id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20817 Minimization failure: KeyError: 'N' chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.7.7-arm64-arm-64bit ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC) Description Replace this text with list of actions that caused this problem to occur Log: UCSF ChimeraX version: 1.12 (2026-06-12) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > ui tool show Registration > open 7B6w fromDatabase ccd format ccd Unknown CCD ligand name > open 7b6w fromDatabase pdbe_bio format mmcif Summary of feedback from opening 7b6w fetched from pdbe_bio --- warnings | Missing or incorrect sequence information. Inferred polymer connectivity. Atom H is not in the residue template for PRO /A:38 notes | Fetching compressed 7b6w bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/7b6w-assembly-1.cif.gz Fetching CCD T0B from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/B/T0B/T0B.cif 7b6w bioassembly 1 title: Crystal structure of the human alpha1B adrenergic receptor in complex with inverse agonist (+)-cyclazosin [more info...] Chain information for 7b6w bioassembly 1 #1 --- Chain | Description A | Alpha-1B adrenergic receptor,alpha1B adrenergic receptor,Alpha-1B adrenergic receptor,alpha1B adrenergic receptor,Alpha-1B adrenergic receptor,alpha1B adrenergic receptor,Alpha-1B adrenergic receptor,alpha1B adrenergic receptor Non-standard residues in 7b6w bioassembly 1 #1 --- T0B — (T0B) 118 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Computing secondary structure Opened 1 biological assemblies for 7b6w > select ::name=""T0B"" 118 atoms, 126 bonds, 2 residues, 1 model selected > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > ui tool show ""Dock Prep"" Populating font family aliases took 183 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Filling out missing side chains /A GLN 39: phi -74.5, psi -29.3 trans /A LEU 40: phi -68.2, psi -25.3 trans /A ASP 41: phi -48.6, psi -35.4 trans /A ILE 42: phi -71.6, psi -51.6 trans /A ARG 44: phi -63.5, psi -35.1 trans /A ARG 74: phi -66.4, psi -30.2 trans /A ARG 115: phi -41.4, psi -34.1 trans /A ILE 145: phi -58.6, psi -37.2 trans /A ARG 148: phi -57.0, psi -52.3 trans /A TYR 150: phi -59.1, psi -49.8 trans /A LEU 151: phi -96.9, psi -6.0 trans /A GLN 152: phi -93.7, psi -34.4 trans /A THR 158: phi -112.9, psi -176.3 trans /A ARG 159: phi -62.7, psi -38.3 trans /A ARG 160: phi -61.1, psi -52.1 trans /A LYS 185: phi -79.6, psi -58.5 trans /A GLU 186: phi -88.7, psi 139.6 trans /A LYS 193: phi -137.8, psi 54.3 trans /A VAL 194: phi -52.1, psi -53.8 trans /A VAL 197: phi -66.6, psi -33.6 trans /A THR 198: phi -56.9, psi 163.3 trans /A GLU 199: phi 179.5, psi -175.5 trans /A PHE 206: phi -54.1, psi -41.1 trans /A TYR 227: phi -55.8, psi -47.1 trans /A LYS 231: phi -73.3, psi -44.2 trans /A ARG 232: phi -64.1, psi -36.6 trans /A THR 234: phi -69.9, psi -43.0 trans /A LYS 235: phi -63.2, psi -49.6 trans /A LEU 237: phi -84.9, psi none trans /A SER 248: phi none, psi 133.7 trans /A LYS 285: phi -47.7, psi -44.9 trans /A ARG 288: phi -93.8, psi -24.4 trans /A LYS 291: phi -65.5, psi -48.2 trans /A LYS 294: phi -71.7, psi -47.7 trans /A LYS 324: phi none, psi -57.4 trans /A VAL 329: phi -70.5, psi -44.8 trans /A GLU 352: phi -97.6, psi 106.4 trans /A LEU 354: phi -57.0, psi -41.0 trans /A GLU 356: phi -72.2, psi -45.6 trans /A LYS 360: phi -76.9, psi -24.6 trans /A GLU 391: phi -59.9, psi -27.0 trans /A LYS 414: phi -60.0, psi -28.5 trans /A GLU 473: phi -59.7, psi -39.1 trans /A LYS 490: phi -66.1, psi -29.5 trans /A GLU 505: phi -65.5, psi -47.9 trans /A LYS 513: phi -59.5, psi -48.1 trans /A ARG 517: phi -60.2, psi -42.5 trans /A GLU 518: phi -64.9, psi -22.4 trans /A GLN 524: phi -127.3, psi none trans Applying GLN rotamer (chi angles: 65.0 -86.1 56.2) to /A GLN 39 Applying LEU rotamer (chi angles: -67.8 174.1) to /A LEU 40 Applying ASP rotamer (chi angles: -71.6 -14.7) to /A ASP 41 Applying ILE rotamer (chi angles: -66.5 168.5) to /A ILE 42 Applying ARG rotamer (chi angles: -68.6 -73.6 -68.1 108.8) to /A ARG 44 Applying ARG rotamer (chi angles: 178.9 65.5 -178.1 84.0) to /A ARG 74 Applying ARG rotamer (chi angles: -178.9 75.0 -85.4 170.0) to /A ARG 115 Applying ILE rotamer (chi angles: -68.1 168.5) to /A ILE 145 Applying ARG rotamer (chi angles: -178.5 178.6 178.4 85.5) to /A ARG 148 Applying TYR rotamer (chi angles: 74.5 111.2) to /A TYR 150 Applying LEU rotamer (chi angles: -61.2 176.5) to /A LEU 151 Applying GLN rotamer (chi angles: -174.7 64.2 73.5) to /A GLN 152 Applying THR rotamer (chi angles: 65.5) to /A THR 158 Applying ARG rotamer (chi angles: -70.7 177.7 -180.0 172.6) to /A ARG 159 Applying ARG rotamer (chi angles: 179.8 76.0 -84.5 167.6) to /A ARG 160 Applying LYS rotamer (chi angles: -178.2 178.5 -70.6 78.8) to /A LYS 185 Applying GLU rotamer (chi angles: -64.4 83.2 -6.6) to /A GLU 186 Applying LYS rotamer (chi angles: -61.1 -66.1 -174.5 -67.0) to /A LYS 193 Applying VAL rotamer (chi angles: 170.9) to /A VAL 194 Applying VAL rotamer (chi angles: 173.2) to /A VAL 197 Applying THR rotamer (chi angles: 60.9) to /A THR 198 Applying GLU rotamer (chi angles: -66.3 179.3 54.2) to /A GLU 199 Applying PHE rotamer (chi angles: 179.8 79.4) to /A PHE 206 Applying TYR rotamer (chi angles: 177.2 79.4) to /A TYR 227 Applying LYS rotamer (chi angles: -70.5 -177.0 175.0 65.8) to /A LYS 231 Applying ARG rotamer (chi angles: 178.6 66.1 -178.0 85.6) to /A ARG 232 Applying THR rotamer (chi angles: -60.5) to /A THR 234 Applying LYS rotamer (chi angles: -179.0 178.1 178.3 180.0) to /A LYS 235 Applying LEU rotamer (chi angles: -64.7 174.5) to /A LEU 237 Applying SER rotamer (chi angles: 179.0) to /A SER 248 Applying LYS rotamer (chi angles: -63.9 -64.8 -87.6 70.8) to /A LYS 285 Applying ARG rotamer (chi angles: -173.4 -88.6 -59.5 -81.9) to /A ARG 288 Applying LYS rotamer (chi angles: 177.8 -92.7 -85.3 47.8) to /A LYS 291 Applying LYS rotamer (chi angles: -70.3 -171.1 -71.7 -174.4) to /A LYS 294 Applying LYS rotamer (chi angles: -66.8 -178.0 -177.5 -65.9) to /A LYS 324 Applying VAL rotamer (chi angles: 173.1) to /A VAL 329 Applying GLU rotamer (chi angles: 66.6 -83.9 15.8) to /A GLU 352 Applying LEU rotamer (chi angles: -69.2 172.7) to /A LEU 354 Applying GLU rotamer (chi angles: -177.8 177.5 -1.2) to /A GLU 356 Applying LYS rotamer (chi angles: -67.2 175.1 70.0 176.2) to /A LYS 360 Applying GLU rotamer (chi angles: -174.7 175.6 -1.2) to /A GLU 391 Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 414 Applying GLU rotamer (chi angles: -67.0 81.2 -0.7) to /A GLU 473 Applying LYS rotamer (chi angles: -66.2 -66.3 -174.8 -67.0) to /A LYS 490 Applying GLU rotamer (chi angles: -66.8 79.9 9.3) to /A GLU 505 Applying LYS rotamer (chi angles: -179.9 63.8 167.7 61.8) to /A LYS 513 Applying ARG rotamer (chi angles: 178.6 66.1 -178.0 85.6) to /A ARG 517 Applying GLU rotamer (chi angles: -64.5 83.4 -3.7) to /A GLU 518 Applying GLN rotamer (chi angles: -68.4 74.8 37.4) to /A GLN 524 Summary of feedback from adding hydrogens to 7b6w bioassembly 1 #1 --- notes | No usable SEQRES records for 7b6w bioassembly 1 (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 38 Chain-initial residues that are not actual N termini: /A SER 248, /A LYS 324 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLN 524, /A LEU 237, /A LEU 319 369 hydrogen bonds /A GLN 524 is not terminus, removing H atom from 'C' 400 hydrogens added Closest equivalent command: addcharge standardizeResidues none Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue T0B (net charge +0) with gasteiger method Running ANTECHAMBER command: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/antechamber -i /var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmpu7uusbz0/ante.in.mol2 -fi mol2 -o /var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmpu7uusbz0/ante.out.mol2 -fo mol2 -c gas -nc 0 -j 5 -s 2 -dr n (T0B) `` (T0B) `Welcome to antechamber 20.0: molecular input file processor.` (T0B) `` (T0B) `Info: Finished reading file (/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmpu7uusbz0/ante.in.mol2); atoms read (59), bonds read (63).` (T0B) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (T0B) `` (T0B) `` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_GAS.AC -o ANTECHAMBER_GAS_AT.AC -d /Applications/ChimeraX-1.12.app/Contents/bin/amber20/dat/antechamber/ATOMTYPE_GAS.DEF` (T0B) `` Charges for residue T0B determined Dock prep finished > ui tool show ""Minimize Structure"" > minimize #1 Starting dock prep Deleting solvent Deleting non-metal-complex ions Deleting non-current alt locs Deleting residues with incomplete backbones Filling out missing side chains /A GLN 524: phi -127.3, psi none trans Applying GLN rotamer (chi angles: -68.4 74.8 37.4) to /A GLN 524 Summary of feedback from adding hydrogens to 7b6w bioassembly 1 #1 --- notes | No usable SEQRES records for 7b6w bioassembly 1 (#1) chain A; guessing termini instead Chain-initial residues that are actual N termini: /A PRO 38 Chain-initial residues that are not actual N termini: /A SER 248, /A LYS 324 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A GLN 524, /A LEU 237, /A LEU 319 365 hydrogen bonds /A GLN 524 is not terminus, removing H atom from 'C' 6 hydrogens added Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue T0B (net charge +0) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmp7fm12t04/ante.in.mol2 -fi mol2 -o /var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmp7fm12t04/ante.out.mol2 -fo mol2 -c bcc -nc 0 -j 5 -s 2 -dr n (T0B) `` (T0B) `Welcome to antechamber 20.0: molecular input file processor.` (T0B) `` (T0B) `Info: Finished reading file (/var/folders/5g/sf3jqpyx7_9dpyckj73r92km0000gn/T/tmp7fm12t04/ante.in.mol2); atoms read (59), bonds read (63).` (T0B) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (T0B) `` (T0B) `` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (T0B) `Info: Total number of electrons: 232; net charge: 0` (T0B) `` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (T0B) `` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /Applications/ChimeraX-1.12.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT -s 2 -j 1` (T0B) `` (T0B) `Running: /Applications/ChimeraX-1.12.app/Contents/bin/amber20/bin/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (T0B) `` Charges for residue T0B determined Dock prep finished Traceback (most recent call last): File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/minimize/tool.py"", line 116, in minimize run(self.session, cmd) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/run.py"", line 49, in run results = command.run(text, log=log, return_json=return_json) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3245, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/minimize/cmd.py"", line 43, in cmd_minimize dock_prep_caller(session, [structure], memorize_name=""minimization"", nogui=True, File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/cmd.py"", line 146, in dock_prep_caller run_steps(session, state, structures) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/cmd.py"", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/prep.py"", line 150, in prep callback(session, state, structures) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/cmd.py"", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/addh/dock_prep.py"", line 56, in run_for_dock_prep callback(session, state, structures) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/cmd.py"", line 161, in run_steps step_mod.run_for_dock_prep(session, state, run_steps, state['memorization'], state['memorize_name'], File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/add_charge/dock_prep.py"", line 58, in run_for_dock_prep callback(session, state, structures) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/cmd.py"", line 156, in run_steps callback() File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/dock_prep/prep.py"", line 149, in state['callback'] = lambda cb=cb, ps=postscript: (ps(), cb()) ^^^^ File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/minimize/cmd.py"", line 45, in steps=max_steps: _minimize(ses, struct, updates, log, steps), **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/minimize/cmd.py"", line 232, in _minimize system = forcefield.createSystem(top, nonbondedCutoff=1*nanometer, constraints=HBonds) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/openmm/app/forcefield.py"", line 1279, in createSystem data.setAtomClasses(self) File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/openmm/app/forcefield.py"", line 683, in setAtomClasses self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/openmm/app/forcefield.py"", line 683, in self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms] ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ KeyError: 'N' KeyError: 'N' File ""/Applications/ChimeraX-1.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/openmm/app/forcefield.py"", line 683, in self.atomClasses = [classNameForType[self.atomType[atom]] for atom in self.atoms] ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M4 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac16,13 Model Number: MW1H3LL/A Chip: Apple M4 Total Number of Cores: 10 (4 performance and 6 efficiency) Memory: 16 GB System Firmware Version: mBoot-18000.120.36 OS Loader Version: 11881.140.96.701.1 Software: System Software Overview: System Version: macOS 15.7.7 (24G720) Kernel Version: Darwin 24.6.0 Time since boot: 20 days, 40 minutes Graphics/Displays: Apple M4: Chipset Model: Apple M4 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2880 x 1864 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.2 aiohttp: 3.13.4 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.4.3 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.67.1 ChimeraX-AtomicLibrary: 14.4 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.2.2 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: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.8.2 ChimeraX-Label: 1.5 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 ChimeraX-Map: 1.3 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-MatchAlign: 1.2 ChimeraX-MatchMaker: 2.4.1 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.9 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.8 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.4.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.14.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.21 decorator: 5.3.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.63.0 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.18 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.2 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.1 narwhals: 2.22.1 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.7 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.10.0 plotly: 6.8.0 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.5.2 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.13.4 pydantic-settings: 2.14.1 pydantic_core: 2.46.4 pydata-sphinx-theme: 0.18.0 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.10.2 PyQt6-Qt6: 6.10.2 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.2 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.32 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 rpds-py: 2026.5.1 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.1.1 sortedcontainers: 2.4.0 soupsieve: 2.8.4 Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.4 stack-data: 0.6.3 starlette: 1.3.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.7 tqdm: 4.68.2 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.7.0 uvicorn: 0.49.0 wcwidth: 0.8.1 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.24.2 }}} " defect closed normal Structure Editing duplicate all ChimeraX