id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14467 Residue NAG is linked to a glycan, but no parameters are available for this type of linkage cnp@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-91-generic-x86_64-with-glibc2.35 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 /u/au591166/Desktop/B0AT1/Refinement/B0AT1_sharpened_map.ccp4 format > ccp4 Opened B0AT1_sharpened_map.ccp4 as #1, grid size 300,300,300, pixel 1.04, shown at level 2.91, step 2, values float32 > open /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_7/RSR7_Leu_CHS- > coot-9.pdb Chain information for RSR7_Leu_CHS-coot-9.pdb #2 --- Chain | Description C | No description available D | No description available > volume #1 step 1 > volume #1 level 5.793 > 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 30 residues in model #2 to IUPAC-IUB standards. Chain information for RSR7_Leu_CHS-coot-9.pdb --- Chain | Description 2.2/C | No description available 2.2/D | No description available > clipper associate #1 toModel #2 Opened B0AT1_sharpened_map.ccp4 as #2.1.1.1, grid size 300,300,300, pixel 1.04, shown at step 1, values float32 > ui mousemode right select Drag select of 627 atoms, 725 residues, 633 bonds, 2 pseudobonds > clipper isolate /C:5-609,621,628,630-632/D maskRadius 4.0 focus false Drag select of 7499 atoms, 725 residues, 7703 bonds, 2 pseudobonds > clipper isolate /C:5-610,615-618,621-635/D maskRadius 4.0 focus false > volume #2.1.1.1 level 2.605 Drag select of 7550 atoms, 725 residues, 7757 bonds, 2 pseudobonds > clipper isolate /C-D maskRadius 4.0 focus false > clipper isolate /C-D maskRadius 5.0 focus false > isolde sim start /C-D Sim termination reason: None ISOLDE: stopped sim > isolde parameterise sel override false Running ANTECHAMBER command: /usr/lib/ucsf- chimerax/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /tmp/tmprwhjacw5/ante.in.mol2 -fi mol2 -o /tmp/tmprwhjacw5/ante.out.mol2 -fo mol2 -c bcc -nc -1 -j 5 -s 2 -dr n (CHS) `` (CHS) `Welcome to antechamber 20.0: molecular input file processor.` (CHS) `` (CHS) `Info: Finished reading file (/tmp/tmprwhjacw5/ante.in.mol2); atoms read (84), bonds read (87).` (CHS) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (CHS) `` (CHS) `` (CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (CHS) `Info: Total number of electrons: 268; net charge: -1` (CHS) `` (CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (CHS) `` (CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /usr/lib/ucsf- chimerax/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (CHS) `` (CHS) `Running: /usr/lib/ucsf-chimerax/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (CHS) `` Charges for residue CHS determined OpenMM ffXML file CHS written to the current working directory. New template added to forcefield as USER_CHS. This ligand should now work in all remaining simulations for this session. To use in future sessions, load the ffXML file with ISOLDE's Load Residue MD Definition(s) button. > view #2.2:LEU > view #2.2:601 > view #2.2:6010 No objects specified. > view #2.2:610 > view #2.2:605 > view #2.2:620 > view #2.2:leu > volume #2.1.1.1 level 12.25 > view #2.2/C:8 > view #2.2/C:48 > clipper spotlight > isolde sim start /C:622 ISOLDE: started sim > volume #2.1.1.1 level 5.072 > ui mousemode right ""isolde tug selection"" [Repeated 1 time(s)] > ui mousemode right ""isolde tug residue"" [Repeated 1 time(s)] > ui mousemode right ""isolde tug atom"" [Repeated 1 time(s)] > 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 > ui mousemode right select Drag select of 449 atoms, 725 residues, 456 bonds, 2 pseudobonds > clipper isolate /C:5-609,629,633/D maskRadius 5.0 focus false Drag select of 7793 atoms, 725 residues, 7997 bonds, 2 pseudobonds > clipper isolate /C:5-610,615-618,621-635/D maskRadius 5.0 focus false Drag select of 7844 atoms, 725 residues, 8051 bonds, 2 pseudobonds > clipper isolate /C-D maskRadius 5.0 focus false > isolde sim start /C-D ISOLDE: started sim > ui tool show ""Ramachandran Plot"" > isolde pepflip /C:282 [Repeated 1 time(s)]Unable to flip peptide bond after 50 rounds. Giving up. > view #2.2/C:48 > volume #2.1.1.1 level 14.2 > view #2.2/C:621 > undo > view #2.2/C:621 > isolde sim pause > open /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_7/RSR7_Leu_CHS- > coot-9.pdb Chain information for RSR7_Leu_CHS-coot-9.pdb #1 --- Chain | Description C | No description available D | No description available > hide #!1 models > isolde sim resume > show #!1 models > hide #!1 models > show #!1 models > isolde sim pause > hide #!1 models > ui mousemode right distance > distance #2.2/C:621@H #2.2/C:277@O Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C LEU 621 H and PHE 277 O: 1.844Å > distance #2.2/C:280@OG #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 280 OG and LEU 621 H: 2.976Å > distance #2.2/C:278@O #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 278 O and LEU 621 H: 3.754Å > ~distance #2.2/C:280@OG #2.2/C:621@H > distance #2.2/C:49@O #2.2/C:280@OG Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C CYS 49 O and SER 280 OG: 4.403Å > undo > select add #2.2 12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected > select add #2.2 12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected > hide #!2.2 models > show #!2.2 models > select add #2.2 12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected > select add #2.2 12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected > select add #2.2 12923 atoms, 13130 bonds, 5 pseudobonds, 748 residues, 16 models selected > ui mousemode right select > select clear > close #3 > ui mousemode right distance > hide #!1 models > distance #2.2/C:49@O #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C CYS 49 O and LEU 621 H: 3.909Å > distance #2.2/C:280@OG #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 280 OG and LEU 621 H: 2.976Å > distance #2.2/C:277@O #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C PHE 277 O and LEU 621 H: 1.844Å > distance #2.2/C:278@O #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 278 O and LEU 621 H: 3.754Å > distance #2.2/C:48@O #2.2/C:621@H Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C PHE 48 O and LEU 621 H: 4.396Å > hide #3.1 models > show #!1 models > hide #!2.2 models > show #!2.2 models > distance #2.2/C:48@O #1/C:621@N Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C PHE 48 O and RSR7_Leu_CHS- coot-9.pdb #1/C LEU 621 N: 2.814Å > ~distance #2.2/C:48@O #1/C:621@N > distance #2.2/C:49@O #1/C:621@N Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C CYS 49 O and RSR7_Leu_CHS- coot-9.pdb #1/C LEU 621 N: 2.970Å > show #3.1 models > ~distance #2.2/C:48@O #2.2/C:621@H > distance #1/C:621@N #2.2/C:48@O Distance between RSR7_Leu_CHS-coot-9.pdb #1/C LEU 621 N and RSR7_Leu_CHS- coot-9.pdb #2.2/C PHE 48 O: 2.814Å > distance #2.2/C:280@OG #1/C:621@N Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 280 OG and RSR7_Leu_CHS- coot-9.pdb #1/C LEU 621 N: 2.291Å > distance #2.2/C:278@O #1/C:621@N Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C SER 278 O and RSR7_Leu_CHS- coot-9.pdb #1/C LEU 621 N: 3.867Å > hide #!3 models > hide #3.1 models > ui mousemode right distance > distance #1/C:129@HH #2.2/C:621@O Distance between RSR7_Leu_CHS-coot-9.pdb #1/C TYR 129 HH and RSR7_Leu_CHS- coot-9.pdb #2.2/C LEU 621 O: 2.553Å > show #!3 models > show #3.1 models > distance #2.2/C:53@H #2.2/C:621@O Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C GLY 53 H and LEU 621 O: 1.916Å > distance #2.2/C:129@HH #2.2/C:621@O Distance between RSR7_Leu_CHS-coot-9.pdb #2.2/C TYR 129 HH and LEU 621 O: 1.814Å > hide #!3 models > hide #!1 models > isolde sim resume > view #2.2/C:622 > volume #2.1.1.1 level 11.47 > view #2.2/C:623 > volume #2.1.1.1 level 10.03 > view #2.2/C:624 > view #2.2/C:625 > volume #2.1.1.1 level 8.594 > isolde sim pause > isolde sim stop Sim termination reason: None ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 9 residues in model #2.2 to IUPAC-IUB standards. ISOLDE: stopped sim > save /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_7/RSR7_Leu_CHS- > coot-9_ISOLDE.pdb models #2 > close #3#2.3#2.1-2 Deleting atomic symmetry model... > close #1 Deleting atomic symmetry model... > hide #2 models > show #2 models > hide #2 models > close Deleting atomic symmetry model... > open /u/au591166/Desktop/B0AT1/Refinement/B0AT1_sharpened_map.ccp4 format > ccp4 Opened B0AT1_sharpened_map.ccp4 as #1, grid size 300,300,300, pixel 1.04, shown at level 2.91, step 2, values float32 > open /u/au591166/Desktop/B0AT1/Refinement/RealSpaceRefine_11/RSR11_Leu_CHS- > coot-10.pdb Chain information for RSR11_Leu_CHS-coot-10.pdb #2 --- Chain | Description C | No description available C | No description available D | No description available ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 40 residues in model #2 to IUPAC-IUB standards. Chain information for RSR11_Leu_CHS-coot-10.pdb --- Chain | Description 2.2/C | No description available 2.2/C | No description available 2.2/D | No description available > clipper associate #1 toModel #2 Opened B0AT1_sharpened_map.ccp4 as #2.1.1.1, grid size 300,300,300, pixel 1.04, shown at step 1, values float32 Traceback (most recent call last): File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/ui/validation_tab/unparameterised.py"", line 84, in _populate_unparameterised_residue_table template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3014, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 269, in find_glycan_anchor_name raise RuntimeError('Residue {} {}{} is linked to a glycan, but no ' RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are available for this type of linkage. File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 269, in find_glycan_anchor_name raise RuntimeError('Residue {} {}{} is linked to a glycan, but no ' See log for complete Python traceback. > view #2.2/C:620 > ui mousemode right select Drag select of 546 atoms, 725 residues, 547 bonds, 4 pseudobonds > clipper isolate /C:5-609/D maskRadius 5.0 focus false Drag select of 7499 atoms, 725 residues, 7703 bonds, 4 pseudobonds > clipper isolate /C:5-610,615-618,621-635/D maskRadius 5.0 focus false Drag select of 7550 atoms, 725 residues, 7757 bonds, 4 pseudobonds > clipper isolate /C-D maskRadius 5.0 focus false > volume #2.1.1.1 level 7.732 > clipper isolate /C-D maskRadius 5.0 focus false > select clear > volume #2.1.1.1 level 6.292 Drag select of 7550 atoms, 725 residues, 7757 bonds, 4 pseudobonds > clipper isolate /C-D maskRadius 5.0 focus false > volume #2.1.1.1 level 4.051 > select clear [Repeated 2 time(s)]Drag select of 7550 atoms, 725 residues, 7757 bonds, 4 pseudobonds > clipper isolate /C-D maskRadius 5.0 focus false > volume #2.1.1.1 level 6.452 > volume #2.1.1.1 level 5.491 > select clear [Repeated 3 time(s)] > ui mousemode right rotate > isolde sim start /C:56 ISOLDE: started sim > isolde pepflip /C:60 [Repeated 4 time(s)] > isolde pepflip /C:56 [Repeated 1 time(s)] > isolde pepflip /C:55 [Repeated 1 time(s)] > isolde sim pause > ui tool show ""Ramachandran Plot"" > view #2.2/C:634 Traceback (most recent call last): File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/ui/validation_tab/unparameterised.py"", line 84, in _populate_unparameterised_residue_table template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3014, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 269, in find_glycan_anchor_name raise RuntimeError('Residue {} {}{} is linked to a glycan, but no ' RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are available for this type of linkage. File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 269, in find_glycan_anchor_name raise RuntimeError('Residue {} {}{} is linked to a glycan, but no ' See log for complete Python traceback. > ui mousemode right select > select /C:634@C09 1 atom, 1 residue, 1 model selected Drag select of 154 atoms, 154 bonds > 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 > /C:187,472,475,477-481,484-485,558-560,578,582,585-586,589,633-634 Sim termination reason: None ISOLDE: stopped sim Traceback (most recent call last): File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/ui/validation_tab/unparameterised.py"", line 84, in _populate_unparameterised_residue_table template_dict = find_residue_templates(residues, ff, ligand_db=ligand_db, logger=self.session.logger) File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/openmm_interface.py"", line 3014, in find_residue_templates templates[residues.index(prot_res)] = find_glycan_anchor_name(prot_res) File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 269, in find_glycan_anchor_name raise RuntimeError('Residue {} {}{} is linked to a glycan, but no ' RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are available for this type of linkage. RuntimeError: Residue NAG C620 is linked to a glycan, but no parameters are available for this type of linkage. File ""/u/au591166/.local/share/ChimeraX/1.6/site- packages/chimerax/isolde/openmm/amberff/glycam.py"", line 269, in find_glycan_anchor_name raise RuntimeError('Residue {} {}{} is linked to a glycan, but no ' See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 545.23.08 OpenGL renderer: NVIDIA RTX A5000/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=xubuntu XDG_SESSION_DESKTOP=xubuntu XDG_CURRENT_DESKTOP=XFCE DISPLAY=:1.0 Manufacturer: LENOVO Model: 30E0003SMT OS: Ubuntu 22.04 Jammy Jellyfish Architecture: 64bit ELF Virtual Machine: none CPU: 32 AMD Ryzen Threadripper PRO 3955WX 16-Cores Cache Size: 512 KB Memory: total used free shared buff/cache available Mem: 62Gi 7.7Gi 48Gi 162Mi 6.8Gi 54Gi Swap: 975Mi 0.0Ki 975Mi Graphics: 61:00.0 VGA compatible controller [0300]: NVIDIA Corporation GA102GL [RTX A5000] [10de:2231] (rev a1) Subsystem: Hewlett-Packard Company GA102GL [RTX A5000] [103c:147e] Kernel driver in use: nvidia 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-LinuxSupport: 1.0.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 distro: 1.7.0 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 pexpect: 4.8.0 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 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 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 zipp: 3.15.0 }}} " defect assigned normal Third Party all ChimeraX