id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17051 ISOLDE add aa problem rohou.alexis@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-14.7.4-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Attempting to add a new aa with isolde gives error ""TypeError: If no anchor residues are specified, chain ID, number and center must be provided! "" But the documentation makes no mention of center needing to be provided. In fact it specifically says the new residue will be centered at cofr. Am I missing something? (it's my first time trying to start a new chain with isolde add aa) Log: Startup Messages --- note | available bundle cache has not been initialized yet > set bgColor white > lighting soft > clipper init > cofr centerOfView showPivot true > camera ortho > lighting simple UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open pdb:6OWE Summary of feedback from opening 6OWE fetched from pdb --- notes | Fetching compressed mmCIF 6owe from http://files.rcsb.org/download/6owe.cif Fetching CCD IMD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/IMD/IMD.cif Fetching CCD N9V from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/V/N9V/N9V.cif Fetching CCD NDP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/NDP/NDP.cif 6owe title: Enoyl-CoA carboxylases/reductases in complex with ethylmalonyl CoA [more info...] Chain information for 6owe #1 --- Chain | Description | UniProt A B C D | Crotonyl-CoA carboxylase/reductase | E4N096_KITSK 1-445 Non-standard residues in 6owe #1 --- IMD — imidazole N9V — 5'-O-[(S)-{[(S)-[(3R)-4-({(1E)-3-[(2-{[(2S)-2-carboxybutanoyl]sulfanyl}ethyl)amino]-3-oxoprop-1-en-1-yl}amino)-3-hydroxy-2,2-dimethyl-4-oxobutoxy](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]adenosine 3'-(dihydrogen phosphate) NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate 208 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > delete ~protein > addh Summary of feedback from adding hydrogens to 6owe #1 --- notes | Termini for 6owe (#1) chain A determined from SEQRES records Termini for 6owe (#1) chain B determined from SEQRES records Termini for 6owe (#1) chain C determined from SEQRES records Termini for 6owe (#1) chain D determined from SEQRES records Chain-initial residues that are actual N termini: /B GLU -3 Chain-initial residues that are not actual N termini: /A ARG -1, /C GLY -2, /D ARG -1 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /A ASN 444, /B ASN 444, /C ASN 444, /D ARG 443 1878 hydrogen bonds Adding 'H' to /A ARG -1 Adding 'H' to /C GLY -2 Adding 'H' to /D ARG -1 /A ASN 444 is not terminus, removing H atom from 'C' /B ASN 444 is not terminus, removing H atom from 'C' /C ASN 444 is not terminus, removing H atom from 'C' /D ARG 443 is not terminus, removing H atom from 'C' 13508 hydrogens added > ~show > isolde start > set selectionWidth 4 Done loading forcefield > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 Removed all altlocs in #1 and reset associated occupancies to 1. ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 142 residues in model #1 to IUPAC-IUB standards. 6owe title: Enoyl-CoA carboxylases/reductases in complex with ethylmalonyl CoA [more info...] Chain information for 6owe --- Chain | Description | UniProt 1.2/A 1.2/B 1.2/C 1.2/D | Crotonyl-CoA carboxylase/reductase | E4N096_KITSK 1-445 > isolde add aa PHE structure #1.2 chainId M number 8 Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 3213, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Users/rohoua/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/chimerax/isolde/atomic/building/cmd.py"", line 132, in add_aa_cmd add_amino_acid_residue(structure, resname.upper(), prev_res=prev_res, next_res=next_res, File ""/Users/rohoua/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/chimerax/isolde/atomic/building/build_utils.py"", line 136, in add_amino_acid_residue raise TypeError('If no anchor residues are specified, chain ID, ' TypeError: If no anchor residues are specified, chain ID, number and center must be provided! TypeError: If no anchor residues are specified, chain ID, number and center must be provided! File ""/Users/rohoua/Library/Application Support/ChimeraX/1.9/lib/python/site- packages/chimerax/isolde/atomic/building/build_utils.py"", line 136, in add_amino_acid_residue raise TypeError('If no anchor residues are specified, chain ID, ' See log for complete Python traceback. OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M2 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,7 Model Number: Z16T0006PLL/A Chip: Apple M2 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 10151.140.19.700.2 Software: System Software Overview: System Version: macOS 14.7.4 (23H420) Kernel Version: Darwin 23.6.0 Time since boot: 4 days, 1 hour, 17 minutes Graphics/Displays: Apple M2: Chipset Model: Apple M2 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 272P7VU: Resolution: 6016 x 3384 UI Looks like: 3008 x 1692 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 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ChimeraX-Clashes: 2.3 ChimeraX-Clipper: 0.23.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-LigandRecognizer: 0.1 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 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ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 importlib_metadata: 8.0.0 importlib_resources: 6.4.0 inflect: 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PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 Send2Trash: 1.8.3 SEQCROW: 1.8.16 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4.2 traitlets: 5.14.3 typeguard: 4.3.0 typing_extensions: 4.12.2 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 zipp: 3.19.2 }}} " defect assigned normal Third Party all ChimeraX