Opened 4 years ago

Closed 3 years ago

#6626 closed defect (limitation)

Backrub requires N- and C-terminal flanking residues to be present

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

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: 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-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-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
    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
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    jupyter-core: 4.7.1
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    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
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    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Backrub requires N- and C-terminal flanking residues to be present

comment:2 by Tristan Croll, 3 years ago

Resolution: → limitation
Status: assigned → closed

I've removed the auto-fit rotamer option (which used this code) from the GUI for the time being. Was never happy with its hit rate - will try to revisit and come up with something better.

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