id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8790 ISOLDE: residue_graph: edges should be a n x 2 array of unsigned ints Jacob.Landeck@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC) Description I am getting a consistant unparameterised Residue error. When I click ""update"" in the unparameterised residue widget I get this error. Log: UCSF ChimeraX version: 1.5 (2022-11-24) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > volume #1 level 0.2017 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel.pdb"" Chain information for J377_startingModel.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > hide atoms > show cartoons > clipper associate #1 toModel #2 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for J377_startingModel.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB standards. > volume #1.1.1.1 level 0.1754 > addh #1.2 Summary of feedback from adding hydrogens to J377_startingModel.pdb #1.2 --- warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy- atom bond partners Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /G GLN 123 OE1 notes | Termini for J377_startingModel.pdb (#1.2) chain A determined from SEQRES records Termini for J377_startingModel.pdb (#1.2) chain B determined from SEQRES records Termini for J377_startingModel.pdb (#1.2) chain C determined from SEQRES records Termini for J377_startingModel.pdb (#1.2) chain D determined from SEQRES records Termini for J377_startingModel.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1960 hydrogen bonds 19191 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Deleted the following atoms from residue ADP B400: H3B, H5', H5'' Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel > set selectionWidth 4 Loading residue template for ADP from internal database ISOLDE: stopped sim > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > close #1 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/postisolde.pdb"" Chain information for postisolde.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > hide atoms > show cartoons > set bgColor white > set bgColor #ffffff00 > lighting simple > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > volume #2 level 0.197 > clipper associate #2 toModel #1 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for postisolde.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > start isolde Unknown command: start isolde > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > select #1 38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 14 models selected > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > select add #1.1 38623 atoms, 39043 bonds, 2419 residues, 6 models selected > isolde sim start sel ISOLDE: stopped sim > close > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > volume #1 level 0.1549 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_CL_SC_ptDNA_J338_start_252-coot-0.pdb"" Chain information for Open_CL_SC_ptDNA_J338_start_252-coot-0.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_ptDNA_J338_start.pdb"" Summary of feedback from opening C:/Users/jtlan/OneDrive - UMass Chan Medical School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_ptDNA_J338_start.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 PRO A 6 GLN A 8 1 3 Start residue of secondary structure not found: HELIX 2 2 ARG A 10 GLN A 12 1 3 Start residue of secondary structure not found: HELIX 3 3 PRO A 28 ASP A 36 1 9 Start residue of secondary structure not found: HELIX 4 4 VAL A 38 ALA A 44 1 7 Start residue of secondary structure not found: HELIX 5 5 TRP A 61 ILE A 64 1 4 200 messages similar to the above omitted Chain information for Open_ptDNA_J338_start.pdb --- Chain | Description 3.1/A 3.3/A | No description available 3.1/B 3.3/B | No description available 3.1/C 3.3/C | No description available 3.1/D 3.3/D | No description available 3.1/E 3.3/E | No description available 3.1/F 3.3/F | No description available 3.1/G 3.3/G | No description available 3.2/G 3.3/J | No description available 3.1/H 3.3/H | No description available 3.1/I 3.3/I | No description available > hide #!2 models > show #!2 models > close #2 > hide #!3.3 models > show #!3.3 models > hide #!3.3 models > delete 33.3 Missing or invalid ""atoms"" argument: invalid atoms specifier > delete #3.3 > hide #3.2 models > show #3.2 models > delete #3.1 > hide #3.2 models > show #3.2 models > hide #3.2 models > hide #!3 models > show #!3 models > show #3.2 models > delete #3 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/Open_CL_fullSC_ptDNA.pdb"" Chain information for Open_CL_fullSC_ptDNA.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available > hide #3 models > show #3 models > hide #3 models > show #3 models > hide #!2 models > show #!2 models > hide #3 models > show #3 models > hide #3 models > close #3 > delete #2/G:1-123 > show cartoons > hide atoms > delete #2/J > volume #1 level 0.2063 > clipper associate #1 toModel #2 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for Open_CL_fullSC_ptDNA.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB standards. > addh #1.2 Summary of feedback from adding hydrogens to Open_CL_fullSC_ptDNA.pdb #1.2 --- warnings | Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners notes | Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain A determined from SEQRES records Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain B determined from SEQRES records Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain C determined from SEQRES records Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain D determined from SEQRES records Termini for Open_CL_fullSC_ptDNA.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1 Chain-initial residues that are not actual N termini: /G SER 124 Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1960 hydrogen bonds Adding 'H' to /G SER 124 19189 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Deleted the following atoms from residue ADP B400: H3B, H5', H5'' Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel ISOLDE: stopped sim > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel ISOLDE: stopped sim > save ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/test.pdb"" > close > open ""C:\Users\jtlan\OneDrive - UMass Chan Medical > School\BacterialClampLoader\ModelBuilding\Open_CL_SC_ptDNA\test.pdb"" format > pdb Chain information for test.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > assoc #2 to #1 Unknown command: assoc #2 to #1 > clipper associate #2 toModel #1 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for test.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel ISOLDE: stopped sim > isolde sim start sel ISOLDE: stopped sim > close > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/PostRefinement/WorkingModel_ptDNA_del- > cha-G-1-123-coot-133.pdb"" Chain information for WorkingModel_ptDNA_del-cha-G-1-123-coot-133.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > lighting simple > hide atoms [Repeated 1 time(s)] > show cartoons > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > ui mousemode right ""rotate selected models"" > select add #1 19426 atoms, 19846 bonds, 1 pseudobond, 2419 residues, 2 models selected > select subtract #1 Nothing selected > select add #1 19426 atoms, 19846 bonds, 1 pseudobond, 2419 residues, 2 models selected > view matrix models > #1,0.9347,0.019254,-0.3549,66.455,-0.029687,-0.99081,-0.13194,359.78,-0.35418,0.13386,-0.92555,355.63 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.9347,0.019254,-0.3549,60.04,-0.029687,-0.99081,-0.13194,345.52,-0.35418,0.13386,-0.92555,348.75 > view matrix models > #1,0.9347,0.019254,-0.3549,50.213,-0.029687,-0.99081,-0.13194,345.63,-0.35418,0.13386,-0.92555,344.19 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.98389,0.15313,-0.092211,-23.895,0.14922,-0.98764,-0.04799,301.41,-0.09842,0.033457,-0.99458,329.85 > toolshed show > ui tool show ""Fit in Map"" > fitmap #1 inMap #2 Fit molecule WorkingModel_ptDNA_del-cha-G-1-123-coot-133.pdb (#1) to map J377_006_volume_map_sharp.mrc (#2) using 19426 atoms average map value = 0.3212, steps = 100 shifted from previous position = 3.15 rotated from previous position = 7.64 degrees atoms outside contour = 3704, contour level = 0.098888 Position of WorkingModel_ptDNA_del-cha-G-1-123-coot-133.pdb (#1) relative to J377_006_volume_map_sharp.mrc (#2) coordinates: Matrix rotation and translation 0.97784985 0.20896876 -0.01190552 -42.80492843 0.20927960 -0.97706676 0.03927582 273.89654349 -0.00342507 -0.04089744 -0.99915748 327.74385785 Axis -0.99444478 -0.10518895 0.00385563 Axis point 0.00000000 142.53424951 160.99615186 Rotation angle (degrees) 177.68974898 Shift along axis 15.01990745 > volume #2 level 0.1802 > save ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/postref_fitJ377.pdb"" > relModel #2 > close #1 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/postref_fitJ377.pdb"" Chain information for postref_fitJ377.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > show cartoons > hide atoms > clipper associate #2 toModel #1 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for postref_fitJ377.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB standards. > addh #1.2 Summary of feedback from adding hydrogens to postref_fitJ377.pdb #1.2 --- warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy- atom bond partners Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /G GLN 123 OE1 notes | Termini for postref_fitJ377.pdb (#1.2) chain A determined from SEQRES records Termini for postref_fitJ377.pdb (#1.2) chain B determined from SEQRES records Termini for postref_fitJ377.pdb (#1.2) chain C determined from SEQRES records Termini for postref_fitJ377.pdb (#1.2) chain D determined from SEQRES records Termini for postref_fitJ377.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1960 hydrogen bonds 19191 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > volume #1.1.1.1 level 0.231 > view matrix models > #1.2,0.90086,-0.34939,0.25765,28.828,0.20337,0.86401,0.46058,-81.584,-0.38353,-0.36252,0.8494,137.56 > view matrix models > #1.2,0.97911,0.17871,0.096979,-39.202,-0.19579,0.95733,0.21257,3.5952,-0.054852,-0.22712,0.97232,47.484 > undo [Repeated 1 time(s)] > ui mousemode right select > volume #1.1.1.1 level 0.1832 > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 182, in _fix_button_clicked_cb indices = [i for i in range(table.rowCount()) if table.item(i, 0).data(USER_ROLE)[0].name == residue.name] File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 182, in indices = [i for i in range(table.rowCount()) if table.item(i, 0).data(USER_ROLE)[0].name == residue.name] AttributeError: 'NoneType' object has no attribute 'data' AttributeError: 'NoneType' object has no attribute 'data' File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 182, in indices = [i for i in range(table.rowCount()) if table.item(i, 0).data(USER_ROLE)[0].name == residue.name] See log for complete Python traceback. Deleted the following atoms from residue ADP B400: H3B, H5', H5'' > isolde sim start sel ISOLDE: stopped sim > isolde sim start sel ISOLDE: started sim > isolde sim pause > select 1 Expected an objects specifier or a keyword > select #1 38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 19 models selected > select #2 Nothing selected > hide #!1.2 models > show #!1.2 models > select #1.2 38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 12 models selected > isolde sim start sel Simulation already running! > isolde sim stop discardTo start reverting to start ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > isolde sim start sel ISOLDE: stopped sim > isolde sim start sel ISOLDE: stopped sim > undo Undo failed, probably because structures have been modified. > undo [Repeated 2 time(s)]Undo failed, probably because structures have been modified. > isolde sim start sel ISOLDE: stopped sim > close > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel- > coot-0.pdb"" Chain information for J377_startingModel-coot-0.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > show cartoons > hide atoms > lighting simple > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > volume #2 level 0.1502 > clipper associate #2 toModel #1 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for J377_startingModel-coot-0.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB standards. > addh #1.2 Summary of feedback from adding hydrogens to J377_startingModel-coot-0.pdb #1.2 --- warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy- atom bond partners Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /G GLN 123 OE1 notes | Termini for J377_startingModel-coot-0.pdb (#1.2) chain A determined from SEQRES records Termini for J377_startingModel-coot-0.pdb (#1.2) chain B determined from SEQRES records Termini for J377_startingModel-coot-0.pdb (#1.2) chain C determined from SEQRES records Termini for J377_startingModel-coot-0.pdb (#1.2) chain D determined from SEQRES records Termini for J377_startingModel-coot-0.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1961 hydrogen bonds 19190 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > close > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel- > coot-1.pdb"" Chain information for J377_startingModel-coot-1.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > volume #1 level 0.193 > show cartoons > hide atoms > clipper associate #1 toModel #2 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for J377_startingModel-coot-1.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 146 residues in model #1.2 to IUPAC-IUB standards. > addh #1.2 Summary of feedback from adding hydrogens to J377_startingModel-coot-1.pdb #1.2 --- warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy- atom bond partners Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /G GLN 123 OE1 notes | Termini for J377_startingModel-coot-1.pdb (#1.2) chain A determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain B determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain C determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain D determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1961 hydrogen bonds 19191 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > isolde sim start sel ISOLDE: started sim > isolde sim pause > isolde sim stop ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > select #1.2 38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 12 models selected > isolde sim start sel ISOLDE: stopped sim > isolde sim start sel ISOLDE: stopped sim > close > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel- > coot-1.pdb"" Chain information for J377_startingModel-coot-1.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #2, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > volume #2 level 0.1631 > clipper associate #2 toModel #1 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for J377_startingModel-coot-1.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 146 residues in model #1.2 to IUPAC-IUB standards. > select 1.2 Expected an objects specifier or a keyword > select #1.2 19426 atoms, 19846 bonds, 1 pseudobond, 2419 residues, 7 models selected > addh #1.2 Summary of feedback from adding hydrogens to J377_startingModel-coot-1.pdb #1.2 --- warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy- atom bond partners Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /G GLN 123 OE1 notes | Termini for J377_startingModel-coot-1.pdb (#1.2) chain A determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain B determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain C determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain D determined from SEQRES records Termini for J377_startingModel-coot-1.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1961 hydrogen bonds 19191 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > close > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377/J377_006_volume_map_sharp.mrc"" Opened J377_006_volume_map_sharp.mrc as #1, grid size 352,352,352, pixel 0.87, shown at level 0.0989, step 2, values float32 > volume #1 level 0.2316 > open ""C:/Users/jtlan/OneDrive - UMass Chan Medical > School/BacterialClampLoader/ModelBuilding/Open_CL_SC_ptDNA/J377_startingModel- > coot-2.pdb"" Chain information for J377_startingModel-coot-2.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available > hide atoms > show cartoons > clipper associate #1 toModel #2 Opened J377_006_volume_map_sharp.mrc as #1.1.1.1, grid size 352,352,352, pixel 0.87, shown at level 0.329, step 1, values float32 Chain information for J377_startingModel-coot-2.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/F | No description available 1.2/G | No description available 1.2/H | No description available 1.2/I | No description available > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 145 residues in model #1.2 to IUPAC-IUB standards. > addh #1.2 Summary of feedback from adding hydrogens to J377_startingModel-coot-2.pdb #1.2 --- warnings | Not adding hydrogens to /G GLN 123 OE1 because it is missing heavy- atom bond partners Not adding hydrogens to /H DG 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /I DT 1 P because it is missing heavy-atom bond partners The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /G GLN 123 OE1 notes | Termini for J377_startingModel-coot-2.pdb (#1.2) chain A determined from SEQRES records Termini for J377_startingModel-coot-2.pdb (#1.2) chain B determined from SEQRES records Termini for J377_startingModel-coot-2.pdb (#1.2) chain C determined from SEQRES records Termini for J377_startingModel-coot-2.pdb (#1.2) chain D determined from SEQRES records Termini for J377_startingModel-coot-2.pdb (#1.2) chain E determined from SEQRES records 4 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B TYR 3, /C GLN 4, /D SER 2, /E MET 1, /F PRO -1, /G GLN 123 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A HIS 333, /B HIS 360, /C PRO 368, /D HIS 360, /E LEU 334, /F LEU 366, /G LEU 366 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A HIS 333 Missing OXT added to C-terminal residue /B HIS 360 Missing OXT added to C-terminal residue /C PRO 368 Missing OXT added to C-terminal residue /D HIS 360 Missing OXT added to C-terminal residue /E LEU 334 1963 hydrogen bonds 19192 hydrogens added Loading residue template for ADP from internal database Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > select #1.2 38623 atoms, 39043 bonds, 1 pseudobond, 2419 residues, 7 models selected > isolde sim start sel ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. Traceback (most recent call last): File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\ui\validation_tab\unparameterised.py"", line 95, in _populate_unparameterised_residue_table by_name, by_comp = ff.find_possible_templates(r) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 317, in find_possible_templates rgraph = self.residue_graph(res) File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) RuntimeError: edges should be a n x 2 array of unsigned ints! RuntimeError: edges should be a n x 2 array of unsigned ints! File ""C:\Users\jtlan\AppData\Local\UCSF\ChimeraX\1.5\site- packages\chimerax\isolde\openmm\forcefields.py"", line 268, in residue_graph return Graph(labels, edges) See log for complete Python traceback. > volume #1.1.1.1 step 2 > volume #1.1.1.1 step 1 OpenGL version: 3.3.0 - Build 31.0.101.4032 OpenGL renderer: Intel(R) Iris(R) Xe Graphics OpenGL vendor: Intel Python: 3.9.11 Locale: en_US.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: LENOVO Model: 21DJ OS: Microsoft Windows 11 Pro (Build 22621) Memory: 16,874,135,552 MaxProcessMemory: 137,438,953,344 CPU: 12 12th Gen Intel(R) Core(TM) i7-1255U OSLanguage: en-US Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 asttokens: 2.1.0 Babel: 2.11.0 backcall: 0.2.0 blockdiag: 3.0.0 build: 0.8.0 certifi: 2022.9.24 cftime: 1.6.2 charset-normalizer: 2.1.1 ChimeraX-AddCharge: 1.4 ChimeraX-AddH: 2.2.1 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.6 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.41.5 ChimeraX-AtomicLibrary: 8.0.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3 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: 2.7.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.1 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.19.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.2 ChimeraX-CommandLine: 1.2.4 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.5 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.3 ChimeraX-DockPrep: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 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: 1.5 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: 1.1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.1 ChimeraX-MatchMaker: 2.0.9 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.8 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.6 ChimeraX-ModelPanel: 1.3.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.1 ChimeraX-MouseModes: 1.1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.9.1 ChimeraX-PDB: 2.6.8 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.7.2 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: 1.1.70 ChimeraX-StdCommands: 1.10 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.1.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.24.3 ChimeraX-uniprot: 2.2.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.1.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.1 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0.1 colorama: 0.4.5 comtypes: 1.1.10 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.32 debugpy: 1.6.4 decorator: 5.1.1 docutils: 0.19 entrypoints: 0.4 executing: 1.2.0 filelock: 3.7.1 fonttools: 4.38.0 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.33 imagecodecs: 2022.7.31 imagesize: 1.4.1 importlib-metadata: 5.1.0 ipykernel: 6.15.3 ipython: 8.4.0 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.1.2 jupyter-client: 7.3.4 jupyter-core: 5.1.0 kiwisolver: 1.4.4 line-profiler: 3.5.1 lxml: 4.9.1 lz4: 4.0.2 MarkupSafe: 2.1.1 matplotlib: 3.5.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.0 networkx: 2.8.5 numexpr: 2.8.4 numpy: 1.23.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 9.2.0 pip: 22.2.2 pkginfo: 1.8.3 platformdirs: 2.5.4 prompt-toolkit: 3.0.33 psutil: 5.9.1 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.12.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 pyqtgraph: 0.13.1 python-dateutil: 2.8.2 pytz: 2022.6 pywin32: 303 pyzmq: 24.0.1 qtconsole: 5.3.1 QtPy: 2.3.0 RandomWords: 0.4.0 requests: 2.28.1 scipy: 1.9.0 setuptools: 65.1.1 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 5.1.1 sphinx-autodoc-typehints: 1.19.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tifffile: 2022.7.31 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.3.0 urllib3: 1.26.13 wcwidth: 0.2.5 webcolors: 1.12 wheel: 0.37.1 wheel-filename: 1.4.1 WMI: 1.5.1 zipp: 3.11.0 }}} " defect closed normal Third Party fixed all ChimeraX