isolde set simFidellityMode: Residue must have the atoms to make at least one of phi, psi or omega!

[singuang.chen@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Error processing trigger "simulation terminated":
ValueError: Residue must have the atoms to make at least one of phi, psi or omega!

File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))

See log for complete Python traceback.

Log:
Startup Messages  
---  
warning | Registration file 'C:\\\Users\\\User\\\AppData\\\Local\\\UCSF\\\ChimeraX\\\registration' has expired  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> F:\\\cryoem_raw_data\\\Guang_isolde_deletion\\\no_Mg\\\Opti\\\Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb

Chain information for
Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

> open
> F:/cryoem_raw_data/Guang_isolde_deletion/no_Mg/Opti/Opti_noMg_II_018_EM2map.mrc

Opened Opti_noMg_II_018_EM2map.mrc as #2, grid size 256,256,256, pixel 1.23,
shown at level 0.0448, step 1, values float32  

> volume #2 level 0.1

> select #1/A:1003-1072

1144 atoms, 1155 bonds, 70 residues, 1 model selected  

> volume #2 level -0.02846

> volume #2 level 0.1

> transparency #2 50

> select #1/A:1047-1072

410 atoms, 410 bonds, 26 residues, 1 model selected  

> delete sel

> show atoms

[Repeated 1 time(s)]

> hide atoms

> select #1/A:1003-1045

714 atoms, 723 bonds, 43 residues, 1 model selected  

> delete sel

> select #1/A:918-920

63 atoms, 62 bonds, 3 residues, 1 model selected  

> delete sel

> select #1/A:945-945

15 atoms, 14 bonds, 1 residue, 1 model selected  

> select #1/A:945-946

29 atoms, 28 bonds, 2 residues, 1 model selected  

> delete sel

> transparency #2 0

> select #1/A:1247-1248

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

> delete sel

> select #1/A:560-586

445 atoms, 447 bonds, 27 residues, 1 model selected  

> delete sel

> select #1/A:204-205

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

> delete sel

> delete #1/A:767

> select #1/A:527-539

218 atoms, 220 bonds, 13 residues, 1 model selected  

> delete sel

> select #1/A:687-690

51 atoms, 51 bonds, 4 residues, 1 model selected  

> delete sel

> select #1/A:674-676

35 atoms, 34 bonds, 3 residues, 1 model selected  

> delete sel

> delete #1/A:669-671

> delete #1/A:714-715

> volume #2 level 1.449

> show atoms

> volume #2 level 1.063

> delete #1/D:100

> volume #2 level 4.018

> volume #2 level 2.412

> volume #2 level 0.1

> addh

Summary of feedback from adding hydrogens to
Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb #1  
---  
warnings | Not adding hydrogens to /B DC 30 P because it is missing heavy-atom bond partners  
Not adding hydrogens to /C DA 1 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /D A 10 P because it is missing heavy-atom bond
partners  
notes | No usable SEQRES records for Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb (#1) chain A; guessing termini instead  
Termini for Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb (#1)
chain B determined from SEQRES records  
Termini for Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb (#1)
chain C determined from SEQRES records  
Termini for Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb (#1)
chain D determined from SEQRES records  
Chain-initial residues that are actual N termini: /A MET 1, /A MET 1, /A VAL
206, /A LEU 540, /A PHE 587, /A ASP 672, /A LYS 677, /A ARG 691, /A GLN 716,
/A LEU 921, /A ASP 947, /A PHE 1046, /A VAL 1073, /A PRO 1249  
Chain-initial residues that are not actual N termini: /A VAL 206, /A LEU 540,
/A PHE 587, /A ASP 672, /A LYS 677, /A ARG 691, /A GLN 716, /A LEU 921, /A ASP
947, /A PHE 1046, /A VAL 1073, /A PRO 1249  
Chain-final residues that are actual C termini: /A ASP 1368, /A ALA 203, /A
LYS 526, /A VAL 559, /A ASN 668, /A LYS 673, /A ASP 686, /A VAL 713, /A GLU
766, /A ASP 944, /A PRO 1002, /A PHE 1046, /A LYS 1246, /A ASP 1368  
Chain-final residues that are not actual C termini: /A ALA 203, /A LYS 526, /A
VAL 559, /A ASN 668, /A LYS 673, /A ASP 686, /A VAL 713, /A GLU 766, /A ASP
944, /A PRO 1002, /A PHE 1046, /A LYS 1246  
Chain-initial residues that are not actual 5' termini: /B DC 30, /D A 10  
Missing OXT added to C-terminal residue /A ALA 203  
Missing OXT added to C-terminal residue /A LYS 526  
Missing OXT added to C-terminal residue /A VAL 559  
Missing OXT added to C-terminal residue /A ASN 668  
Missing OXT added to C-terminal residue /A LYS 673  
7 messages similar to the above omitted  
1269 hydrogen bonds  
/C DT 22 is not terminus, removing H atom from O3'  
/D U 99 is not terminus, removing H atom from O3'  
0 hydrogens added  
  

> hbonds

1265 hydrogen bonds found  

> hide HC

> clipper associate #2 toModel #1

Opened Opti_noMg_II_018_EM2map.mrc as #1.1.1.1, grid size 256,256,256, pixel
1.23, shown at level 7.61, step 1, values float32  
Chain information for
Opti_noMg_II_018_final_pdb_251027_level_0.1_1st_del_iso.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/D | No description available  
  

> set bgColor white

> lighting full

> isolde start

> set selectionWidth 4

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

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
Traceback (most recent call last):  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 144, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  

> isolde sim start /B-D,A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 91, in sim_end_cb  
self.update()  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 144, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
Error processing trigger "simulation terminated":  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B-D,A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 91, in sim_end_cb  
self.update()  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 144, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
Error processing trigger "simulation terminated":  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B-D,A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 91, in sim_end_cb  
self.update()  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 144, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
Error processing trigger "simulation terminated":  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B-D,A

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.9\bin\Lib\site-
packages\chimerax\core\triggerset.py", line 149, in invoke  
return self._func(self._name, data)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 91, in sim_end_cb  
self.update()  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\ui.py", line 120, in update  
clusters, noise = pa.problem_zones(m, restraint_types=restraint_types,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 71, in
problem_zones  
sites.extend(vm(structure, outliers_only=validation_outliers_only))  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\problem_regions\problems.py", line 144, in
get_protein_backbone_problems  
problems = f(residues)  
^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1057, in non_favored  
scores, cases = self.validate(residues)  
^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
Error processing trigger "simulation terminated":  
ValueError: Residue must have the atoms to make at least one of phi, psi or
omega!  
  
File "C:\Users\User\AppData\Local\UCSF\ChimeraX\1.9\Python311\site-
packages\chimerax\isolde\molobject.py", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
  
See log for complete Python traceback.  
  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 5 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  




OpenGL version: 3.3.0 NVIDIA 561.09
OpenGL renderer: NVIDIA GeForce RTX 4090 D/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 137,132,670,976
MaxProcessMemory: 137,438,953,344
CPU: 32 Intel(R) Core(TM) i9-14900K
OSLanguage: en-US

Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    autocommand: 2.2.2
    babel: 2.16.0
    backports.tarfile: 1.2.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2024.8.30
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-Clipper: 0.24.0
    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: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    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: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ISOLDE: 1.9
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    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-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    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-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: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    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: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    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: 1.18.1
    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
    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: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    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: 1.4.5
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    importlib_metadata: 8.0.0
    importlib_resources: 6.4.0
    inflect: 7.3.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jaraco.context: 5.3.0
    jaraco.functools: 4.0.1
    jaraco.text: 3.12.1
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    more-itertools: 10.3.0
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    ordered-set: 4.1.0
    packaging: 23.2
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    platformdirs: 4.2.2
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pywin32: 306
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    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: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4.2
    traitlets: 5.14.3
    typeguard: 4.3.0
    typing_extensions: 4.12.2
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
    WMI: 1.5.1
    zipp: 3.19.2

[Eric Pettersen]

Reported by Sin Guang Chen