Opened 21 months ago

Last modified 21 months ago

#14588 assigned defect

ISOLDE: start sim: No dihedral with that name is registered for this residue type

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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

Change History (2)

comment:1 by Eric Pettersen, 21 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: start sim: No dihedral with that name is registered for this residue type

...and possible follow-on errors.

comment:2 by Tristan Croll, 21 months ago

Ugh... my memory's playing tricks on me. I could have sworn I fixed that first error for ISOLDE 1.7, but I just checked and it's still there. The Problem Zones widget will fail with this error if (a) the "Protein backbone" option is checked (which it is by default) and (b) there is a non-standard amino acid in your protein chain.

The chain of "Index out of range" errors at the end is something that gets reported very occasionally, but so far I've never been able to reproduce it nor figure out the root cause.

Note: See TracTickets for help on using tickets.