id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
14588	ISOLDE: start sim: No dihedral with that name is registered for this residue type	chimerax-bug-report@…	Tristan Croll	"{{{
The following bug report has been submitted:
Platform:        Windows-10-10.0.19044
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open M:/Users/Natalia-Dana/models/Src-Barr/J532_Bar120-Src95-SH3_isolde.pdb

Chain information for J532_Bar120-Src95-SH3_isolde.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
H | No description available  
L | No description available  
V | No description available  
  

> open M:/Users/Natalia-Dana/models/Src-Barr/Bar120-Src_J532_zflip.mrc

Opened Bar120-Src_J532_zflip.mrc as #2, grid size 300,300,300, pixel 1.44,
shown at level 0.135, step 2, values float32  

> clipper associate #2 toModel #1

Opened Bar120-Src_J532_zflip.mrc as #1.1.1.1, grid size 300,300,300, pixel
1.44, shown at level 1.05, step 1, values float32  
Chain information for J532_Bar120-Src95-SH3_isolde.pdb  
---  
Chain | Description  
1.2/A | No description available  
1.2/B | No description available  
1.2/C | No description available  
1.2/H | No description available  
1.2/L | No description available  
1.2/V | No description available  
  

> isolde start

> set selectionWidth 4

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

> 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  

> ui tool show ""Ramachandran Plot""

> isolde sim start /A:97

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:94-100

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:91-103

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:229

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:226-232

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:97

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:94-100

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:70

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /B:107

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /L:48

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B:229

ISOLDE: started sim  
Traceback (most recent call last):  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\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\dkb35\AppData\Local\UCSF\ChimeraX\1.6\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\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\problem_regions\problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\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 resume

[Repeated 1 time(s)]

> set selectionWidth 4

No simulation is currently running!  

> 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 sim resume

No simulation is currently running!  

> isolde sim resume

No simulation is currently running!  

> isolde sim resume

No simulation is currently running!  

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py"", line 638, in <lambda>  
gw.mousePressEvent = lambda e, s=self: s._dispatch_mouse_event(e,
""mouse_down"")  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\mouse_modes\mousemodes.py"", line 538, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\tugging.py"", line 124, in mouse_down  
pa = self._pick_atoms(pick)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\tugging.py"", line 154, in _pick_atoms  
if self.atoms.index(a) != -1:  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\tugging.py"", line 55, in atoms  
return self.session.isolde.sim_manager.sim_construct.mobile_atoms  
AttributeError: 'NoneType' object has no attribute 'sim_construct'  
  
AttributeError: 'NoneType' object has no attribute 'sim_construct'  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\tugging.py"", line 55, in atoms  
return self.session.isolde.sim_manager.sim_construct.mobile_atoms  
  
See log for complete Python traceback.  
  

> isolde sim resume

No simulation is currently running!  

> isolde sim start /B:234

ISOLDE: started sim  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> ui tool show ""Ramachandran Plot""

> isolde sim start /A:97

ISOLDE: started sim  

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:94-100

ISOLDE: started sim  

> ui tool show ""Ramachandran Plot""

Traceback (most recent call last):  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\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\dkb35\AppData\Local\UCSF\ChimeraX\1.6\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\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\problem_regions\problems.py"", line 141, in
get_protein_backbone_problems  
problems = f(residues)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\molobject.py"", line 1057, in non_favored  
scores, cases = self.validate(residues)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\molobject.py"", line 1107, in validate  
return self._validate_by_residue(residues_or_ramas)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\molobject.py"", line 1124, in _validate_by_residue  
f(self._c_pointer, residues._c_pointers, n, pointer(scores), pointer(cases))  
IndexError: No dihedral with that name is registered for this residue type!  
  
IndexError: No dihedral with that name is registered for this residue type!  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\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 resume

> isolde cisflip #!1.2/A:97

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  

> isolde sim resume

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde cisflip #1.2/A:97

ISOLDE: started sim  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  

> isolde cisflip #1.2/A:97

> isolde sim pause

> isolde cisflip #1.2/A:97

> isolde sim resume

> isolde cisflip #1.2/A:97

[Repeated 3 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:101

ISOLDE: started sim  

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:97

ISOLDE: started sim  

> isolde cisflip #1.2/A:97

> isolde sim stop discardTo start

Sim termination reason: None  
reverting to start  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> isolde sim start /A:94-100

ISOLDE: started sim  

> isolde cisflip #1.2/A:97

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  

> isolde cisflip #1.2/A:97

Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 909, in
_dihe_r_changed_cb  
self.sim_handler.update_dihedral_restraints(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 1816, in
update_dihedral_restraints  
force.update_targets(restraints.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomTorsionForce.cpp:118. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1301, in
update_targets  
_openmm_force_ext.customtorsionforce_update_torsion_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File ""C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\triggerset.py"", line 138, in invoke  
return self._func(self._name, data)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 978, in
_tug_changed_cb  
self.sim_handler.update_tuggables(all_changeds)  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py"", line 2301, in
update_tuggables  
force.update_targets(tuggables.sim_indices,  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
Error processing trigger ""changes"":  
RuntimeError: Assertion failure at CustomExternalForce.cpp:104. Index out of
range  
  
File ""C:\Users\dkb35\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py"", line 1156, in
update_targets  
_openmm_force_ext.customexternalforce_update_particle_parameters(int(self.this),
indices, params)  
  
See log for complete Python traceback.  
  

> isolde sim pause




OpenGL version: 3.3.0 - Build 31.0.101.2115
OpenGL renderer: Intel(R) UHD Graphics 630
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.cp1252
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 11CR003NUS
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 16,866,512,896
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700 CPU @ 2.90GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.21.0
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.6.1
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.1
    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: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.6.0
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    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: 2.0.12
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.3.7
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.8.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    comtypes: 1.1.14
    contourpy: 1.0.7
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.39.3
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0

}}}
"	defect	assigned	normal		Third Party								all	ChimeraX