id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5669 ISOLDE: restrain torsions: Each residue selection must be from a single chain Eric Pettersen Tristan Croll "The following bug report has been submitted: Platform: Linux-3.10.0-1160.6.1.el7.x86_64-x86_64-with-glibc2.14 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 /data1/cryoem/cryoem_krios/002-02/Phenix_refine61 format dicom open /data1/cryoem/cryoem_krios/002-02/Phenix_refine61/spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb Chain information for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available F I | No description available G J | No description available show cartoons style stick Changed 32765 atom styles open /data1/cryoem/cryoem_krios/002-02/Phenix_refine52/spike_mab_002_02_composite_box.ccp4 Opened spike_mab_002_02_composite_box.ccp4 as #2, grid size 145,145,231, pixel 1.07, shown at level 17.8, step 1, values float32 volume #2 level 8.797 clipper associate #2 toModel #1 Opened spike_mab_002_02_composite_box.ccp4 as #1.1.1.1, grid size 145,145,231, pixel 1.07, shown at level 13.2, step 1, values float32 Chain information for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb --- Chain | Description 1.2/A | No description available 1.2/B | No description available 1.2/C | No description available 1.2/F 1.2/I | No description available 1.2/G 1.2/J | No description available addh Summary of feedback from adding hydrogens to spike2up1downRBD_compositemap_SOLDE_NAG-coot_real_space_refined_061.pdb #1.2 --- notes | No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb (#1.2) chain A; guessing termini instead No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb (#1.2) chain B; guessing termini instead No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb (#1.2) chain F; guessing termini instead No usable SEQRES records for spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb (#1.2) chain G; guessing termini instead 2 messages similar to the above omitted Chain-initial residues that are actual N termini: /A GLN 14, /B GLN 14, /C GLN 14, /F GLU 1, /G GLU 1, /I GLU 1, /J GLU 1 Chain-initial residues that are not actual N termini: /A THR 76, /A ASN 544, /A TRP 633, /A GLN 690, /A ALA 852, /B THR 76, /B TYR 451, /B ASN 487, /B VAL 503, /B THR 630, /B GLN 690, /B ALA 852, /C THR 76, /C PRO 631, /C GLN 690, /C CYS 743, /C ALA 852 Chain-final residues that are actual C termini: /F CYS 214, /G LYS 222, /I CYS 214, /J LYS 222 Chain-final residues that are not actual C termini: /A LYS 1149, /A VAL 70, /A ASN 542, /A ALA 623, /A GLN 675, /A LEU 828, /B LYS 1149, /B VAL 70, /B LEU 441, /B ALA 475, /B PHE 497, /B ALA 623, /B GLN 675, /B LEU 828, /C LYS 1149, /C VAL 70, /C ILE 624, /C GLN 675, /C TYR 741, /C LEU 828 2937 hydrogen bonds Adding 'H' to /A THR 76 Adding 'H' to /A ASN 544 Adding 'H' to /A TRP 633 Adding 'H' to /A GLN 690 Adding 'H' to /A ALA 852 11 messages similar to the above omitted /A LYS 1149 is not terminus, removing H atom from 'C' /B LYS 1149 is not terminus, removing H atom from 'C' /C LYS 1149 is not terminus, removing H atom from 'C' 32068 hydrogens added hide HC select #1 64833 atoms, 65631 bonds, 17 pseudobonds, 4163 residues, 8 models selected open /data1/cryoem/cryoem_krios/RBD_model1.pdb Summary of feedback from opening /data1/cryoem/cryoem_krios/RBD_model1.pdb --- note | Combining 2 symmetry atoms into HOH /Z:779 O Chain information for RBD_model1.pdb #2 --- Chain | Description Z | No description available select #2 1629 atoms, 1599 bonds, 274 residues, 1 model selected hide #2 models show #2 models hide #2 models show #2 models hide #2 models show #2 models hide #2 models show #2 models show target m ui tool show Matchmaker matchmaker #2 to #1.2/A pairing bs Parameters --- Chain pairing | bs 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 spike2up1downRBD_compositemap_SOLDE_NAG- coot_real_space_refined_061.pdb, chain A (#1.2) with RBD_model1.pdb, chain Z (#2), sequence alignment score = 939.5 RMSD between 169 pruned atom pairs is 1.139 angstroms; (across all 194 pairs: 1.473) isolde restrain torsions #1/A:334-527/B The ""isolde restrain torsions"" command only applies to protein chains. Other residues have been ignored. 334-527/c334-527 tempelate #2/Z Unknown command: 334-527/c334-527 tempelate #2/Z isolde restrain torsions #1/A:334-527/B The ""isolde restrain torsions"" command only applies to protein chains. Other residues have been ignored. 334-527/C:334-527 tempelate #2/Z Unknown command: 334-527/C:334-527 tempelate #2/Z isolde restrain torsions #1/A:334-527/B:334-527/C:334-527 tempelate #2/Z Expected a keyword isolde restrain torsions #1/A:334-527/B:334-527/C:334-527 templateResidues #2/Z Traceback (most recent call last): File ""/usr/libexec/UCSF-ChimeraX/lib/python3.8/site- packages/chimerax/cmd_line/tool.py"", line 280, in execute cmd.run(cmd_text) File ""/usr/libexec/UCSF-ChimeraX/lib/python3.8/site- packages/chimerax/core/commands/cli.py"", line 2852, in run result = ci.function(session, **kw_args) File ""/home/cryoem/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/restraints/cmd.py"", line 171, in restrain_torsions restrain_torsions_to_template(session, tres, pres, File ""/home/cryoem/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 159, in restrain_torsions_to_template trs, rrs = sequence_align_all_residues( File ""/home/cryoem/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 317, in sequence_align_all_residues raise TypeError('Each residue selection must be from a single chain!') TypeError: Each residue selection must be from a single chain! TypeError: Each residue selection must be from a single chain! File ""/home/cryoem/.local/share/ChimeraX/1.2/site- packages/chimerax/isolde/restraints/restraint_utils.py"", line 317, in sequence_align_all_residues raise TypeError('Each residue selection must be from a single chain!') See log for complete Python traceback. OpenGL version: 3.3.0 NVIDIA 450.80.02 OpenGL renderer: GeForce GTX 1080 Ti/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Manufacturer: Supermicro Model: SYS-7048GR-TR OS: CentOS Linux 7 Core Architecture: 64bit ELF Virutal Machine: none CPU: 24 Intel(R) Xeon(R) CPU E5-2620 v3 @ 2.40GHz Cache Size: 15360 KB Memory: total used free shared buff/cache available Mem: 125G 7.2G 5.3G 79M 113G 117G Swap: 15G 462M 15G Graphics: 02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1) Subsystem: ZOTAC International (MCO) Ltd. Device [19da:1470] 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: 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-Clipper: 0.16.0 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-ISOLDE: 1.2.2 ChimeraX-Label: 1.0 ChimeraX-LinuxSupport: 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-Phenix: 0.3 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 distro: 1.5.0 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 pexpect: 4.8.0 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 ptyprocess: 0.7.0 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 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 Send2Trash: 1.8.0 SEQCROW: 1.2.2 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: 1.2.0" defect closed moderate Third Party fixed all ChimeraX