H-Bonds: acc_phi_psi() takes N positional arguments

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.26100
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\au759858\\\OneDrive - Aarhus
> universitet\\\Documents\\\Projects\\\SM_GM_Erk2-Tornado\\\HDOCK prediction
> Tornado C5 Broccoli_Erk2.pdb"

Summary of feedback from opening C:\\\Users\\\au759858\\\OneDrive - Aarhus
universitet\\\Documents\\\Projects\\\SM_GM_Erk2-Tornado\\\HDOCK prediction
Tornado C5 Broccoli_Erk2.pdb  
---  
warnings | Duplicate atom serial number found: 1  
Duplicate atom serial number found: 5  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 8  
Duplicate atom serial number found: 10  
1916 messages similar to the above omitted  
  
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/cryosparc_P1502_J96_003_volume_map.mrc"

Opened cryosparc_P1502_J96_003_volume_map.mrc as #2, grid size 300,300,300,
pixel 1.29, shown at level 0.00838, step 2, values float32  

> open "C:/Users/au759858/OneDrive - Aarhus
> universitet/Documents/Projects/SM_GM_Erk2-Tornado/cryosparc_P1502_J96_003_volume_map.mrc"

Opened cryosparc_P1502_J96_003_volume_map.mrc as #3, grid size 300,300,300,
pixel 1.29, shown at level 0.00838, step 2, values float32  

> volume #3 step 1

> volume #2 step 1

> volume #2 level 0.25

> volume #3 level 0.25

> select add #1

7444 atoms, 8049 bonds, 15 pseudobonds, 566 residues, 2 models selected  

> ui mousemode right "move picked models"

> view matrix models #1,1,0,0,142.77,0,1,0,140.64,0,0,1,172.27

> view matrix models
> #1,0.37094,0.1055,-0.92265,173.91,-0.7815,-0.50123,-0.37151,273.41,-0.50166,0.85886,-0.10348,151.97

> view matrix models
> #1,0.37094,0.1055,-0.92265,196.75,-0.7815,-0.50123,-0.37151,244.84,-0.50166,0.85886,-0.10348,156.12

> ui tool show "Fit in Map"

> fitmap #1 inMap #2

Fit molecule HDOCK prediction Tornado C5 Broccoli_Erk2.pdb (#1) to map
cryosparc_P1502_J96_003_volume_map.mrc (#2) using 7444 atoms  
average map value = 0.1259, steps = 288  
shifted from previous position = 13.2  
rotated from previous position = 24.3 degrees  
atoms outside contour = 5727, contour level = 0.25  
  
Position of HDOCK prediction Tornado C5 Broccoli_Erk2.pdb (#1) relative to
cryosparc_P1502_J96_003_volume_map.mrc (#2) coordinates:  
Matrix rotation and translation  
0.10155381 -0.21379116 -0.97158642 228.14047314  
-0.86790481 -0.49638557 0.01850973 242.84000215  
-0.48623870 0.84136479 -0.23596023 148.80755906  
Axis 0.71070128 -0.41919563 -0.56495904  
Axis point 0.00000000 158.32556511 217.33046653  
Rotation angle (degrees) 144.62653532  
Shift along axis -23.72791885  
  
Drag select of 3 residues, 1 shapes  

> view matrix models
> #1,0.10155,-0.21379,-0.97159,228.49,-0.8679,-0.49639,0.01851,242.8,-0.48624,0.84136,-0.23596,148.54

> select up

4557 atoms, 5094 bonds, 213 residues, 1 model selected  

> select up

7444 atoms, 8049 bonds, 566 residues, 1 model selected  

> view matrix models
> #1,0.77859,0.50336,-0.37474,146.25,-0.31703,-0.19984,-0.92712,238.47,-0.54156,0.84065,0.0039854,142.78

> view matrix models
> #1,0.77859,0.50336,-0.37474,156.6,-0.31703,-0.19984,-0.92712,232.27,-0.54156,0.84065,0.0039854,134.17

> isolde start

> set selectionWidth 4

Done loading forcefield  

> isolde set simFidelityMode Medium/Medium

ISOLDE: setting sim fidelity mode to Medium/Medium  
nonbonded_cutoff_distance = 0.900000  
use_gbsa = True  
gbsa_cutoff = 1.100000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 19 residues in model #1 to IUPAC-IUB
standards.  
Chain information for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
  

> clipper associate #2 toModel #1

Opened cryosparc_P1502_J96_003_volume_map.mrc as #1.1.1.1, grid size
300,300,300, pixel 1.29, shown at step 1, values float32  

> hide #!3 models

> isolde restrain basepairs sel

donor: /B C 44 N4 acceptor: /B G 45 O6  
Traceback (most recent call last):  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\ui\restraints_tab\base_pairing.py", line 33, in
<lambda>  
bp.triggered.connect(lambda *_:run(session, 'isolde restrain basepair sel'))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\cmd.py", line 51, in restrain_basepairs  
restrain_base_pairs(session, residues, dist_slop=dist_slop,
angle_slop=angle_slop)  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\restraint_utils.py", line 1026, in
restrain_base_pairs  
hbonds.extend(find_hbonds(session, [s], donors=target_donors,
acceptors=ref_acceptors, dist_slop=dist_slop, angle_slop=angle_slop))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde restrain basepairs sel

donor: /B C 44 N4 acceptor: /B G 45 O6  
Traceback (most recent call last):  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\ui\restraints_tab\base_pairing.py", line 33, in
<lambda>  
bp.triggered.connect(lambda *_:run(session, 'isolde restrain basepair sel'))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\cmd.py", line 51, in restrain_basepairs  
restrain_base_pairs(session, residues, dist_slop=dist_slop,
angle_slop=angle_slop)  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\restraint_utils.py", line 1026, in
restrain_base_pairs  
hbonds.extend(find_hbonds(session, [s], donors=target_donors,
acceptors=ref_acceptors, dist_slop=dist_slop, angle_slop=angle_slop))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select clear

[Repeated 2 time(s)]

> select up

4557 atoms, 5094 bonds, 213 residues, 1 model selected  

> isolde restrain basepairs sel

donor: /B C 44 N4 acceptor: /B G 45 O6  
Traceback (most recent call last):  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\ui\restraints_tab\base_pairing.py", line 33, in
<lambda>  
bp.triggered.connect(lambda *_:run(session, 'isolde restrain basepair sel'))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\cmd.py", line 51, in restrain_basepairs  
restrain_base_pairs(session, residues, dist_slop=dist_slop,
angle_slop=angle_slop)  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\restraint_utils.py", line 1026, in
restrain_base_pairs  
hbonds.extend(find_hbonds(session, [s], donors=target_donors,
acceptors=ref_acceptors, dist_slop=dist_slop, angle_slop=angle_slop))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> isolde restrain distances strand

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances helix

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances nucleic

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> isolde restrain distances protein

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  

> select up

141 atoms, 141 bonds, 16 residues, 1 model selected  

> select up

1433 atoms, 1462 bonds, 177 residues, 1 model selected  

> select up

1472 atoms, 1499 bonds, 182 residues, 1 model selected  

> select up

2887 atoms, 2955 bonds, 353 residues, 1 model selected  

> select up

7444 atoms, 8049 bonds, 566 residues, 2 models selected  

> isolde restrain basepairs sel

donor: /B C 44 N4 acceptor: /B G 45 O6  
Traceback (most recent call last):  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\ui\restraints_tab\base_pairing.py", line 33, in
<lambda>  
bp.triggered.connect(lambda *_:run(session, 'isolde restrain basepair sel'))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\cmd.py", line 51, in restrain_basepairs  
restrain_base_pairs(session, residues, dist_slop=dist_slop,
angle_slop=angle_slop)  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\restraints\restraint_utils.py", line 1026, in
restrain_base_pairs  
hbonds.extend(find_hbonds(session, [s], donors=target_donors,
acceptors=ref_acceptors, dist_slop=dist_slop, angle_slop=angle_slop))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> view matrix models #1.2,1,0,0,-1.057,0,1,0,-8.4562,0,0,1,2.7226

> view matrix models #1.2,1,0,0,0.29261,0,1,0,-9.1115,0,0,1,-0.73663

> addh #1.2

Summary of feedback from adding hydrogens to HDOCK prediction Tornado C5
Broccoli_Erk2.pdb #1.2  
---  
warnings | Not adding hydrogens to /B G 1 P because it is missing heavy-atom bond partners  
Not adding hydrogens to /B G 45 C2 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B G 45 N3 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B G 45 C6 because it is missing heavy-atom bond
partners  
Not adding hydrogens to /B G 46 C5 because it is missing heavy-atom bond
partners  
2 messages similar to the above omitted  
notes | No usable SEQRES records for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb (#1.2) chain A; guessing termini instead  
No usable SEQRES records for HDOCK prediction Tornado C5 Broccoli_Erk2.pdb
(#1.2) chain B; guessing termini instead  
Chain-initial residues that are actual N termini: /A ALA 6  
Chain-initial residues that are not actual N termini: /A VAL 186  
Chain-final residues that are actual C termini: /A SER 358  
Chain-final residues that are not actual C termini: /A GLU 184  
donor: /B A 72 N6 acceptor: /B G 46 N7  
  
Traceback (most recent call last):  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 76, in
_populate_unparameterised_residue_table  
self._ask_to_add_hydrogens_if_necessary(residues)  
File "C:\Users\au759858\AppData\Local\UCSF\ChimeraX\1.8\Python311\site-
packages\chimerax\isolde\ui\validation_tab\unparameterised.py", line 226, in
_ask_to_add_hydrogens_if_necessary  
run(self.session, f'addh #{residues.unique_structures[0].id_string}')  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 Core Profile Context 23.20.40.01.231124
OpenGL renderer: AMD Radeon(TM) 780M
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: da_DK.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: LENOVO
Model: 21K8S0BJ00
OS: Microsoft Windows 11 Enterprise (Build 26100)
Memory: 15,801,827,328
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 PRO 7840U w/ Radeon 780M Graphics  
OSLanguage: en-US

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: 2024.6.2
    cftime: 1.6.4
    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: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    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: 1.2.7
    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-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    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: 1.8
    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: 1.2.4
    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-ISOLDE: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    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-MatchMaker: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    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: 1.13.5
    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: 3.0.15
    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: 1.16.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    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
    comtypes: 1.4.1
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    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: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    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: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    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
    pywin32: 306
    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: 6.4.1
    traitlets: 5.14.2
    typing-extensions: 4.12.2
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.11
    WMI: 1.5.1