id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20858 ChimeraX bug report submission Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.7.9-arm64-arm-64bit ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC) Description alphafold search produces no output 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 > alphafold search > MAGGGGAERVRVGAAAAGLLPPSCRQPRRRESRERLSVCSKLCYAVGGAPYQTTGCALGFFLQIYLLDVAQLDPFYASIILFVGRAWDAITDPMVGFFISKTPWTRFGRLMPWIIFSTPFAVISYFLIWFVPDISTGQVMWYLIFYCIFQTLVTCFHVPYSALTMFISREQSERDSATAYRMTVEVLGTVLGTAIQGQIVGKAVTPCIENPPFLSETNFSVAIRNVNMTHYTGSLADTRNAYMVAAGVIGGLYILCAVILSVGVREKRESSELQSDEPVSFFRGLKLVMNHGAYIKLITGFLFTSLAFMLLEGNFALFCTYTLGFRNEFQNILLAIMLSATLTIPFWQWFLTRFGKKTAVYVGISSAVPFLITVVVLDSNLVVTYIVAVAAGISVAAAFLLPWSMLPDVIDDFKLQHPESRGHEAIFFSFYVFFTKFTSGVSLGISTLSLDFAGYQTRGCSQPSEVNITLKLLVSAVPVGLILLGLLLFKLYPIDEEKRRENKKALQDLREESNSSSESDSTELANIV > open /Users/pett/src/chimerax/src/bundles/seqalign/test-data/nonassoc.fa > format fasta Summary of feedback from opening /Users/pett/src/chimerax/src/bundles/seqalign/test-data/nonassoc.fa --- notes | Alignment identifier is nonassoc.fa Showing conservation header (""seq_conservation"" residue attribute) for alignment nonassoc.fa Opened 5 sequences from nonassoc.fa > open 1qvc 1kaw 1eyg 3ull 1qvc title: Crystal structure analysis of single stranded DNA binding protein (SSB) from E.coli [more info...] Chain information for 1qvc #1 --- Chain | Description | UniProt A B C D | SINGLE STRANDED DNA BINDING PROTEIN MONOMER | SSB_ECOLI 1-145 201-345 401-545 601-745 1kaw title: Structure of single stranded DNA binding protein (SSB) [more info...] Chain information for 1kaw #2 --- Chain | Description | UniProt A B C D | SINGLE-STRANDED DNA BINDING PROTEIN | SSB_ECOLI 1-135 1eyg title: Crystal structure of chymotryptic fragment of E. coli ssb bound to two 35-mer single strand DNAS [more info...] Chain information for 1eyg #3 --- Chain | Description | UniProt A B C D | SINGLE-STRAND DNA-BINDING PROTEIN | SSB_ECOLI 1000-1115 2000-2115 3000-3115 4000-4115 Q R | SINGLE STRANDED 28-MER OF D(C) | 1eyg mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3ull title: Human mitochondrial single-stranded DNA binding protein [more info...] Chain information for 3ull #4 --- Chain | Description | UniProt A B | DNA BINDING PROTEIN | SSB_HUMAN 1-132 3ull mmCIF Assemblies --- 1| author_defined_assembly Associated 1qvc chain A to 1qvc with 0 mismatches Associated 1qvc chain B to 1qvc with 0 mismatches Associated 1qvc chain C to 1qvc with 0 mismatches Associated 1qvc chain D to 1qvc with 0 mismatches Associated 1kaw chain A to 1qvc with 0 mismatches Associated 1kaw chain B to 1qvc with 0 mismatches Associated 1kaw chain C to 1qvc with 0 mismatches Associated 1kaw chain D to 1qvc with 0 mismatches Associated 1eyg chain A to 1eyg with 0 mismatches Associated 1eyg chain B to 1eyg with 0 mismatches Associated 1eyg chain C to 1eyg with 0 mismatches Associated 1eyg chain D to 1eyg with 0 mismatches Associated 3ull chain A to 3ull with 0 mismatches Associated 3ull chain B to 3ull with 0 mismatches > ui tool show ""Modeller Comparative"" Populating font family aliases took 183 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > modeller comparative nonassoc.fa:4 numModels 3 fast false multichain true > hetPreserve false hydrogens false waterPreserve false directory > /Users/pett/rm Webservices job id: 5CLNCC1KEKXYIZHI Webservices job finished: 5CLNCC1KEKXYIZHI Modeller job (ID 5CLNCC1KEKXYIZHI) finished Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 198.9 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 225.9 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 208.7 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 194.8 RMSD between 249 pruned atom pairs is 0.774 angstroms; (across all 545 pairs: 9.039) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 169.9 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 221.5 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 196 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 203.1 RMSD between 242 pruned atom pairs is 0.751 angstroms; (across all 540 pairs: 9.499) Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 1qvc, chain A (#1) with T0151, chain A (#), sequence alignment score = 189.6 Matchmaker 1qvc, chain B (#1) with T0151, chain B (#), sequence alignment score = 218.7 Matchmaker 1qvc, chain C (#1) with T0151, chain C (#), sequence alignment score = 208.7 Matchmaker 1qvc, chain D (#1) with T0151, chain D (#), sequence alignment score = 204.3 RMSD between 254 pruned atom pairs is 0.688 angstroms; (across all 547 pairs: 8.841) Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Associated T0151 chain A to T0151 with 0 mismatches Associated T0151 chain B to T0151 with 0 mismatches Associated T0151 chain C to T0151 with 0 mismatches Associated T0151 chain D to T0151 with 0 mismatches Chain information for T0151 --- Chain | Description 5.1/A 5.2/A 5.3/A 5.1/B 5.2/B 5.3/B 5.1/C 5.2/C 5.3/C 5.1/D 5.2/D 5.3/D | No description available > close > alphafold search > MAGGGGAERVRVGAAAAGLLPPSCRQPRRRESRERLSVCSKLCYAVGGAPYQTTGCALGFFLQIYLLDVAQLDPFYASIILFVGRAWDAITDPMVGFFISKTPWTRFGRLMPWIIFSTPFAVISYFLIWFVPDISTGQVMWYLIFYCIFQTLVTCFHVPYSALTMFISREQSERDSATAYRMTVEVLGTVLGTAIQGQIVGKAVTPCIENPPFLSETNFSVAIRNVNMTHYTGSLADTRNAYMVAAGVIGGLYILCAVILSVGVREKRESSELQSDEPVSFFRGLKLVMNHGAYIKLITGFLFTSLAFMLLEGNFALFCTYTLGFRNEFQNILLAIMLSATLTIPFWQWFLTRFGKKTAVYVGISSAVPFLITVVVLDSNLVVTYIVAVAAGISVAAAFLLPWSMLPDVIDDFKLQHPESRGHEAIFFSFYVFFTKFTSGVSLGISTLSLDFAGYQTRGCSQPSEVNITLKLLVSAVPVGLILLGLLLFKLYPIDEEKRRENKKALQDLREESNSSSESDSTELANIV OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Max 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: Mac Studio Model Identifier: Mac13,1 Model Number: Z14J0008FLL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: mBoot-18000.161.10 OS Loader Version: 11881.140.96.701.1 Software: System Software Overview: System Version: macOS 15.7.9 (24G830) Kernel Version: Darwin 24.6.0 Time since boot: 6 hours, 34 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: PHL 279P1: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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-ArtiaX: 0.7.0 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-ChopChopMF: 1.2 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-DAQplugin: 0.13.60 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-Gamepad: 0.3.0 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-SelTools: 0.1.0 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 coloredlogs: 15.0.1 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: 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