Opened 2 years ago

Closed 2 years ago

#9127 closed defect (can't reproduce)

ISOLDE: a couple of errors

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-10-10.0.22621
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
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 "C:\Users\Anthony
> Nguyen\Documents\B2V2R_Barr1\volume\class4\NEW_J4502_4503_4510_class4_max.mrc"
> format mrc

Opened NEW_J4502_4503_4510_class4_max.mrc as #1, grid size 300,300,300, pixel
0.844, shown at level 0.0156, step 2, values float32  

> set bgColor white

> open "C:/Users/Anthony
> Nguyen/Phenix/B2V2R_Barr1_Phenix/RealSpaceRefine_675/NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb"

Chain information for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2  
---  
Chain | Description  
B | No description available  
H | No description available  
L | No description available  
R | No description available  
V | No description available  
  

> isolde start

> set selectionWidth 4

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 41 residues in model #2 to IUPAC-IUB
standards.  
Chain information for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb  
---  
Chain | Description  
2.2/B | No description available  
2.2/H | No description available  
2.2/L | No description available  
2.2/R | No description available  
2.2/V | No description available  
  

> clipper associate #1 toModel #2

Opened NEW_J4502_4503_4510_class4_max.mrc as #2.1.1.1, grid size 300,300,300,
pixel 0.844, shown at step 1, values float32  

> addh #2.2

Summary of feedback from adding hydrogens to
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2.2  
---  
warnings | Not adding hydrogens to /H GLN 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L GLN 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L MET 5 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L SER 15 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L GLN 28 CB because it is missing heavy-atom bond
partners  
38 messages similar to the above omitted  
notes | No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain B; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain H; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain L; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain R; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain V; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 6, /H VAL 5, /L SER
1, /R GLU 30, /V GLU 356  
Chain-initial residues that are not actual N termini: /B ARG 312, /R GLN 179,
/R CYS 265  
Chain-final residues that are actual C termini: /B PRO 361, /H SER 122, /L ILE
107, /R CYS 341, /V ASP 368  
Chain-final residues that are not actual C termini: /B GLU 308, /R ARG 175, /R
GLN 229  
732 hydrogen bonds  
Adding 'H' to /B ARG 312  
Adding 'H' to /R GLN 179  
Adding 'H' to /R CYS 265  
6573 hydrogens added  
  
Loading residue template for P0G from internal database  
Deleted the following atoms from residue P0G R1601: HAE, HAM1, HAA2, HAP1,
HAM2, HAP2, HAB1, HAN2, HAN1, HAO1, HAB2, HAF, HAC1, HAC3, HAA3, HAO2, HAA1,
HAQ, HAB3, HAC2  

> isolde restrain ligands #2.2

> volume #2.1.1.1 level 0.09493

> select up

16 atoms, 15 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

> set selectionWidth 4

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\toolbar\tool.py", line 205, in callback  
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 386, in run_provider  
return api._api_caller.run_provider(api, session, name, mgr, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\\__init__.py", line 1289, in run_provider  
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\\__init__.py", line 183, in run_provider  
toolbar_command(session, name)  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\toolbar.py", line 21, in toolbar_command  
run(session, f'isolde sim start {_current_residue_sel_string(session)}')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\cmd\cmd.py", line 122, in isolde_sim  
isolde.start_sim()  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\isolde.py", line 896, in start_sim  
sm.start_sim()  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 401, in start_sim  
sh.start_sim()  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1432, in start_sim  
self._prepare_sim()  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 1364, in
_prepare_sim  
platform = openmm.Platform.getPlatformByName(params.platform)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\openmm\openmm.py", line
16445, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
openmm.OpenMMException: There is no registered Platform called "HIP"  
  
openmm.OpenMMException: There is no registered Platform called "HIP"  
  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\openmm\openmm.py", line
16445, in getPlatformByName  
return _openmm.Platform_getPlatformByName(name)  
  
See log for complete Python traceback.  
  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> select up

16 atoms, 15 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

ISOLDE: started sim  

> isolde pepflip /B:70

> 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  

> select up

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

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

ISOLDE: started sim  

> isolde pepflip /B:71

[Repeated 1 time(s)]

> isolde pepflip /B:70

> isolde pepflip /B:71

> 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  

> select up

16 atoms, 15 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

ISOLDE: started sim  

> isolde pepflip /B:70

> isolde pepflip /B:71

[Repeated 1 time(s)]

> isolde pepflip /B:69

[Repeated 1 time(s)]

> isolde pepflip /B:70

> isolde pepflip /B:71

> 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  

> select up

16 atoms, 15 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

ISOLDE: started sim  

> isolde pepflip /B:70

[Repeated 1 time(s)]

> isolde pepflip /B:71

> volume #2.1.1.1 level 0.1749

> isolde pepflip /B:68

> volume #2.1.1.1 level 0.07612

> isolde pepflip /B:71

[Repeated 1 time(s)]

> ui tool show "Ramachandran Plot"

> isolde sim resume

> isolde pepflip /B:71

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B:82

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 #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> select H

6572 atoms, 866 residues, 1 model selected  

> delete atoms (#!2.2 & sel)

> delete bonds (#!2.2 & sel)

> save "C:/Users/Anthony
> Nguyen/Phenix/B2V2R_Barr1_Phenix/RealSpaceRefine_675/NEW_from567_forClass4_ISOLDE6_rsr675_2ndFL.pdb"

> addh

Summary of feedback from adding hydrogens to
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2.2  
---  
warnings | Not adding hydrogens to /H GLN 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L GLN 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L MET 5 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L SER 15 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L GLN 28 CB because it is missing heavy-atom bond
partners  
38 messages similar to the above omitted  
notes | No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain B; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain H; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain L; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain R; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain V; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 6, /H VAL 5, /L SER
1, /R GLU 30, /V GLU 356  
Chain-initial residues that are not actual N termini: /B ARG 312, /R GLN 179,
/R CYS 265  
Chain-final residues that are actual C termini: /B PRO 361, /H SER 122, /L ILE
107, /R CYS 341, /V ASP 368  
Chain-final residues that are not actual C termini: /B GLU 308, /R ARG 175, /R
GLN 229  
736 hydrogen bonds  
Adding 'H' to /B ARG 312  
Adding 'H' to /R GLN 179  
Adding 'H' to /R CYS 265  
6573 hydrogens added  
  
Loading residue template for P0G from internal database  
Deleted the following atoms from residue P0G R1601: HAP2, HAN2, HAA1, HAA3,
HAB2, HAC1, HAC3, HAF, HAN1, HAC2, HAM1, HAE, HAO1, HAM2, HAQ, HAB1, HAP1,
HAO2, HAA2, HAB3  

> isolde sim start /B:70

ISOLDE: started sim  

> isolde pepflip /B:71

> volume #2.1.1.1 level 0.1514

> 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 #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B:76

ISOLDE: started sim  

> isolde sim stop

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

> select #2.2/B:86

11 atoms, 10 bonds, 1 residue, 1 model selected  

> view sel

> isolde sim start /B:86

ISOLDE: started sim  

> isolde pepflip /B:86

[Repeated 1 time(s)]

> isolde pepflip /B:87

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 3 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select clear

> isolde sim start /B:70

ISOLDE: started sim  

> isolde pepflip /B:70

[Repeated 1 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 /B:76

ISOLDE: started sim  

> isolde pepflip /B:76

[Repeated 1 time(s)]

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select H

6572 atoms, 866 residues, 1 model selected  

> delete atoms (#!2.2 & sel)

> delete bonds (#!2.2 & sel)

> save "C:/Users/Anthony
> Nguyen/Phenix/B2V2R_Barr1_Phenix/RealSpaceRefine_675/NEW_from567_forClass4_ISOLDE6_rsr675_2ndFL_2.pdb"

> addh

Summary of feedback from adding hydrogens to
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2.2  
---  
warnings | Not adding hydrogens to /H GLN 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L GLN 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L MET 5 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L SER 15 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L GLN 28 CB because it is missing heavy-atom bond
partners  
38 messages similar to the above omitted  
notes | No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain B; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain H; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain L; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain R; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain V; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 6, /H VAL 5, /L SER
1, /R GLU 30, /V GLU 356  
Chain-initial residues that are not actual N termini: /B ARG 312, /R GLN 179,
/R CYS 265  
Chain-final residues that are actual C termini: /B PRO 361, /H SER 122, /L ILE
107, /R CYS 341, /V ASP 368  
Chain-final residues that are not actual C termini: /B GLU 308, /R ARG 175, /R
GLN 229  
735 hydrogen bonds  
Adding 'H' to /B ARG 312  
Adding 'H' to /R GLN 179  
Adding 'H' to /R CYS 265  
6573 hydrogens added  
  
Deleted the following atoms from residue P0G R1601: HAB2, HAA1, HAB1, HAC3,
HAO1, HAB3, HAO2, HAE, HAP2, HAQ, HAM1, HAN1, HAC1, HAN2, HAA3, HAM2, HAF,
HAP1, HAC2, HAA2  

> select up

19 atoms, 18 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

ISOLDE: started sim  

> volume #2.1.1.1 level 0.08082

> isolde pepflip /B:69

[Repeated 1 time(s)]

> isolde pepflip /B:70

[Repeated 1 time(s)]

> isolde pepflip /B:71

> volume #2.1.1.1 level 0.2031

> isolde sim stop

Sim termination reason: None  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select H

6572 atoms, 866 residues, 1 model selected  

> delete atoms (#!2.2 & sel)

> delete bonds (#!2.2 & sel)

> save "C:/Users/Anthony
> Nguyen/Phenix/B2V2R_Barr1_Phenix/RealSpaceRefine_675/NEW_from567_forClass4_ISOLDE6_rsr675_2ndFL_3.pdb"

> select #2.2/B:79

8 atoms, 7 bonds, 1 residue, 1 model selected  

> view sel

> volume #2.1.1.1 level 0.4242

> save "C:/Users/Anthony
> Nguyen/Phenix/B2V2R_Barr1_Phenix/RealSpaceRefine_675/NEW_from567_forClass4_ISOLDE6_rsr675_2ndFL_4.pdb"

> volume #2.1.1.1 level 0.1449

> volume #2.1.1.1 level 0.04319

> addh

Summary of feedback from adding hydrogens to
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2.2  
---  
warnings | Not adding hydrogens to /H GLN 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L GLN 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L MET 5 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L SER 15 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L GLN 28 CB because it is missing heavy-atom bond
partners  
38 messages similar to the above omitted  
notes | No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain B; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain H; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain L; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain R; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain V; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 6, /H VAL 5, /L SER
1, /R GLU 30, /V GLU 356  
Chain-initial residues that are not actual N termini: /B ARG 312, /R GLN 179,
/R CYS 265  
Chain-final residues that are actual C termini: /B PRO 361, /H SER 122, /L ILE
107, /R CYS 341, /V ASP 368  
Chain-final residues that are not actual C termini: /B GLU 308, /R ARG 175, /R
GLN 229  
735 hydrogen bonds  
Adding 'H' to /B ARG 312  
Adding 'H' to /R GLN 179  
Adding 'H' to /R CYS 265  
6573 hydrogens added  
  

> addh

Summary of feedback from adding hydrogens to
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2.2  
---  
warnings | Not adding hydrogens to /H GLN 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L GLN 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L MET 5 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L SER 15 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L GLN 28 CB because it is missing heavy-atom bond
partners  
38 messages similar to the above omitted  
notes | No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain B; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain H; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain L; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain R; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain V; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 6, /H VAL 5, /L SER
1, /R GLU 30, /V GLU 356  
Chain-initial residues that are not actual N termini: /B ARG 312, /R GLN 179,
/R CYS 265  
Chain-final residues that are actual C termini: /B PRO 361, /H SER 122, /L ILE
107, /R CYS 341, /V ASP 368  
Chain-final residues that are not actual C termini: /B GLU 308, /R ARG 175, /R
GLN 229  
706 hydrogen bonds  
0 hydrogens added  
  
Deleted the following atoms from residue P0G R1601: HAP1, HAM2, HAN1, HAA1,
HAO2, HAF, HAC1, HAC3, HAB3, HAN2, HAE, HAB1, HAB2, HAP2, HAQ, HAA2, HAC2,
HAA3, HAM1, HAO1  

> select #2.2/B:63-75

205 atoms, 206 bonds, 13 residues, 1 model selected  

> select up

16 atoms, 15 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

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 2 residues in model #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> select H

6572 atoms, 866 residues, 1 model selected  

> delete atoms (#!2.2 & sel)

> delete bonds (#!2.2 & sel)

> save "C:/Users/Anthony
> Nguyen/Phenix/B2V2R_Barr1_Phenix/RealSpaceRefine_675/NEW_from567_forClass4_ISOLDE6_rsr675_2ndFL_5.pdb"

> select H

Nothing selected  

> addh

Summary of feedback from adding hydrogens to
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
#2.2  
---  
warnings | Not adding hydrogens to /H GLN 6 CB because it is missing heavy-
atom bond partners  
Not adding hydrogens to /L GLN 4 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L MET 5 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L SER 15 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /L GLN 28 CB because it is missing heavy-atom bond
partners  
38 messages similar to the above omitted  
notes | No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain B; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain H; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain L; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain R; guessing termini instead  
No usable SEQRES records for
NEW_from567_forClass4_ISOLDE6_rsr669_Isolde3_coot2_real_space_refined_675.pdb
(#2.2) chain V; guessing termini instead  
Chain-initial residues that are actual N termini: /B THR 6, /H VAL 5, /L SER
1, /R GLU 30, /V GLU 356  
Chain-initial residues that are not actual N termini: /B ARG 312, /R GLN 179,
/R CYS 265  
Chain-final residues that are actual C termini: /B PRO 361, /H SER 122, /L ILE
107, /R CYS 341, /V ASP 368  
Chain-final residues that are not actual C termini: /B GLU 308, /R ARG 175, /R
GLN 229  
736 hydrogen bonds  
Adding 'H' to /B ARG 312  
Adding 'H' to /R GLN 179  
Adding 'H' to /R CYS 265  
6573 hydrogens added  
  
Deleted the following atoms from residue P0G R1601: HAC3, HAO1, HAN1, HAA3,
HAB3, HAN2, HAE, HAB2, HAP1, HAC2, HAB1, HAO2, HAF, HAM1, HAP2, HAQ, HAC1,
HAA2, HAM2, HAA1  

> select clear

> select up

16 atoms, 15 bonds, 1 residue, 2 models selected  

> select up

205 atoms, 206 bonds, 13 residues, 2 models selected  

> isolde sim start /B:63-75

ISOLDE: started sim  

> volume #2.1.1.1 level 0.2313

> volume #2.1.1.1 level 0.1043

> 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 #2.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  

> isolde sim start /B:70

ISOLDE: started sim  

> isolde sim stop

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

> select #2.2

13267 atoms, 13427 bonds, 3 pseudobonds, 866 residues, 15 models selected  

> isolde sim start /H-L,V,R,B

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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 839, in
_dr_changed_cb  
self.sim_handler.update_distance_restraints(all_changeds)  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2013, in
update_distance_restraints  
force.update_targets(restraints.sim_indices,  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1013, in
update_targets  
_openmm_force_ext.custombondforce_update_bond_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomBondForce.cpp:118. Index out of range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomBondForce.cpp:118. Index out of range  
  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1013, in
update_targets  
_openmm_force_ext.custombondforce_update_bond_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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 839, in
_dr_changed_cb  
self.sim_handler.update_distance_restraints(all_changeds)  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\openmm_interface.py", line 2013, in
update_distance_restraints  
force.update_targets(restraints.sim_indices,  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1013, in
update_targets  
_openmm_force_ext.custombondforce_update_bond_parameters(int(self.this),
indices, params)  
RuntimeError: Assertion failure at CustomBondForce.cpp:118. Index out of range  
  
Error processing trigger "changes":  
RuntimeError: Assertion failure at CustomBondForce.cpp:118. Index out of range  
  
File "C:\Users\Anthony Nguyen\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\isolde\openmm\custom_forces.py", line 1013, in
update_targets  
_openmm_force_ext.custombondforce_update_bond_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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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\Anthony Nguyen\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.  
  




OpenGL version: 3.3.0 NVIDIA 528.24
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

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: Dell Inc.
Model: XPS 8950
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 137,149,734,912
MaxProcessMemory: 137,438,953,344
CPU: 24 12th Gen Intel(R) Core(TM) i9-12900K
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-PhenixUI: 1.1.11
    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-StarMap: 1.1.75
    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
    pyqtgraph: 0.13.3
    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, 2 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: a couple of errors

OpenMMException: There is no registered Platform called "HIP

-and-

Assertion failure at CustomExternalForce.cpp:104. Index out of
range

comment:2 by Tristan Croll, 2 years ago

Resolution: → can't reproduce
Status: assigned → closed

The first exception is extremely perplexing - the "HIP" Platform is the new Metal implementation, and is only valid on the Mac. The only "official" way for the user to choose the Platform is via the "Computational Platform" combo box that appears when the user sets the Experience level to advanced - an\d that auto-populates with only the platforms that OpenMM was able to successfully load. The only way I can imagine it being set to "HIP" in Windows is if the user has been reading the source code, saw the new "HIP" option, thought "what's that?" and set it via the Python shell.

I can't recall ever seeing those assertion failures either (not just for the CustomExternalForce (tugging/position restraints) - also CustomTorsionForce and CustomBondForce (dihedral and distance restraints respectively)). My best bet is that the user has been experimenting with some scripting in the shell and got something wrong... honestly not sure what, though. I've tried a few different possibilities, but I don't think I'll be able to replicate any of this without a test case.

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