id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9127 ISOLDE: a couple of errors chimerax-bug-report@… Tristan Croll "{{{ 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 }}} " defect closed normal Third Party can't reproduce all ChimeraX