id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 9710 Possible MD template error arotsch@… Tristan Croll "{{{ The following bug report has been submitted: Platform: macOS-10.15.7-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Failed to add atoms ['H23'] to atom N2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_MGT). Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/arotsch/Documents/combination_lastframe_7qtl_7kl3-coot-3_2.pdb Summary of feedback from opening /Users/arotsch/Documents/combination_lastframe_7qtl_7kl3-coot-3_2.pdb --- warnings | Cannot find LINK/SSBOND residue RQA (101 ) PDB SEQRES record for chain G is incomplete. Ignoring input sequence records as basis for sequence. Chain information for combination_lastframe_7qtl_7kl3-coot-3_2.pdb #1 --- Chain | Description B | No description available C | No description available D | No description available E | No description available G | No description available R | No description available V | No description available X | No description available Y | No description available > open /Users/arotsch/Downloads/cryosparc_P202_J378_005_volume_map_sharp.mrc Opened cryosparc_P202_J378_005_volume_map_sharp.mrc as #2, grid size 448,448,448, pixel 1.05, shown at level 0.263, step 2, values float32 > volume #2 step 1 > volume #2 level 0.6363 > hide atoms > show cartoons > style stick Changed 18221 atom styles > show atoms > isolde start > set selectionWidth 4 > isolde set simFidelityMode Medium/Medium ISOLDE: setting sim fidelity mode to Medium/Medium nonbonded_cutoff_distance = 0.900000 use_gbsa = True gbsa_cutoff = 1.100000 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 191 residues in model #1 to IUPAC-IUB standards. Chain information for combination_lastframe_7qtl_7kl3-coot-3_2.pdb --- Chain | Description 1.2/B | No description available 1.2/C | No description available 1.2/D | No description available 1.2/E | No description available 1.2/G | No description available 1.2/R | No description available 1.2/V | No description available 1.2/X | No description available 1.2/Y | No description available > clipper associate #2 toModel #1 Opened cryosparc_P202_J378_005_volume_map_sharp.mrc as #1.1.1.1, grid size 448,448,448, pixel 1.05, shown at step 1, values float32 > isolde sim start /B,R-Y,G,D-E,C Loading residue template for MGT from internal database Sim termination reason: None ISOLDE: stopped sim > addh #1.2 Summary of feedback from adding hydrogens to combination_lastframe_7qtl_7kl3-coot-3_2.pdb #1.2 --- warnings | Not adding hydrogens to /B A 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /R C 6 P because it is missing heavy-atom bond partners Not adding hydrogens to /R U 13 P because it is missing heavy-atom bond partners Not adding hydrogens to /Y PRO 13 N because it is missing heavy-atom bond partners Not adding hydrogens to /Y PRO 13 CB because it is missing heavy-atom bond partners 1 messages similar to the above omitted Unknown hybridization for atom (PG) of residue type MGT; not adding hydrogens to it The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: /Y PRO 13 N notes | Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain B determined from SEQRES records No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain C; guessing termini instead No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain D; guessing termini instead No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain E; guessing termini instead No usable SEQRES records for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain G; guessing termini instead Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain R determined from SEQRES records Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain V determined from SEQRES records Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain X determined from SEQRES records Termini for combination_lastframe_7qtl_7kl3-coot-3_2.pdb (#1.2) chain Y determined from SEQRES records Chain-initial residues that are actual N termini: /C MET 1, /D GLY 0, /E MET 1, /X TYR 1, /D GLY 0, /D LEU 72, /E MET 1, /E LYS 207, /E ASN 676, /C MET 1, /C GLU 492 Chain-initial residues that are not actual N termini: /C GLU 492, /D LEU 72, /E LYS 207, /E ASN 676, /Y PRO 13 Chain-final residues that are actual C termini: /C ARG 737, /D ARG 716, /E LYS 757, /D ILE 63, /D ARG 716, /E HIS 184, /E SER 673, /E LYS 757, /C MET 483, /C ARG 737 Chain-final residues that are not actual C termini: /C MET 483, /D ILE 63, /E HIS 184, /E SER 673, /X PRO 6, /Y TYR 22 Chain-initial residues that are not actual 5' termini: /R C 6 1559 hydrogen bonds Adding 'H' to /C GLU 492 Adding 'H' to /D LEU 72 Adding 'H' to /E LYS 207 Adding 'H' to /E ASN 676 /X PRO 6 is not terminus, removing H atom from 'C' /Y TYR 22 is not terminus, removing H atom from 'C' /B G 2 is not terminus, removing H atom from O3' /V G 15 is not terminus, removing H atom from O3' 17893 hydrogens added Fetching CCD PCA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/PCA/PCA.cif Fetching CCD HY3 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif Fetching CCD AYA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif Fetching CCD CSO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/CSO/CSO.cif Fetching CCD ORN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ORN/ORN.cif Fetching CCD CSS from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/S/CSS/CSS.cif Deleted the following atoms from residue A V1: OP1 Residue U R13 has only 2 atoms in common with the template. At least 3 are needed to rebuild automatically. Adding of nucleic acid residues is not currently possible in ISOLDE. To move forward, just delete this residue. [Repeated 1 time(s)]Deleted the following atoms from residue MGT G1: H1G, H5'', H8, H1, H2G, H21, H5', H22 Failed to add atoms ['H23'] to atom N2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_MGT). If this template is built into ISOLDE, please report this using Help/Report a bug MD template PRO for residue PRO Y13 contains extra atoms that are not in a coordinate template, and are not directly connected to existing atoms. Since MD templates do not explicitly provide geometry,these atoms will not be built. > delete sel Fetching CCD N7P from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/N7P/N7P.cif Fetching CCD FME from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/FME/FME.cif MD template PRO for residue PRO Y13 contains extra atoms that are not in a coordinate template, and are not directly connected to existing atoms. Since MD templates do not explicitly provide geometry,these atoms will not be built. The atom CG in MD template PRO bonds to more than one existing atom in residue PRO. Since MD templates do not explicitly specify geometry, this type of atom addition is not currently supported. The resulting residue will contain only those atoms which the MD and coordinate templates have in common > delete sel Failed to add atoms ['H23'] to atom N2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_MGT). If this template is built into ISOLDE, please report this using Help/Report a bug > isolde sim start /G:1 Sim termination reason: None ISOLDE: stopped sim Failed to add atoms ['H23'] to atom N2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_MGT). If this template is built into ISOLDE, please report this using Help/Report a bug > ui mousemode right select > select /G:1@N2 1 atom, 1 residue, 1 model selected > select /G:1@N2 1 atom, 1 residue, 1 model selected > select /G:1@N2 1 atom, 1 residue, 1 model selected > select clear > select /G:1@N3 1 atom, 1 residue, 1 model selected > select /G:1@N3 1 atom, 1 residue, 1 model selected Failed to add atoms ['H23'] to atom N2 because this will lead to having 4 atoms attached, which is more than its assigned geometry can support. This is probably due to an error in the MD template (MC_MGT). If this template is built into ISOLDE, please report this using Help/Report a bug [Repeated 7 time(s)] OpenGL version: 4.1 ATI-3.10.23 OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: iMac Model Identifier: iMac19,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3,7 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Memory: 32 GB Boot ROM Version: 1731.140.1.0.0 SMC Version (system): 2.46f13 Software: System Software Overview: System Version: macOS 10.15.7 (19H2026) Kernel Version: Darwin 19.6.0 Time since boot: 4 days 21:57 Graphics/Displays: Radeon Pro 580X: Chipset Model: Radeon Pro 580X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D0008A-042 VBIOS Version: 113-D0008A1X-009 EFI Driver Version: 01.B1.042 Metal: Supported, feature set macOS GPUFamily2 v1 Displays: iMac: Display Type: Built-In Retina LCD Resolution: 5120 x 2880 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 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-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PhenixUI: 1.1.13 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 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sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect assigned normal Third Party all ChimeraX