id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6626 Backrub requires N- and C-terminal flanking residues to be present chimerax-bug-report@… Tristan Croll "{{{ 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 C:/Users/DELL/Desktop/0414-NEW- > ABPairsComb_real_space_refined_004-coot-0.pdb > C:/Users/DELL/Desktop/cryosparc_P1_J198_004_volume_map_sharp.mrc Summary of feedback from opening C:/Users/DELL/Desktop/0414-NEW- ABPairsComb_real_space_refined_004-coot-0.pdb --- warning | Ignored bad PDB record found on line 62857 END Chain information for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb #1 --- Chain | Description A | No description available B C | No description available D E F | No description available H | No description available I | No description available J K | No description available M | No description available N | No description available O | No description available Opened cryosparc_P1_J198_004_volume_map_sharp.mrc as #2, grid size 448,448,448, pixel 1.11, shown at level 0.246, step 2, values float32 > clipper associate #2 toModel #1 Opened cryosparc_P1_J198_004_volume_map_sharp.mrc as #1.1.1.1, grid size 448,448,448, pixel 1.11, shown at level 0.934, step 1, values float32 Chain information for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb --- Chain | Description 1.2/A | No description available 1.2/B 1.2/C | No description available 1.2/D 1.2/E 1.2/F | No description available 1.2/H | No description available 1.2/I | No description available 1.2/J 1.2/K | No description available 1.2/M | No description available 1.2/N | No description available 1.2/O | No description available > isolde start > set selectionWidth 4 Done loading forcefield > addh Summary of feedback from adding hydrogens to 0414-NEW- ABPairsComb_real_space_refined_004-coot-0.pdb #1.2 --- notes | Termini for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb (#1.2) chain A determined from SEQRES records Termini for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb (#1.2) chain B determined from SEQRES records Termini for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb (#1.2) chain C determined from SEQRES records Termini for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb (#1.2) chain D determined from SEQRES records Termini for 0414-NEW-ABPairsComb_real_space_refined_004-coot-0.pdb (#1.2) chain E determined from SEQRES records 8 messages similar to the above omitted Chain-initial residues that are actual N termini: /A THR 17, /B THR 17, /C THR 17, /D TYR 39, /E TYR 39, /F TYR 39, /H LYS 4, /I GLN 71, /J GLN 66, /K GLN 66, /M ALA 71, /N GLY 67, /O GLY 64 Chain-initial residues that are not actual N termini: /H ALA 149 Chain-final residues that are actual C termini: /H ILE 211, /M ARG 115 Chain-final residues that are not actual C termini: /A LEU 615, /B LEU 615, /C LEU 615, /D PRO 505, /E PRO 505, /F PRO 505, /H ILE 52, /I PHE 225, /J PHE 225, /K PHE 225, /N ARG 115, /O ARG 115 3564 hydrogen bonds /A LEU 615 is not terminus, removing H atom from 'C' /B LEU 615 is not terminus, removing H atom from 'C' /C LEU 615 is not terminus, removing H atom from 'C' /D PRO 505 is not terminus, removing H atom from 'C' /E PRO 505 is not terminus, removing H atom from 'C' 6 messages similar to the above omitted 0 hydrogens added > select #1 62010 atoms, 62573 bonds, 1 pseudobond, 3932 residues, 13 models selected Loading residue template for ADP from internal database ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim > select clear ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: paused sim ISOLDE: resumed sim Unable to flip peptide bond after 50 rounds. Giving up. Unable to flip peptide bond after 50 rounds. Giving up. Unable to flip peptide bond after 50 rounds. Giving up. Unable to flip peptide bond after 50 rounds. Giving up. ISOLDE: paused sim ISOLDE: resumed sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim > select clear ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim ISOLDE: started sim ISOLDE: stopped sim Traceback (most recent call last): File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\isolde.py"", line 2148, in _backrub_rotamer self._apply_backrub(None, None) File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\isolde.py"", line 2158, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\refine\backrub_rotamer.py"", line 410, in apply_backrub b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight) File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\refine\backrub_rotamer.py"", line 81, in __init__ raise TypeError('Backrub requires N- and C-terminal flanking residues to be present!') TypeError: Backrub requires N- and C-terminal flanking residues to be present! TypeError: Backrub requires N- and C-terminal flanking residues to be present! File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\refine\backrub_rotamer.py"", line 81, in __init__ raise TypeError('Backrub requires N- and C-terminal flanking residues to be present!') See log for complete Python traceback. > save C:/Users/DELL/Desktop/0415-NEW- > ABPairsComb_real_space_refined_004-coot-0.pdb relModel #1.2 Traceback (most recent call last): File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\isolde.py"", line 2148, in _backrub_rotamer self._apply_backrub(None, None) File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\isolde.py"", line 2158, in _apply_backrub apply_backrub(self, mdff_mgr, res) File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\refine\backrub_rotamer.py"", line 410, in apply_backrub b = Backrub(r, mdff_p, clash_weight=clash_weight, map_weight=map_weight) File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\refine\backrub_rotamer.py"", line 81, in __init__ raise TypeError('Backrub requires N- and C-terminal flanking residues to be present!') TypeError: Backrub requires N- and C-terminal flanking residues to be present! TypeError: Backrub requires N- and C-terminal flanking residues to be present! File ""C:\Users\DELL\AppData\Local\UCSF\ChimeraX\1.2\site- packages\chimerax\isolde\refine\backrub_rotamer.py"", line 81, in __init__ raise TypeError('Backrub requires N- and C-terminal flanking residues to be present!') See log for complete Python traceback. OpenGL version: 3.3.0 - Build 27.20.100.9664 OpenGL renderer: Intel(R) UHD Graphics 630 OpenGL vendor: Intel Manufacturer: Dell Inc. Model: XPS 8930 OS: Microsoft Windows 10 家庭中文版 (Build 19044) Memory: 68,513,140,736 MaxProcessMemory: 137,438,953,344 CPU: 12 Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz OSLanguage: zh-CN Locale: ('zh_CN', 'cp936') 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: 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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 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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 Third Party limitation all ChimeraX