id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 7512 Tautomers in alt locs Tristan Croll Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Something's a bit funky about the handling of hydrogen altlocs in histidines (this is the second ultra-high-res structure I've seen this in today). open 7tgt show view /X:132 The histidine is shown as altloc B for all atoms other than HE2, which has altloc A shown, appearing with a very long bond to NE2. Playing with the altloc explorer, it looks like this might be because HE2 only appears in altloc A. Log: 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 7v5u structureFactors true Summary of feedback from opening 7v5u fetched from pdb --- warning | WARNING: multiple experimental reflection datasets found: F_meas_au, F_meas_sigma_au, phase_calc, fom Automatically choosing ""F_meas_au, F_meas_sigma_au"". notes | Fetching compressed mmCIF 7v5u from http://files.rcsb.org/download/7v5u.cif Fetching CCD HA4 from http://ligand-expo.rcsb.org/reports/H/HA4/HA4.cif Fetching CCD P6G from http://ligand-expo.rcsb.org/reports/P/P6G/P6G.cif Fetching compressed 7v5u structure factors from http://files.rcsb.org/download/7v5u-sf.cif Resolution: 0.9190125273225865 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 82,84,80, pixel 0.303,0.289,0.301, shown at level 1.33, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 82,84,80, pixel 0.303,0.289,0.301, shown at level -0.225,0.225, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_29 as #1.1.1.4, grid size 82,84,80, pixel 0.303,0.289,0.301, shown at level 0.244, step 1, values float32 Opened (STATIC) F_calc_au, phase_calc as #1.1.1.5, grid size 82,84,80, pixel 0.303,0.289,0.301, shown at level -1.69,1.69, step 1, values float32 Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.6, grid size 82,84,80, pixel 0.303,0.289,0.301, shown at level -0.373,0.373, step 1, values float32 Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.7, grid size 82,84,80, pixel 0.303,0.289,0.301, shown at level -1.62,1.62, step 1, values float32 7v5u title: The 0.92 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with 2-cyclohexadecylacetic acid (CYC16AA) [more info...] Chain information for 7v5u --- Chain | Description | UniProt 1.2/A | Fatty acid-binding protein, heart | FABPH_HUMAN Non-standard residues in 7v5u #1.2 --- HA4 — 2-cyclohexadecylethanoic acid (2-cyclohexadecylacetic acid) P6G — hexaethylene glycol (polyethylene glycol PEG400) > set bgColor white > cbo Unknown command: cbo > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} > cbo 1308 atoms, 351 residues, atom occupancy range 0.29 to 1 > cbc > cbo 1308 atoms, 351 residues, atom occupancy range 0.29 to 1 > select /A:1002@O 1 atom, 1 residue, 1 model selected > ui tool show ""Selection Inspector"" > select /A:107@CD 1 atom, 1 residue, 1 model selected > cbc > close #1 Deleting Crystallographic maps(7v5u-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_29 > open 7th6 structureFactors true Summary of feedback from opening 7th6 fetched from pdb --- warning | Atom HCS is not in the residue template for I56 /A:301 notes | Fetching compressed mmCIF 7th6 from http://files.rcsb.org/download/7th6.cif Fetching CCD I56 from http://ligand-expo.rcsb.org/reports/I/I56/I56.cif Fetching compressed 7th6 structure factors from http://files.rcsb.org/download/7th6-sf.cif Resolution: 0.9700031604813305 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 78,76,78, pixel 0.322,0.322,0.308, shown at level 1.47, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 78,76,78, pixel 0.322,0.322,0.308, shown at level -0.276,0.276, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_28 as #1.1.1.4, grid size 78,76,78, pixel 0.322,0.322,0.308, shown at level 0.256, step 1, values float32 Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 78,76,78, pixel 0.322,0.322,0.308, shown at level -1.21,1.21, step 1, values float32 Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 78,76,78, pixel 0.322,0.322,0.308, shown at level -4.28,4.28, step 1, values float32 7th6 title: Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B21 [more info...] Chain information for 7th6 --- Chain | Description | UniProt 1.2/A | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | PPIF_HUMAN Non-standard residues in 7th6 #1.2 --- I56 — 4'-{[(4S,7S,11R,13E,19S)-19-{[2-(2-aminoethoxy)ethyl]carbamoyl}-7-benzyl-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosin-4-yl]methyl}-2-methyl[1,1'-biphenyl]-4-carboxylic acid > cbo 2785 atoms, 359 residues, atom occupancy range 0.402 to 1 > cbc > close #1 Deleting Crystallographic maps(7th6-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_28 > open 7tgt structureFactors true Summary of feedback from opening 7tgt fetched from pdb --- notes | Fetching compressed mmCIF 7tgt from http://files.rcsb.org/download/7tgt.cif Fetching CCD I4F from http://ligand-expo.rcsb.org/reports/I/I4F/I4F.cif Fetching compressed 7tgt structure factors from http://files.rcsb.org/download/7tgt-sf.cif Resolution: 1.0550024172682124 Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 90,70,72, pixel 0.334,0.349,0.345, shown at level 1.29, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 90,70,72, pixel 0.334,0.349,0.345, shown at level -0.256,0.256, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_28 as #1.1.1.4, grid size 90,70,72, pixel 0.334,0.349,0.345, shown at level 0.235, step 1, values float32 Opened (STATIC) pdbx_DELFWT, pdbx_DELPHWT as #1.1.1.5, grid size 90,70,72, pixel 0.334,0.349,0.345, shown at level -0.453,0.453, step 1, values float32 Opened (STATIC) pdbx_FWT, pdbx_PHWT as #1.1.1.6, grid size 90,70,72, pixel 0.334,0.349,0.345, shown at level -1.59,1.59, step 1, values float32 7tgt title: Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor A26 [more info...] Chain information for 7tgt --- Chain | Description | UniProt 1.2/X | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | PPIF_HUMAN Non-standard residues in 7tgt #1.2 --- I4F — (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide > cbo 2821 atoms, 421 residues, atom occupancy range 0.453 to 1 > cbc > select /X:132@HE2 1 atom, 1 residue, 1 model selected > ui tool show ""Selection Inspector"" > ui tool show Shell Populating font family aliases took 189 ms. Replace uses of missing font family ""Monaco"" with one that exists to avoid this cost. > select /X:132@NE2 1 atom, 1 residue, 1 model selected > close #1 Deleting Crystallographic maps(7tgt-sf.cif) Deleting (LIVE) 2mFo-DFc Deleting (LIVE) mFo-DFc Deleting (LIVE) 2mFo-DFc_smooth_28 > open 7tgt 7tgt title: Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor A26 [more info...] Chain information for 7tgt #1 --- Chain | Description | UniProt X | Peptidyl-prolyl cis-trans isomerase F, mitochondrial | PPIF_HUMAN Non-standard residues in 7tgt #1 --- I4F — (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[(furan-2-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide > show > view /X:132 > select /X:132@NE2 1 atom, 1 residue, 1 model selected > select up 18 atoms, 18 bonds, 1 residue, 1 model selected > select down 1 atom, 1 residue, 1 model selected > select up 18 atoms, 18 bonds, 1 residue, 1 model selected > ui tool show ""Altloc Explorer"" > altlocs change A /X:132 Changed /X HIS 132 to alternate location A > altlocs change B /X:132 Changed /X HIS 132 to alternate location B > altlocs change A /X:132 Changed /X HIS 132 to alternate location A > altlocs change B /X:132 Changed /X HIS 132 to alternate location B > altlocs change A /X:132 Changed /X HIS 132 to alternate location A > altlocs change B /X:132 Changed /X HIS 132 to alternate location B > altlocs change A /X:132 Changed /X HIS 132 to alternate location A > altlocs change B /X:132 Changed /X HIS 132 to alternate location B OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,1 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 10 L2 Cache: 20 MB Memory: 32 GB Software: System Software Overview: System Version: macOS 12.5.1 (21G83) Kernel Version: Darwin 21.6.0 Time since boot: 6 days 3:11 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 Displays: HP Z27k G3: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 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: 0.19.0.dev0 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: 1.4 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 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 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: 21.0 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 Core limitation Elaine Meng all ChimeraX