id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7180 ISOLDE restrain distances: ffi_prep_cif_var failed sean.connell@… Tristan Croll "{{{ The following bug report has been submitted: Platform: Linux-5.15.0-37-generic-x86_64-with-glibc2.35 ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description isolde restrain distances #1.2/G template #4/G adjustForConfidence true Log: > set selectionWidth 4 UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /home/xhan/Downloads/RsmA_ebic/ISOLDE/RsmA-001-job456/7k00-30S-body- > aln-trim-RimPRsmAAF-modh45-coot-3.pdb Chain information for 7k00-30S-body-aln-trim-RimPRsmAAF-modh45-coot-3.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 K | No description available L | No description available O | No description available P | No description available Q | No description available R | No description available T | No description available U | No description available > open > /home/xhan/Downloads/RsmA_ebic/ISOLDE/RsmA-001-job456/job456_deephancer.mrc > /home/xhan/Downloads/RsmA_ebic/ISOLDE/RsmA-001-job456/Refine3D-job456-run_class001.mrc Opened job456_deephancer.mrc as #2.1, grid size 416,416,416, pixel 1.02, shown at level 0.000145, step 2, values float32 Opened Refine3D-job456-run_class001.mrc as #2.2, grid size 416,416,416, pixel 1.02, shown at level 0.00501, step 2, values float32 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Chain information for 7k00-30S-body-aln-trim-RimPRsmAAF-modh45-coot-3.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/K | No description available 1.2/L | No description available 1.2/O | No description available 1.2/P | No description available 1.2/Q | No description available 1.2/R | No description available 1.2/T | No description available 1.2/U | No description available > clipper associate #2.2 toModel #1 Opened Refine3D-job456-run_class001.mrc as #1.1.1.1, grid size 416,416,416, pixel 1.02, shown at step 1, values float32 > clipper associate #2.1 toModel #1 Opened job456_deephancer.mrc as #1.1.1.2, grid size 416,416,416, pixel 1.02, shown at step 1, values float32 > addh Summary of feedback from adding hydrogens to 7k00-30S-body-aln-trim- RimPRsmAAF-modh45-coot-3.pdb #1.2 --- warning | Not adding hydrogens to /A A 2 P because it is missing heavy-atom bond partners notes | No usable SEQRES records for 7k00-30S-body-aln-trim-RimPRsmAAF- modh45-coot-3.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for 7k00-30S-body-aln-trim-RimPRsmAAF- modh45-coot-3.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for 7k00-30S-body-aln-trim-RimPRsmAAF- modh45-coot-3.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for 7k00-30S-body-aln-trim-RimPRsmAAF- modh45-coot-3.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for 7k00-30S-body-aln-trim-RimPRsmAAF- modh45-coot-3.pdb (#1.2) chain E; guessing termini instead 11 messages similar to the above omitted Chain-initial residues that are actual N termini: /B VAL 4, /C MET 1, /D ALA 2, /E GLU 10, /F MET 1, /G MET 1, /H SER 2, /K ARG 13, /L ALA 2, /O SER 2, /P MET 1, /Q LYS 4, /R LYS 9, /T ALA 2, /U PRO 2 Chain-initial residues that are not actual N termini: /K GLY 120 Chain-final residues that are actual C termini: /B GLN 227, /C PHE 150, /D LYS 206, /E LEU 165, /F VAL 103, /G SER 273, /H ALA 130, /K VAL 129, /L ALA 124, /O ARG 89, /P ALA 81, /Q ALA 82, /R HIS 74, /T ALA 87, /U TYR 71 Chain-final residues that are not actual C termini: /K HIS 118 3960 hydrogen bonds /K HIS 118 is not terminus, removing H atom from 'C' 36 hydrogens added > help help:index.html > alphafold fetch P0A8A8 alignTo #1.2/C AlphaFold chains matching chain C --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id C | | P0A8A8 | 0.00 | 150 | 150 | 100 > isolde restrain torsions #1.2/C templateResidues #3/C adjustForConfidence > true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 24 residues in model #3 to IUPAC-IUB standards. > isolde restrain distances #1.2/C templateAtoms #3/C adjustForConfidence true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]RMSD between 150 pruned atom pairs is 0.000 angstroms; (across all 150 pairs: 0.000) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 673, in restrain_atom_distances_to_template apply_restraints(tr, rr, adjust_for_confidence, confidence_type) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > isolde restrain distances #1.2/C ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 653, in restrain_atom_distances_to_template return [apply_restraints(trs, rrs, adjust_for_confidence, confidence_type) for trs, rrs in zip(template_residues, restrained_residues)] File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 653, in return [apply_restraints(trs, rrs, adjust_for_confidence, confidence_type) for trs, rrs in zip(template_residues, restrained_residues)] File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > isolde restrain distances #1.2/G ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 653, in restrain_atom_distances_to_template return [apply_restraints(trs, rrs, adjust_for_confidence, confidence_type) for trs, rrs in zip(template_residues, restrained_residues)] File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 653, in return [apply_restraints(trs, rrs, adjust_for_confidence, confidence_type) for trs, rrs in zip(template_residues, restrained_residues)] File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > alphafold fetch P06992 alignTo #1.2/G AlphaFold chains matching chain G --- Chain| UniProt Name| UniProt Id| RMSD| Length| Seen| % Id G | | P06992 | 0.00 | 273 | 273 | 100 > isolde restrain torsions #1.2/G templateResidues #4/G adjustForConfidence > true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]ISOLDE: Corrected atom nomenclature of 35 residues in model #4 to IUPAC-IUB standards. > isolde tutorial > isolde restrain distances #1.2/G templateAtoms #4/G adjustForConfidence true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]RMSD between 273 pruned atom pairs is 0.000 angstroms; (across all 273 pairs: 0.000) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 673, in restrain_atom_distances_to_template apply_restraints(tr, rr, adjust_for_confidence, confidence_type) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > isolde restrain distances #1.2/G templateAtoms #4/G adjustForConfidence true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]RMSD between 273 pruned atom pairs is 0.000 angstroms; (across all 273 pairs: 0.000) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 673, in restrain_atom_distances_to_template apply_restraints(tr, rr, adjust_for_confidence, confidence_type) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > isolde restrain distances #1.2/G templateAtoms #4/G adjustForConfidence true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]RMSD between 273 pruned atom pairs is 0.000 angstroms; (across all 273 pairs: 0.000) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 673, in restrain_atom_distances_to_template apply_restraints(tr, rr, adjust_for_confidence, confidence_type) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. > isolde restrain distances #1.2/G templateAtoms #4/G adjustForConfidence true ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... [Repeated 1 time(s)]RMSD between 273 pruned atom pairs is 0.000 angstroms; (across all 273 pairs: 0.000) Traceback (most recent call last): File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/usr/lib/ucsf-chimerax/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2897, in run result = ci.function(session, **kw_args) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/cmd.py"", line 47, in restrain_distances restraint_utils.restrain_atom_distances_to_template(session, template_residues, File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 673, in restrain_atom_distances_to_template apply_restraints(tr, rr, adjust_for_confidence, confidence_type) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 637, in apply_restraints dr = adrm.add_restraint(ra1, ra2) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2883, in add_restraint r = self._get_restraints(Atoms([atom1]), Atoms([atom2]), True) File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) RuntimeError: ffi_prep_cif_var failed RuntimeError: ffi_prep_cif_var failed File ""/home/xhan/.local/share/ChimeraX/1.4/site- packages/chimerax/isolde/molobject.py"", line 2863, in _get_restraints num = f(self._c_pointer, atoms1._c_pointers, atoms2._c_pointers, create, n, pointer(ret)) See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 470.129.06 OpenGL renderer: NVIDIA GeForce GTX 1070/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.9.11 Locale: en_US.UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: xcb XDG_SESSION_TYPE=x11 DESKTOP_SESSION=ubuntu XDG_SESSION_DESKTOP=ubuntu XDG_CURRENT_DESKTOP=ubuntu:GNOME DISPLAY=:1 Manufacturer: Hewlett-Packard Model: HP Z440 Workstation OS: Ubuntu 22.04 jammy Architecture: 64bit ELF Virtual Machine: none CPU: 8 Intel(R) Xeon(R) CPU E5-1620 v3 @ 3.50GHz Cache Size: 10240 KB Memory: total used free shared buff/cache available Mem: 62Gi 12Gi 19Gi 247Mi 31Gi 49Gi Swap: 2.0Gi 0.0Ki 2.0Gi Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1070] [10de:1b81] (rev a1) Subsystem: ASUSTeK Computer Inc. GP104 [GeForce GTX 1070] [1043:8596] Kernel driver in use: nvidia Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2022.5.18.1 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4b1 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 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: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 distro: 1.6.0 docutils: 0.17.1 entrypoints: 0.4 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openvr: 1.16.802 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 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 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Third Party fixed all ChimeraX