id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5617 Morph segmentSieve: empty rList chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Windows-10-10.0.19041 ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.2.5 (2021-05-24) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 6n2y 6n2y title: Bacillus PS3 ATP synthase class 1 [more info...] Chain information for 6n2y #1 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | ATP synthase subunit δ a | ATP synthase subunit a b1 | ATP synthase subunit b b2 | ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2y #1 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > sequence chain #1/A Alignment identifier is 1/A > log metadata #1 Metadata for 6n2y #1 --- Title | Bacillus PS3 ATP synthase class 1 Citation | Guo, H., Suzuki, T., Rubinstein, J.L. (2019). Structure of a bacterial ATP synthase. Elife, 8. PMID: 30724163. DOI: 10.7554/eLife.43128 Non-standard residues | ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion Gene source | Bacillus sp. (strain PS3) Experimental method | Electron microscopy Resolution | 3.0Å > hide atoms > show cartoons > select :ADP 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 27 atom styles > select /H 928 atoms, 938 bonds, 129 residues, 1 model selected > color sel red > preset cylinders Changed 34914 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick 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 cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > save C:\Users\emhab/Desktop/image1.png Directory ""C:\Users\emhab/Desktop"" does not exist > open 6n2z Summary of feedback from opening 6n2z fetched from pdb --- note | Fetching compressed mmCIF 6n2z from http://files.rcsb.org/download/6n2z.cif 6n2z title: Bacillus PS3 ATP synthase class 2 [more info...] Chain information for 6n2z #2 --- Chain | Description A B C | ATP synthase subunit α D E F | ATP synthase subunit β G | ATP synthase γ chain H | ATP synthase ε chain I | Bacillus PS3 ATP synthase subunit δ a | Bacillus PS3 ATP synthase subunit a b1 | Bacillus PS3 ATP synthase subunit b b2 | Bacillus PS3 ATP synthase subunit b c0 c1 c2 c3 c4 c5 c6 c7 c8 c9 | ATP synthase subunit c Non-standard residues in 6n2z #2 --- ADP — adenosine-5'-diphosphate ATP — adenosine-5'-triphosphate MG — magnesium ion PO4 — phosphate ion > open 6n3O Summary of feedback from opening 6n3O fetched from pdb --- notes | Fetching compressed mmCIF 6n3o from http://files.rcsb.org/download/6n3o.cif Fetching CCD KA7 from http://ligand-expo.rcsb.org/reports/K/KA7/KA7.cif 6n3o title: Identification of novel, potent and selective GCN2 inhibitors as first-in- class anti-tumor agents [more info...] Chain information for 6n3o #3 --- Chain | Description A | eIF-2-alpha kinase GCN2 Non-standard residues in 6n3o #3 --- KA7 — N-{3-[(2-aminopyrimidin-5-yl)ethynyl]-2,4-difluorophenyl}-5-chloro-2-methoxypyridine-3-sulfonamide > morph #1,2 Computed 21 frame morph #4 > coordset #4 1,21 > hide cartoons > show atoms > lighting simple > coordset #4,1,21 > close #4 > morph #1,2,3 wrap true same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 280, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\morph.py"", line 73, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\motion.py"", line 107, in interpolate results = segment.segmentHingeSame(sm, m, cf, mhs, log=log) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 88, in segmentHingeSame segments = find_hinges(parts, fraction, min_hinge_spacing, log) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 298, in find_hinges segs = segmentHingeResidues(rList0, rList1, fraction, min_hinge_spacing) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 306, in segmentHingeResidues segments = segmentSieve(rList0, rList1, fraction) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 41, in segmentSieve chain = rList0[0].chain_id IndexError: list index out of range IndexError: list index out of range File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 41, in segmentSieve chain = rList0[0].chain_id See log for complete Python traceback. > morph #1,2,3 wrap true same true Traceback (most recent call last): File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\cmd_line\tool.py"", line 280, in execute cmd.run(cmd_text) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\core\commands\cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\morph.py"", line 73, in morph traj = compute_morph(structures, session.logger, method=method, rate=rate, frames=frames, File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\motion.py"", line 25, in compute_morph res_groups = motion.interpolate(mol, res_interp) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\motion.py"", line 107, in interpolate results = segment.segmentHingeSame(sm, m, cf, mhs, log=log) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 88, in segmentHingeSame segments = find_hinges(parts, fraction, min_hinge_spacing, log) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 298, in find_hinges segs = segmentHingeResidues(rList0, rList1, fraction, min_hinge_spacing) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 306, in segmentHingeResidues segments = segmentSieve(rList0, rList1, fraction) File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 41, in segmentSieve chain = rList0[0].chain_id IndexError: list index out of range IndexError: list index out of range File ""C:\Program Files\ChimeraX 1.2.5\bin\lib\site- packages\chimerax\morph\segment.py"", line 41, in segmentSieve chain = rList0[0].chain_id See log for complete Python traceback. OpenGL version: 3.3.0 - Build 25.20.100.6446 OpenGL renderer: Intel(R) UHD Graphics 620 OpenGL vendor: Intel Manufacturer: HP Model: HP ENVY x360 Convertible 15m-cn0xxx OS: Microsoft Windows 10 Home (Build 19043) Memory: 12,711,006,208 MaxProcessMemory: 137,438,953,344 CPU: 8 Intel(R) Core(TM) i7-8550U CPU @ 1.80GHz OSLanguage: en-US Locale: ('en_US', 'cp1252') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2020.12.5 cftime: 1.5.0 chardet: 3.0.4 ChimeraX-AddCharge: 1.0.1 ChimeraX-AddH: 2.1.6 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.13.2 ChimeraX-AtomicLibrary: 3.1.3 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.5.2 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.1 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.1 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.2.1 ChimeraX-CommandLine: 1.1.4 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.2.5 ChimeraX-CoreFormats: 1.0 ChimeraX-coulombic: 1.1.1 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.1 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.3 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.0 ChimeraX-Hbonds: 2.1 ChimeraX-Help: 1.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.0 ChimeraX-ImageFormats: 1.1 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-Label: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.0.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.0 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 1.2.1 ChimeraX-MDcrds: 2.2 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.3 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.0.1 ChimeraX-ModelPanel: 1.0.1 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: 2.0.1 ChimeraX-OpenCommand: 1.5 ChimeraX-PDB: 2.4.1 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.1 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.0.1 ChimeraX-ReadPbonds: 1.0 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.4 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SeqView: 2.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.0 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.0.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.3.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.0.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.7.6 ChimeraX-uniprot: 2.1 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 5.0.9 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 2.0.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.18 psutil: 5.7.2 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 pywin32: 228 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 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-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0 WMI: 1.5.1 }}} " defect closed normal Structure Comparison fixed all ChimeraX