamer (chi angles: -173.4 -88.6 -59.5 -81.9) to /A ARG 288  
Applying LYS rotamer (chi angles: 177.8 -92.7 -85.3 47.8) to /A LYS 291  
Applying LYS rotamer (chi angles: -70.3 -171.1 -71.7 -174.4) to /A LYS 294  
Applying LYS rotamer (chi angles: -66.8 -178.0 -177.5 -65.9) to /A LYS 324  
Applying VAL rotamer (chi angles: 173.1) to /A VAL 329  
Applying GLU rotamer (chi angles: 66.6 -83.9 15.8) to /A GLU 352  
Applying LEU rotamer (chi angles: -69.2 172.7) to /A LEU 354  
Applying GLU rotamer (chi angles: -177.8 177.5 -1.2) to /A GLU 356  
Applying LYS rotamer (chi angles: -67.2 175.1 70.0 176.2) to /A LYS 360  
Applying GLU rotamer (chi angles: -174.7 175.6 -1.2) to /A GLU 391  
Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 414  
Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to /A GLU 473  
Applying LYS rotamer (chi angles: -66.2 -66.3 -174.8 -67.0) to /A LYS 490  
Applying GLU rotamer (chi angles: -66.8 79.9 9.3) to /A GLU 505  
Applying LYS rotamer (chi angles: -179.9 63.8 167.7 61.8) to /A LYS 513  
Applying ARG rotamer (chi angles: 178.6 66.1 -178.0 85.6) to /A ARG 517  
Applying GLU rotamer (chi angles: -64.5 83.4 -3.7) to /A GLU 518  
Applying GLN rotamer (chi angles: -68.4 74.8 37.4) to /A GLN 524  
Summary of feedback from adding hydrogens to 7b6w bioassembly 1 #1  
---  
notes | No usable SEQRES records for 7b6w bioassembly 1 (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A PRO 38  
Chain-initial residues that are not actual N termini: /A SER 248, /A LYS 324  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLN 524, /A LEU 237, /A
LEU 319  
369 hydrogen bonds  
/A GLN 524 is not terminus, removing H atom from 'C'  
400 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue T0B (net charge +0) with gasteiger method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/antechamber -i
/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmpu7uusbz0/ante.in.mol2 -fi
mol2 -o
/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmpu7uusbz0/ante.out.mol2 -fo
mol2 -c gas -nc 0 -j 5 -s 2 -dr n  
(T0B) ``  
(T0B) `Welcome to antechamber 20.0: molecular input file processor.`  
(T0B) ``  
(T0B) `Info: Finished reading file
(/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmpu7uusbz0/ante.in.mol2);
atoms read (59), bonds read (63).`  
(T0B) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(T0B) ``  
(T0B) ``  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF`  
(T0B) ``  
Charges for residue T0B determined  
Dock prep finished  

> ui tool show "Minimize Structure"

> minimize #1

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Deleting residues with incomplete backbones  
Filling out missing side chains  
/A GLN 524: phi -127.3, psi none trans  
Applying GLN rotamer (chi angles: -68.4 74.8 37.4) to /A GLN 524  
Summary of feedback from adding hydrogens to 7b6w bioassembly 1 #1  
---  
notes | No usable SEQRES records for 7b6w bioassembly 1 (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A PRO 38  
Chain-initial residues that are not actual N termini: /A SER 248, /A LYS 324  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLN 524, /A LEU 237, /A
LEU 319  
365 hydrogen bonds  
/A GLN 524 is not terminus, removing H atom from 'C'  
6 hydrogens added  
  
Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue T0B (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmp7fm12t04/ante.in.mol2 -fi
mol2 -o
/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmp7fm12t04/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(T0B) ``  
(T0B) `Welcome to antechamber 20.0: molecular input file processor.`  
(T0B) ``  
(T0B) `Info: Finished reading file
(/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmp7fm12t04/ante.in.mol2);
atoms read (59), bonds read (63).`  
(T0B) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(T0B) ``  
(T0B) ``  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(T0B) `Info: Total number of electrons: 232; net charge: 0`  
(T0B) ``  
(T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(T0B) ``  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(T0B) ``  
(T0B) `Running:
/Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc
-o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(T0B) ``  
Charges for residue T0B determined  
Dock prep finished  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/tool.py", line 116, in minimize  
run(self.session, cmd)  
File
"/Applications/ChimeraX-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 43, in cmd_minimize  
dock_prep_caller(session, [structure], memorize_name="minimization",
nogui=True,  
File
"/Applications/ChimeraX-1.12.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-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 150, in prep  
callback(session, state, structures)  
File
"/Applications/ChimeraX-1.12.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-1.12.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-1.12.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-1.12.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-1.12.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-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/dock_prep/prep.py", line 149, in <lambda>  
state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb())  
^^^^  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 45, in <lambda>  
steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/minimize/cmd.py", line 232, in _minimize  
system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer,
constraints=HBonds)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 1279, in createSystem  
data.setAtomClasses(self)  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in setAtomClasses  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in <listcomp>  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
KeyError: 'N'  
  
KeyError: 'N'  
  
File
"/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openmm/app/forcefield.py", line 683, in  
self.atomClasses = [classNameForType[self.atomType[atom]] for atom in
self.atoms]  
~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M4
OpenGL vendor: Apple

Python: 3.11.9
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: Mac16,13
      Model Number: MW1H3LL/A
      Chip: Apple M4
      Total Number of Cores: 10 (4 performance and 6 efficiency)
      Memory: 16 GB
      System Firmware Version: mBoot-18000.120.36
      OS Loader Version: 11881.140.96.701.1

Software:

    System Software Overview:

      System Version: macOS 15.7.7 (24G720)
      Kernel Version: Darwin 24.6.0
      Time since boot: 20 days, 40 minutes

Graphics/Displays:

    Apple M4:

      Chipset Model: Apple M4
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2880 x 1864 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    accessible-pygments: 0.0.5
    aiohappyeyeballs: 2.6.2
    aiohttp: 3.13.4
    aiosignal: 1.4.0
    alabaster: 1.0.0
    annotated-types: 0.7.0
    anyio: 4.13.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.1
    attrs: 26.1.0
    babel: 2.18.0
    beautifulsoup4: 4.13.5
    blockdiag: 3.0.0
    blosc2: 4.4.3
    bs4: 0.0.2
    build: 1.3.0
    certifi: 2025.7.14
    cftime: 1.6.5
    charset-normalizer: 3.4.7
    ChimeraX-AddCharge: 1.5.20
    ChimeraX-AddH: 2.2.8
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.2
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.2
    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: 1.67.1
    ChimeraX-AtomicLibrary: 14.4
    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: 1.4.1
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.5
    ChimeraX-ChemGroup: 2.0.2
    ChimeraX-Clashes: 2.4
    ChimeraX-Cluster: 1.0
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.8
    ChimeraX-CommandLine: 1.3.1
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.12
    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: 1.2.2
    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: 1.8.2
    ChimeraX-Label: 1.5
    ChimeraX-LightingGUI: 1.0
    ChimeraX-ListInfo: 1.3.1
    ChimeraX-Log: 1.2.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.3
    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-MatchAlign: 1.2
    ChimeraX-MatchMaker: 2.4.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MCPServer: 0.2.0
    ChimeraX-MDcrds: 2.19
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.3.9
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.23
    ChimeraX-ModelPanel: 1.6.1
    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: 1.15.4
    ChimeraX-OpenFold: 1.0
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.13
    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: 1.6
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.8.2
    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: 3.5.12
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.18
    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-SNFG: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.19.3
    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: 2.5.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.4
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.50.8
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.6.2
    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: 8.4.1
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.14.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.2.4
    debugpy: 1.8.21
    decorator: 5.3.1
    docutils: 0.21.2
    executing: 2.2.1
    filelock: 3.19.1
    fonttools: 4.63.0
    frozenlist: 1.8.0
    funcparserlib: 2.0.0a0
    glfw: 2.10.0
    grako: 3.16.5
    h11: 0.16.0
    h5py: 3.16.0
    html2text: 2025.4.15
    httpcore: 1.0.9
    httpx: 0.28.1
    httpx-sse: 0.4.3
    idna: 3.18
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 2.0.0
    iniconfig: 2.3.0
    ipykernel: 7.1.0
    ipython: 9.9.0
    ipython_pygments_lexers: 1.1.1
    jedi: 0.19.2
    Jinja2: 3.1.6
    jsonschema: 4.26.0
    jsonschema-specifications: 2025.9.1
    jupyter_client: 8.8.0
    jupyter_core: 5.9.1
    kiwisolver: 1.5.0
    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: 0.2.2
    mcp: 1.18.0
    msgpack: 1.1.1
    multidict: 6.7.1
    narwhals: 2.22.1
    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: 8.4.0
    openvr: 1.26.701
    packaging: 25.0
    ParmEd: 4.2.2
    parso: 0.8.7
    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: 4.10.0
    plotly: 6.8.0
    pluggy: 1.6.0
    prompt_toolkit: 3.0.52
    propcache: 0.5.2
    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: 2.13.4
    pydantic-settings: 2.14.1
    pydantic_core: 2.46.4
    pydata-sphinx-theme: 0.18.0
    pydicom: 2.4.4
    Pygments: 2.18.0
    pynmrstar: 3.5.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.10
    PyOpenGL-accelerate: 3.1.10
    pyopenxr: 1.1.4501
    pyparsing: 3.3.2
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.10.2
    PyQt6-Qt6: 6.10.2
    PyQt6-WebEngine-commercial: 6.10.0
    PyQt6-WebEngine-Qt6: 6.10.2
    PyQt6_sip: 13.10.3
    pytest: 9.0.3
    pytest-cov: 7.1.0
    python-dateutil: 2.9.0.post0
    python-dotenv: 1.2.2
    python-multipart: 0.0.32
    pyzmq: 27.1.0
    qtconsole: 5.7.0
    QtPy: 2.4.3
    qtshim: 1.2.2
    RandomWords: 0.4.0
    referencing: 0.37.0
    requests: 2.32.5
    roman-numerals: 4.1.0
    rpds-py: 2026.5.1
    scipy: 1.14.0
    setuptools: 80.9.0
    sfftk-rw: 0.8.1
    six: 1.17.0
    snowballstemmer: 3.1.1
    sortedcontainers: 2.4.0
    soupsieve: 2.8.4
    Sphinx: 9.0.4
    sphinx-autodoc-typehints: 3.6.1
    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: 3.4.4
    stack-data: 0.6.3
    starlette: 1.3.0
    superqt: 0.7.6
    tables: 3.10.2
    tcia_utils: 3.2.1
    threadpoolctl: 3.6.0
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tornado: 6.5.7
    tqdm: 4.68.2
    traitlets: 5.14.3
    typing-inspection: 0.4.2
    typing_extensions: 4.15.0
    Unidecode: 1.4.0
    urllib3: 2.7.0
    uvicorn: 0.49.0
    wcwidth: 0.8.1
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    yarl: 1.24.2