id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6776 Tolman cone angle not implemented for tridentate or more ligands nxb318@… Tony Schaefer "{{{ The following bug report has been submitted: Platform: Linux-5.4.0-107-generic-x86_64-with-glibc2.31 ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description (Describe the actions that caused this problem to occur here) Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > cd /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo Current working directory is: /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo > open *coot*.pdb No such file/path: *coot*.pdb > select #1:550-584, 630-665, 817-839 Nothing selected > select ~sel Nothing selected > delete sel > save > /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo/TMD- > pore/apo-TMD-porealt.pdb No structures to save > close > cd /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo Current working directory is: /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo > open *coot*.pdb Chain information for FINAL_apo- fromcls5-input_real_space_refined_022-coot-0.pdb #1 --- Chain | Description A B C D | No description available > select #1:550-584, 630-665, 817-839 2776 atoms, 2840 bonds, 4 pseudobonds, 360 residues, 2 models selected > select ~sel 21352 atoms, 21838 bonds, 4 pseudobonds, 2655 residues, 2 models selected > delete sel > save > /mnt/data0/Data_processing/FROM_EXX/Final_phenix_refinement/Holes/apo/TMD- > pore/apo-TMD-porealt.pdb > close [Repeated 2 time(s)] > tool show ""Side View"" > open 3w7f Summary of feedback from opening 3w7f fetched from pdb --- notes | Fetching compressed mmCIF 3w7f from http://files.rcsb.org/download/3w7f.cif Fetching CCD FPS from http://ligand-expo.rcsb.org/reports/F/FPS/FPS.cif Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif 3w7f title: Crystal structure of the C(30) carotenoid dehydrosqualene synthase from staphylococcus aureus complexed with farnesyl thiopyrophosphate [more info...] Chain information for 3w7f #1 --- Chain | Description | UniProt A B | Dehydrosqualene synthase | CRTM_STAAU Non-standard residues in 3w7f #1 --- FPS — S-[(2E,6E)-3,7,11-trimethyldodeca-2,6,10-trienyl] trihydrogen thiodiphosphate (farnesyl thiopyrophosphate) MG — magnesium ion 3w7f mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > delete /b > view ligand > label ligand > label height 1.0 > lighting soft > delete solvent > label @@display > view #1:21 > select /A:21@OG 1 atom, 1 residue, 1 model selected > select add /A:302@O1B 2 atoms, 2 residues, 1 model selected > distance /A:21@OG /A:302@O1B Distance between /A SER 21 OG and FPS 302 O1B: 2.405Å > distance :21@OG :302@O1B Distance already exists; modify distance properties with 'distance style' > distance :248@OH :302@O1B Distance between /A TYR 248 OH and FPS 302 O1B: 2.996Å > hbonds 312 hydrogen bonds found > hbonds hide Expected a keyword > hide hbonds > select :FPS 48 atoms, 46 bonds, 2 residues, 1 model selected > hbonds sel restrict cross reveal true log true Finding intermodel H-bonds Finding intramodel H-bonds Constraints relaxed by 0.4 angstroms and 20 degrees Models used: 1 3w7f 13 H-bonds H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist): /A SER 19 OG /A FPS 302 O2A no hydrogen 2.886 N/A /A SER 21 N /A FPS 302 O2B no hydrogen 3.185 N/A /A SER 21 OG /A FPS 302 O1B no hydrogen 2.405 N/A /A SER 21 OG /A FPS 302 O2B no hydrogen 3.332 N/A /A TYR 41 OH /A FPS 302 O2A no hydrogen 2.585 N/A /A ARG 45 NH1 /A FPS 301 O2B no hydrogen 3.428 N/A /A ARG 45 NH1 /A FPS 301 O3B no hydrogen 2.585 N/A /A ARG 45 NH2 /A FPS 301 O2B no hydrogen 3.175 N/A /A ARG 45 NH2 /A FPS 302 O1A no hydrogen 3.052 N/A /A ARG 171 NH1 /A FPS 302 O1B no hydrogen 2.685 N/A /A ARG 171 NH1 /A FPS 302 O3B no hydrogen 3.412 N/A /A ARG 171 NH2 /A FPS 302 O3B no hydrogen 3.129 N/A /A TYR 248 OH /A FPS 302 O1B no hydrogen 2.996 N/A 13 hydrogen bonds found > ~hbonds > ~distance > contacts sel restrict cross reveal true log true select true Allowed overlap: -0.4 H-bond overlap reduction: 0.4 Ignore contacts between atoms separated by 4 bonds or less Detect intra-residue contacts: False Detect intra-molecule contacts: True 86 contacts atom1 atom2 overlap distance /A FPS 301 C10 /A CYS 44 CB 0.472 3.288 /A FPS 302 O2A /A SER 19 CB 0.387 2.913 /A FPS 301 PB /A ARG 45 NH1 0.248 3.492 /A FPS 302 O2A /A SER 19 CA 0.242 3.058 /A FPS 302 O1B /A SER 21 CB 0.215 3.085 /A FPS 302 C14 /A ALA 157 CB 0.208 3.552 /A FPS 301 C7 /A CYS 44 CB 0.207 3.433 /A FPS 302 C14 /A ALA 157 CA 0.191 3.569 /A FPS 301 C6 /A ASP 48 CB 0.166 3.474 /A FPS 301 C15 /A TYR 41 CD2 0.158 3.482 /A FPS 301 O2A /A MG 303 MG 0.156 1.834 /A FPS 302 PB /A ARG 171 NH1 0.139 3.601 /A FPS 301 PA /A ASN 168 ND2 0.116 3.624 /A FPS 301 C14 /A LEU 141 CD1 0.106 3.654 /A FPS 302 O1A /A MG 304 MG 0.098 1.892 /A FPS 301 C8 /A CYS 44 CB 0.097 3.393 /A FPS 301 O2A /A ASN 168 OD1 0.097 2.743 /A FPS 301 O2A /A ASP 172 OD2 0.088 2.752 /A FPS 302 O1B /A SER 21 OG 0.075 2.405 /A FPS 301 O3B /A ARG 45 NH1 0.075 2.585 /A FPS 302 PB /A SER 21 OG 0.073 3.487 /A FPS 302 O3B /A MG 304 MG 0.039 1.951 /A FPS 301 C15 /A TYR 41 CE2 0.036 3.604 /A FPS 302 C4 /A GLN 165 OE1 -0.007 3.307 /A FPS 302 PA /A ARG 45 NH2 -0.011 3.751 /A FPS 301 C12 /A TYR 41 CD2 -0.015 3.535 /A FPS 302 PB /A SER 21 CB -0.023 4.003 /A FPS 302 O1B /A ARG 171 NH1 -0.025 2.685 /A FPS 302 C2 /A PHE 22 CE2 -0.038 3.558 /A FPS 301 C12 /A VAL 137 CG1 -0.048 3.688 /A FPS 301 O2B /A MG 304 MG -0.054 2.044 /A FPS 301 C2 /A ASP 48 CG -0.073 3.713 /A FPS 302 C10 /A GLY 161 CA -0.084 3.844 /A FPS 301 C11 /A TYR 41 CD2 -0.091 3.611 /A FPS 302 C5 /A ALA 134 CB -0.095 3.855 /A FPS 301 O1A /A MG 304 MG -0.097 2.087 /A FPS 301 O3B /A MG 305 MG -0.103 2.093 /A FPS 302 C5 /A LEU 164 CB -0.104 3.864 /A FPS 302 O2A /A TYR 41 OH -0.105 2.585 /A FPS 301 O3B /A ASP 48 OD2 -0.105 2.945 /A FPS 301 C13 /A TYR 41 CD2 -0.106 3.476 /A FPS 302 C15 /A LEU 145 CD1 -0.106 3.866 /A FPS 301 C11 /A TYR 41 CE2 -0.107 3.627 /A FPS 302 C12 /A LEU 160 CD2 -0.110 3.750 /A FPS 301 C9 /A ARG 45 NH2 -0.149 3.669 /A FPS 302 C11 /A LEU 164 CD1 -0.154 3.794 /A FPS 301 C5 /A ASP 48 CG -0.159 3.919 /A FPS 302 C1 /A PHE 22 CE2 -0.161 3.681 /A FPS 301 C9 /A TYR 41 CE2 -0.162 3.802 /A FPS 302 C1 /A TYR 248 OH -0.174 3.394 /A FPS 301 C9 /A ARG 45 CA -0.175 3.935 /A FPS 302 C4 /A ASN 168 CB -0.185 3.945 /A FPS 302 PB /A ARG 265 NH2 -0.191 3.931 /A FPS 302 C14 /A PHE 233 CZ -0.192 3.832 /A FPS 302 C4 /A ASN 168 ND2 -0.193 3.713 /A FPS 302 C15 /A LEU 141 CD1 -0.205 3.965 /A FPS 302 C4 /A GLN 165 CA -0.212 3.972 /A FPS 301 C15 /A MET 15 CE -0.215 3.975 /A FPS 302 PA /A SER 19 CB -0.217 4.197 /A FPS 302 O1B /A TYR 248 CE2 -0.227 3.407 /A FPS 302 C11 /A GLY 161 CA -0.230 3.870 /A FPS 302 C10 /A GLY 138 CA -0.231 3.991 /A FPS 302 PA /A SER 19 CA -0.232 4.212 /A FPS 302 C12 /A GLY 138 CA -0.237 3.877 /A FPS 302 PA /A SER 19 OG -0.239 3.799 /A FPS 301 C15 /A PHE 22 CD2 -0.249 3.889 /A FPS 301 C5 /A ASP 48 CB -0.250 4.010 /A FPS 301 PA /A ASN 168 OD1 -0.251 3.771 /A FPS 302 PA /A TYR 41 OH -0.259 3.819 /A FPS 302 C13 /A LEU 160 CD2 -0.264 3.754 /A FPS 302 C15 /A LEU 160 CD2 -0.279 4.039 /A FPS 301 C6 /A ASP 48 CG -0.284 3.924 /A FPS 301 C10 /A TYR 41 CD2 -0.296 3.936 /A FPS 301 C9 /A ARG 45 CZ -0.312 3.802 /A FPS 302 C10 /A LEU 141 CD1 -0.317 4.077 /A FPS 302 O2A /A TYR 41 CE2 -0.327 3.507 /A FPS 302 C7 /A ALA 134 CB -0.333 3.973 /A FPS 302 PB /A TYR 248 OH -0.356 3.916 /A FPS 302 C10 /A GLY 138 N -0.356 3.876 /A FPS 301 O2A /A ASN 168 CG -0.361 3.391 /A FPS 302 C7 /A GLY 161 CA -0.379 4.019 /A FPS 302 C14 /A PHE 233 CE1 -0.382 4.022 /A FPS 302 O2A /A HIS 18 O -0.390 3.230 /A FPS 302 C9 /A LEU 164 CD1 -0.390 4.150 /A FPS 302 O1A /A ARG 45 NH2 -0.392 3.052 /A FPS 302 C6 /A ALA 134 CB -0.396 4.036 86 contacts > ui tool show ""Cone Angle"" > select clear > select FPS Expected an objects specifier or a keyword > select FPS Expected an objects specifier or a keyword > select :FPS 48 atoms, 46 bonds, 2 residues, 1 model selected WARNING AaronTools.atoms.Atom._set_saturation Saturation not found for element: Mg Traceback (most recent call last): File ""/home/user/.local/share/ChimeraX/1.3/site- packages/SEQCROW/tools/cone_angle.py"", line 307, in calc_cone cone_angle = comp.cone_angle( File ""/home/user/.local/share/ChimeraX/1.3/site- packages/AaronTools/component.py"", line 494, in cone_angle raise NotImplementedError( NotImplementedError: Tolman cone angle not implemented for tridentate or more ligands NotImplementedError: Tolman cone angle not implemented for tridentate or more ligands File ""/home/user/.local/share/ChimeraX/1.3/site- packages/AaronTools/component.py"", line 494, in cone_angle raise NotImplementedError( See log for complete Python traceback. > select clear > select /A:FPS 48 atoms, 46 bonds, 2 residues, 1 model selected > select /A:301 24 atoms, 23 bonds, 1 residue, 1 model selected WARNING AaronTools.atoms.Atom._set_saturation Saturation not found for element: Mg Traceback (most recent call last): File ""/home/user/.local/share/ChimeraX/1.3/site- packages/SEQCROW/tools/cone_angle.py"", line 307, in calc_cone cone_angle = comp.cone_angle( File ""/home/user/.local/share/ChimeraX/1.3/site- packages/AaronTools/component.py"", line 494, in cone_angle raise NotImplementedError( NotImplementedError: Tolman cone angle not implemented for tridentate or more ligands NotImplementedError: Tolman cone angle not implemented for tridentate or more ligands File ""/home/user/.local/share/ChimeraX/1.3/site- packages/AaronTools/component.py"", line 494, in cone_angle raise NotImplementedError( See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 470.103.01 OpenGL renderer: NVIDIA T600/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: System manufacturer Model: System Product Name OS: Linux Mint 20.3 una Architecture: 64bit ELF Virutal Machine: none CPU: 20 Intel(R) Core(TM) i9-10900X CPU @ 3.70GHz Cache Size: 19712 KB Memory: total used free shared buff/cache available Mem: 31Gi 24Gi 5.2Gi 449Mi 1.3Gi 5.6Gi Swap: 8.0Gi 8.0Gi 47Mi Graphics: 65:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU117GL [T600] [10de:1fb1] (rev a1) Subsystem: NVIDIA Corporation Device [10de:1488] Kernel driver in use: nvidia Locale: ('en_US', 'UTF-8') 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: 2021.10.8 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 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: 2.2.2 ChimeraX-Clipper: 0.17.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 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: 1.0 ChimeraX-DistMonitor: 1.1.5 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: 1.1 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: 1.3 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1 ChimeraX-LinuxSupport: 1.0 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 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: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 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: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 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 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 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: 1.6.1 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: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 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: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 distro: 1.6.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 line-profiler: 3.3.0 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.3 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 Send2Trash: 1.8.0 SEQCROW: 1.3.2 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 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: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect assigned normal Third Party all ChimeraX