Molecular Dynamics Viewer not handling hexadecimal residue numbers

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.11.dev202508050120 (2025-08-05 01:20:22 UTC)
Description
Replace this text with list of actions that caused this problem to occur

Log:
You can double click a model's Name or ID in the model panel to edit those
fields  
UCSF ChimeraX version: 1.11.dev202508050120 (2025-08-05)  
© 2016-2025 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/fogy/Documents/4MBS.pdb

4MBS.pdb title:  
Crystal structure of the CCR5 chemokine receptor [more info...]  
  
Chain information for 4MBS.pdb #1  
---  
Chain | Description | UniProt  
A B | chimera protein of C-C chemokine receptor type 5 and rubredoxin | CCR5_HUMAN 2-223 227-352, RUBR_CLOPA 1001-1054  
  
Non-standard residues in 4MBS.pdb #1  
---  
MRV —
4,4-difluoro-N-[(1S)-3-{(3-exo)-3-[3-methyl-5-(propan-2-yl)-4H-1,2,4-triazol-4-yl]-8-azabicyclo[3.2.1]oct-8-yl}-1-phenylpropyl]cyclohexanecarboxamide  
OLC — (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate (1-oleoyl-R-glycerol)  
ZN — zinc ion  
  
5486 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select add #1.1

8 pseudobonds, 1 model selected  

> select subtract #1.1

Nothing selected  

> select add #1

5764 atoms, 5871 bonds, 8 pseudobonds, 754 residues, 2 models selected  

> select ::name="HOH"::name="MRV"::name="OLC"::name="ZN"

278 atoms, 226 bonds, 62 residues, 1 model selected  

> delete atoms sel

> delete bonds sel

> select add #1

5486 atoms, 5645 bonds, 692 residues, 1 model selected  

> ui tool show "Dock Prep"

Populating font family aliases took 158 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 21: phi -60.5, psi 89.9 trans  
/A LYS 22: phi -67.1, psi 161.1 trans  
/A ILE 23: phi -82.6, psi 149.2 trans  
/A LYS 26: phi -65.2, psi -36.1 trans  
/A LYS 59: phi -72.2, psi -25.0 trans  
/A LYS 138: phi -97.6, psi -26.3 trans  
/A SER 179: phi -148.0, psi 169.9 trans  
/A LYS 191: phi -56.9, psi -49.2 trans  
/A LYS 1002: phi -61.5, psi 126.4 trans  
/A LYS 1031: phi -66.9, psi -21.4 trans  
/A LYS 228: phi -68.3, psi 122.6 trans  
/A LYS 229: phi -59.0, psi -38.7 trans  
/A GLU 262: phi -71.1, psi -25.3 trans  
/A PHE 263: phi -100.8, psi -39.2 trans  
/A LEU 266: phi -114.8, psi 113.7 trans  
/A ASN 267: phi -107.3, psi -11.0 trans  
/A SER 272: phi -65.2, psi -38.1 trans  
/A GLN 277: phi -67.7, psi -36.8 trans  
/A GLN 280: phi -63.9, psi -47.4 trans  
/A ARG 305: phi -79.9, psi -29.7 trans  
/A LEU 308: phi -58.2, psi -34.9 trans  
/A GLN 313: phi -68.6, psi none trans  
/B GLN 21: phi -60.6, psi 90.6 trans  
/B LYS 22: phi -66.4, psi 160.2 trans  
/B ILE 23: phi -82.9, psi 149.1 trans  
/B LYS 26: phi -64.9, psi -35.6 trans  
/B GLN 27: phi -68.7, psi -34.2 trans  
/B LEU 137: phi -58.4, psi -36.1 trans  
/B LYS 138: phi -98.6, psi -25.4 trans  
/B HIS 175: phi -116.3, psi 148.6 trans  
/B SER 179: phi -147.0, psi 169.6 trans  
/B LYS 191: phi -58.9, psi -48.4 trans  
/B LYS 1031: phi -67.6, psi -21.3 trans  
/B GLU 1050: phi -126.7, psi 145.9 trans  
/B LYS 228: phi -67.7, psi 125.4 trans  
/B LYS 229: phi -61.7, psi -39.1 trans  
/B PHE 263: phi -100.5, psi -39.3 trans  
/B LEU 266: phi -114.8, psi 114.0 trans  
/B SER 272: phi -66.6, psi -36.4 trans  
/B ASN 273: phi -75.8, psi -43.1 trans  
/B GLN 277: phi -67.5, psi -37.1 trans  
/B ARG 305: phi -64.6, psi -49.3 trans  
/B LEU 308: phi -70.2, psi -38.7 trans  
/B VAL 310: phi -75.6, psi -33.5 trans  

The following atoms were skipped as donors/acceptors due to missing heavy-atom
bond partners: /A ARG 305 NE; /B ARG 305 NE  

Applying GLN rotamer (chi angles: -179.1 65.8 51.5) to /A GLN 21  
Applying LYS rotamer (chi angles: 66.0 -173.9 -70.3 -174.3) to /A LYS 22  
Applying ILE rotamer (chi angles: 62.6 170.5) to /A ILE 23  
Applying LYS rotamer (chi angles: -177.8 66.0 175.8 178.5) to /A LYS 26  
Applying LYS rotamer (chi angles: -69.0 174.6 69.9 176.2) to /A LYS 59  
Applying LYS rotamer (chi angles: 67.1 178.5 72.8 65.5) to /A LYS 138  
Applying SER rotamer (chi angles: 66.7) to /A SER 179  
Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 191  
Applying LYS rotamer (chi angles: -178.2 91.4 -75.3 -174.6) to /A LYS 1002  
Applying LYS rotamer (chi angles: -66.4 -173.5 -71.8 -66.9) to /A LYS 1031  
Applying LYS rotamer (chi angles: -61.5 -67.4 -176.2 -178.3) to /A LYS 228  
Applying LYS rotamer (chi angles: -177.6 176.5 -176.1 -64.3) to /A LYS 229  
Applying GLU rotamer (chi angles: -174.5 174.6 -1.2) to /A GLU 262  
Applying PHE rotamer (chi angles: -68.1 102.4) to /A PHE 263  
Applying LEU rotamer (chi angles: -58.6 176.6) to /A LEU 266  
Applying ASN rotamer (chi angles: -66.1 -98.6) to /A ASN 267  
Applying SER rotamer (chi angles: 64.6) to /A SER 272  
Applying GLN rotamer (chi angles: -69.0 176.9 64.2) to /A GLN 277  
Applying GLN rotamer (chi angles: -69.9 176.2 64.1) to /A GLN 280  
Applying ARG rotamer (chi angles: -177.6 176.3 63.4 81.7) to /A ARG 305  
Applying LEU rotamer (chi angles: -68.4 173.8) to /A LEU 308  
Applying GLN rotamer (chi angles: -65.8 -178.9 75.3) to /A GLN 313  
Applying GLN rotamer (chi angles: -179.1 65.8 51.5) to /B GLN 21  
Applying LYS rotamer (chi angles: -66.3 -178.9 -179.9 179.3) to /B LYS 22  
Applying ILE rotamer (chi angles: 62.6 170.5) to /B ILE 23  
Applying LYS rotamer (chi angles: -178.6 66.3 175.8 178.5) to /B LYS 26  
Applying GLN rotamer (chi angles: -173.9 63.3 74.0) to /B GLN 27  
Applying LEU rotamer (chi angles: -69.2 172.7) to /B LEU 137  
Applying LYS rotamer (chi angles: 67.1 178.5 72.8 65.5) to /B LYS 138  
Applying HIS rotamer (chi angles: 64.7 -31.7) to /B HIS 175  
Applying SER rotamer (chi angles: 66.7) to /B SER 179  
Applying LYS rotamer (chi angles: -174.7 178.4 -68.9 -68.5) to /B LYS 191  
Applying LYS rotamer (chi angles: -66.4 -173.5 -71.8 -66.9) to /B LYS 1031  
Applying GLU rotamer (chi angles: -178.9 65.5 79.6) to /B GLU 1050  
Applying LYS rotamer (chi angles: -61.6 -67.4 -176.1 -178.2) to /B LYS 228  
Applying LYS rotamer (chi angles: -177.6 176.5 -176.1 -64.3) to /B LYS 229  
Applying PHE rotamer (chi angles: -68.1 102.4) to /B PHE 263  
Applying LEU rotamer (chi angles: -58.6 176.6) to /B LEU 266  
Applying SER rotamer (chi angles: 64.6) to /B SER 272  
Applying ASN rotamer (chi angles: -72.0 -81.1) to /B ASN 273  
Applying GLN rotamer (chi angles: -175.0 62.7 106.7) to /B GLN 277  
Applying ARG rotamer (chi angles: -179.4 65.3 178.1 173.5) to /B ARG 305  
Applying LEU rotamer (chi angles: -68.3 173.0) to /B LEU 308  
Applying VAL rotamer (chi angles: 173.7) to /B VAL 310  
Summary of feedback from adding hydrogens to 4MBS.pdb #1  
---  
notes | Termini for 4MBS.pdb (#1) chain A determined from SEQRES records  
Termini for 4MBS.pdb (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini:  
Chain-initial residues that are not actual N termini: /A PRO 19, /B PRO 19  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A GLN 313, /B GLN 313  
/A GLN 313 is not terminus, removing H atom from 'C'  
/B GLN 313 is not terminus, removing H atom from 'C'  
5686 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Dock prep finished  

> select subtract #1.1

5414 atoms, 5573 bonds, 692 residues, 1 model selected  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> select subtract #1.1

5414 atoms, 5573 bonds, 692 residues, 1 model selected  

> select add #1

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #1.1 models

> select add #1

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> select subtract #1

Nothing selected  

> select subtract #1.1

Nothing selected  

> save /Users/fogy/Documents/4MBS.pdb relModel #1

> hide #1.1 models

> select subtract #1.1

Nothing selected  

> select add #1

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> select subtract #1.1

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> select add #1.1

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> select subtract #1

Nothing selected  

> show #1.1 models

> delete atoms

> delete bonds

> open /Users/fogy/Documents/4MBS.pdb format pdb

4MBS.pdb title:  
Crystal structure of the CCR5 chemokine receptor [more info...]  
  
Chain information for 4MBS.pdb #1  
---  
Chain | Description | UniProt  
A B | chimera protein of C-C chemokine receptor type 5 and rubredoxin | CCR5_HUMAN 2-223 227-352, RUBR_CLOPA 1001-1054  
  
5414 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.  

> select add #1

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> select main

11306 atoms, 11468 bonds, 692 residues, 1 model selected  

> save /Users/fogy/Documents/4MBS.pdb relModel #1

> close session

> open /Users/fogy/Documents/trajectory.pdb

Summary of feedback from opening /Users/fogy/Documents/trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 115121  
HETATMA3B0E O HOH C 1A 103.481 76.798 28.913 1.00 0.00 O  
  
Ignored bad PDB record found on line 115122  
HETATMA3B0F H1 HOH C 1A 103.568 77.567 29.565 1.00 0.00 H  
  
Ignored bad PDB record found on line 115123  
HETATMA3B10 H2 HOH C 1A 104.339 76.263 28.940 1.00 0.00 H  
  
Ignored bad PDB record found on line 115124  
HETATMA3B11 O HOH C 1B 112.052 81.847 35.789 1.00 0.00 O  
  
Ignored bad PDB record found on line 115125  
HETATMA3B12 H1 HOH C 1B 111.699 80.936 36.054 1.00 0.00 H  
  
15655 messages similar to the above omitted  
  
Chain information for trajectory.pdb #1  
---  
Chain | Description  
A B | No description available  
  
Computing secondary structure  

> select add #1

127399 atoms, 88852 bonds, 39397 residues, 1 model selected  

> select subtract #1

Nothing selected  

> close session

> open /Users/fogy/Documents/trajectory.pdb

Summary of feedback from opening /Users/fogy/Documents/trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 115121  
HETATMA3B0E O HOH C 1A 103.481 76.798 28.913 1.00 0.00 O  
  
Ignored bad PDB record found on line 115122  
HETATMA3B0F H1 HOH C 1A 103.568 77.567 29.565 1.00 0.00 H  
  
Ignored bad PDB record found on line 115123  
HETATMA3B10 H2 HOH C 1A 104.339 76.263 28.940 1.00 0.00 H  
  
Ignored bad PDB record found on line 115124  
HETATMA3B11 O HOH C 1B 112.052 81.847 35.789 1.00 0.00 O  
  
Ignored bad PDB record found on line 115125  
HETATMA3B12 H1 HOH C 1B 111.699 80.936 36.054 1.00 0.00 H  
  
31315 messages similar to the above omitted  
  
Chain information for trajectory.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.1/B 1.2/B | No description available  
  
Computing secondary structure  
[Repeated 1 time(s)]

> select add #1.1

127399 atoms, 88852 bonds, 39397 residues, 1 model selected  

> select subtract #1.1

Nothing selected  

> select add #1.2

127399 atoms, 88852 bonds, 39397 residues, 1 model selected  

> select subtract #1.2

Nothing selected  

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> hide #!1 models

> show #!1 models

> show #1.1 models

> hide #1.1 models

> show #1.1 models

> hide #1.1 models

> hide #1.2 models

> show #1.2 models

> show #1.1 models

> select add #1

254798 atoms, 177704 bonds, 78794 residues, 3 models selected  

> select subtract #1

Nothing selected  

> select add #1

254798 atoms, 177704 bonds, 78794 residues, 3 models selected  

> reference #1

Unknown command: reference #1  

> reference 1.1

Unknown command: reference 1.1  

> rmsd #2 to #1 atom :CA per-frame true plot true

Expected a keyword  

> close session

> open /Users/fogy/Documents/trajectory.pdb

Summary of feedback from opening /Users/fogy/Documents/trajectory.pdb  
---  
warnings | Ignored bad PDB record found on line 115121  
HETATMA3B0E O HOH C 1A 103.481 76.798 28.913 1.00 0.00 O  
  
Ignored bad PDB record found on line 115122  
HETATMA3B0F H1 HOH C 1A 103.568 77.567 29.565 1.00 0.00 H  
  
Ignored bad PDB record found on line 115123  
HETATMA3B10 H2 HOH C 1A 104.339 76.263 28.940 1.00 0.00 H  
  
Ignored bad PDB record found on line 115124  
HETATMA3B11 O HOH C 1B 112.052 81.847 35.789 1.00 0.00 O  
  
Ignored bad PDB record found on line 115125  
HETATMA3B12 H1 HOH C 1B 111.699 80.936 36.054 1.00 0.00 H  
  
78295 messages similar to the above omitted  
  
Chain information for trajectory.pdb  
---  
Chain | Description  
1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.1/B 1.2/B 1.3/B 1.4/B 1.5/B | No description available  
  
Computing secondary structure  
[Repeated 4 time(s)]

> select add #1

636995 atoms, 444280 bonds, 196985 residues, 6 models selected  

> toolshed show

> ui tool show "Map Coordinates"

> select subtract #1

Nothing selected  

> select add #1

636995 atoms, 444280 bonds, 196985 residues, 6 models selected  

> select subtract #1

Nothing selected  

> select add #1.1

127399 atoms, 88856 bonds, 39397 residues, 1 model selected  

> select add #1.2

254798 atoms, 177712 bonds, 78794 residues, 2 models selected  

> select subtract #1.1

127399 atoms, 88856 bonds, 39397 residues, 1 model selected  

> select add #1.1

254798 atoms, 177712 bonds, 78794 residues, 2 models selected  

> select add #1

636995 atoms, 444280 bonds, 196985 residues, 6 models selected  

> select subtract #1

Nothing selected  

> select add #1

636995 atoms, 444280 bonds, 196985 residues, 6 models selected  

> models

Unknown command: models  

> info models

model id #1 type Model name "trajectory.pdb group"  
model id #1.1 type AtomicStructure name trajectory.pdb  
model id #1.2 type AtomicStructure name trajectory.pdb  
model id #1.3 type AtomicStructure name trajectory.pdb  
model id #1.4 type AtomicStructure name trajectory.pdb  
model id #1.5 type AtomicStructure name trajectory.pdb  

> rmsd #1.2-#1.5 to #1.1 atoms :CA

Missing or invalid "atoms" argument: only initial part "#1.2" of atom
specifier valid  

> rmsd #1.2 to #1.1 atoms :CA

Expected a keyword  

> rmsd #1.3 to #1.1 atoms :CA

Expected a keyword  

> rmsd #1.4 to #1.1 atoms :CA

Expected a keyword  

> rmsd #1.5 to #1.1 atoms :CA

Expected a keyword  

> md rmsd #1 ref #1.1 atoms :CA plot true

Unknown command: md rmsd #1 ref #1.1 atoms :CA plot true  

> select subtract #1.1

509596 atoms, 355424 bonds, 157588 residues, 5 models selected  

> select add #1.1

636995 atoms, 444280 bonds, 196985 residues, 6 models selected  

> select subtract #1

Nothing selected  

> align #1.2 toAtoms #1.1 atoms :CA

Expected a keyword  

> align #1.3 toAtoms #1.1 atoms :CA

Expected a keyword  

> align #1.4 toAtoms #1.1 atoms :CA

Expected a keyword  

> align #1.5 toAtoms #1.1 atoms :CA

Expected a keyword  

> toolshed show

> md movie

Unknown command: md movie  

> toolshed show

Installed MolecularDynamicsViewer (1.6)  

QWebEngineUrlScheme::registerScheme: Too late to register scheme kmd  

Installed MolecularDynamicsViewer (1.6)  

QWebEngineUrlScheme::registerScheme: Too late to register scheme kmd  

> ui tool show "Molecular Dynamics Viewer"

Please register the custom scheme 'kmd' via
QWebEngineUrlScheme::registerScheme() before installing the custom scheme
handler.  

Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 479, in thread_safe  
func(*args, **kw)  
File "/Users/fogy/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/Users/fogy/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 225, in openFile  
res = self.atomStruct.new_residue(resName, chain, int(resSeq))  
^^^^^^^^^^^  
ValueError: invalid literal for int() with base 10: 'A000'  
  
ValueError: invalid literal for int() with base 10: 'A000'  
  
File "/Users/fogy/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 225, in openFile  
res = self.atomStruct.new_residue(resName, chain, int(resSeq))  
^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select add #1

636995 atoms, 444280 bonds, 196985 residues, 6 models selected  

> select subtract #1

Nothing selected  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 316, in interceptRequest  
self._callback(info)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/widgets/htmlview.py", line 93, in _intercept  
return interceptor(request_info, *args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/htmltool.py", line 112, in _navigate  
self.session.ui.thread_safe(self.handle_scheme, url)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/ui/gui.py", line 479, in thread_safe  
func(*args, **kw)  
File "/Users/fogy/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 57, in handle_scheme  
self.openFile()  
File "/Users/fogy/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 183, in openFile  
self.deleteModel()  
File "/Users/fogy/Library/Application Support/ChimeraX/1.11/lib/python/site-
packages/com/kdiller/dynamics/viewer/gui.py", line 129, in deleteModel  
self.session.models.remove([self.atomStruct])  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 1012, in remove  
mlist.sort(key=lambda m: len(m.id), reverse=True)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 1012, in <lambda>  
mlist.sort(key=lambda m: len(m.id), reverse=True)  
^^^^^^^^^  
TypeError: object of type 'NoneType' has no len()  
  
TypeError: object of type 'NoneType' has no len()  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/models.py", line 1012, in  
mlist.sort(key=lambda m: len(m.id), reverse=True)  
^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 89.4
OpenGL renderer: Apple M1
OpenGL vendor: Apple

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

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir10,1
      Model Number: MGN93HN/A
      Chip: Apple M1
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 11881.121.1
      OS Loader Version: 11881.121.1

Software:

    System Software Overview:

      System Version: macOS 15.5 (24F74)
      Kernel Version: Darwin 24.5.0
      Time since boot: 5 hours, 43 minutes

Graphics/Displays:

    Apple M1:

      Chipset Model: Apple M1
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 7
      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: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 1.0.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    babel: 2.17.0
    beautifulsoup4: 4.13.4
    blockdiag: 3.0.0
    blosc2: 3.6.1
    build: 1.2.2.post1
    certifi: 2025.7.14
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.2
    ChimeraX-AddCharge: 1.5.19
    ChimeraX-AddH: 2.2.7
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.6.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 3.0
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Aniso: 1.3.2
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.60.10
    ChimeraX-AtomicLibrary: 14.1.21
    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: 1.5.1
    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.dev202508050120
    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: 1.7.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    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: 1.0
    ChimeraX-MatchMaker: 2.2.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.15
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-Minimize: 1.2
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.16
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.22
    ChimeraX-ModelPanel: 1.5.1
    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: 1.15.1
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.10
    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: 1.1.3
    ChimeraX-ProfileGrids: 1.1.4
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.4
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    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-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.3
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.7
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.17.2
    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: 1.47
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDock: 1.2
    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
    colorama: 0.4.6
    comm: 0.2.3
    contourpy: 1.3.3
    coverage: 7.10.2
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.1.2
    debugpy: 1.8.15
    decorator: 5.2.1
    docutils: 0.21.2
    executing: 2.2.0
    filelock: 3.18.0
    fonttools: 4.59.0
    funcparserlib: 2.0.0a0
    glfw: 2.9.0
    grako: 3.16.5
    h5py: 3.14.0
    html2text: 2024.2.26
    idna: 3.10
    ihm: 2.2
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    iniconfig: 2.1.0
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.7
    jedi: 0.19.1
    Jinja2: 3.1.6
    jupyter_client: 8.6.3
    jupyter_core: 5.8.1
    jupyterlab_widgets: 3.0.15
    kiwisolver: 1.4.8
    line_profiler: 5.0.0
    lxml: 5.3.1
    lz4: 4.3.2
    Markdown: 3.8.2
    MarkupSafe: 3.0.2
    matplotlib: 3.10.1
    matplotlib-inline: 0.1.7
    MolecularDynamicsViewer: 1.6
    msgpack: 1.1.0
    narwhals: 2.1.2
    ndindex: 1.10.0
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.11.0
    numpy: 2.2.6
    numpy: 1.26.4
    OpenMM: 8.2.0
    openvr: 1.26.701
    packaging: 24.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pickleshare: 0.7.5
    pillow: 10.4.0
    pip: 25.2
    pkginfo: 1.11.1
    platformdirs: 4.3.8
    plotly: 6.0.1
    pluggy: 1.6.0
    prompt_toolkit: 3.0.51
    psutil: 7.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    Pygments: 2.18.0
    pyKVFinder: 0.8.1
    pynmrstar: 3.3.5
    pynrrd: 1.0.0
    PyOpenGL: 3.1.9
    PyOpenGL-accelerate: 3.1.9
    pyopenxr: 1.1.4501
    pyparsing: 3.2.3
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.9.1
    PyQt6-Qt6: 6.9.1
    PyQt6-WebEngine-commercial: 6.9.0
    PyQt6-WebEngine-Qt6: 6.9.1
    PyQt6_sip: 13.10.2
    pytest: 8.4.1
    pytest-cov: 6.2.1
    python-dateutil: 2.9.0.post0
    pytz: 2025.2
    pyzmq: 27.0.1
    qtconsole: 5.5.2
    QtPy: 2.4.3
    qtshim: 1.1
    RandomWords: 0.4.0
    requests: 2.32.4
    roman-numerals-py: 3.1.0
    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: 2.7
    Sphinx: 8.2.3
    sphinx-autodoc-typehints: 3.1.0
    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
    stack-data: 0.6.3
    superqt: 0.7.5
    tables: 3.10.2
    tcia_utils: 1.5.1
    tifffile: 2025.3.13
    tinyarray: 1.2.5
    tomlkit: 0.13.2
    tornado: 6.5.1
    traitlets: 5.14.3
    typing_extensions: 4.14.1
    tzdata: 2025.2
    urllib3: 2.5.0
    wcwidth: 0.2.13
    webcolors: 24.11.1
    wheel: 0.45.1
    wheel-filename: 1.4.2
    widgetsnbextension: 4.0.14

[Eric Pettersen]

Not that it *should* necessarily handle them...