Opened 3 years ago

Last modified 3 years ago

#8206 feedback defect

hbonds: acc_phi_psi() takes 8 positional arguments but 10 were given

Reported by: leofrancalima@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Structure Analysis Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-5.15.0-53-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open Non-Modified-From-Leo-To-Ewe-post6TAchiralityFIxing-FINALnoH.pdb.pdb

Chain information for Non-Modified-From-Leo-To-Ewe-post6TAchiralityFIxing-
FINALnoH.pdb.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
A | No description available  
C | No description available  
D | No description available  
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l | No description available  
n | No description available  
  

> hide

> ribbon

> set bgColor white

> open /srv/home/leonardo/Downloads/M6A-from-Leo-to-Ewe-
> After6TAchiralityFixing-FINAL-new.pdb

Chain information for M6A-from-Leo-to-Ewe-After6TAchiralityFixing-FINAL-
new.pdb #2  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
A | No description available  
C | No description available  
D | No description available  
E | No description available  
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n | No description available  
  

> hide

> ribbon

> open /srv/home/leonardo/Downloads/M6A-P-FromLeo-for-Ewe-
> After6TAChiralityFixingFINAL.pdb

Chain information for M6A-P-FromLeo-for-Ewe-After6TAChiralityFixingFINAL.pdb
#3  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
A | No description available  
C | No description available  
D | No description available  
E | No description available  
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n | No description available  
  

> hide

> ribbon

> color #1 #e01b24 transparency 0

> color #2 #33d17a transparency 0

> color #3 #1c71d8 transparency 0

> hide #!2 models

> hide #!1 models

> close

> open /srv/home/leonardo/Documents/RNA-initialization-modification-
> steps/From_Ewe_To_Leo/No-modification/Post-Phenix/After-Correction-
> QuadrisulfideBond-in-Chain-e/After-coot-R55-chiAngles-updating/with-all-the-
> nucle-modifications/ConsideringExplicitly-withAMBERmoderna08/After-
> discovering-13PwasWrongAndFixing-25-11-2022/newAproach-considerin-13P-a-
> ligand/First-Part-treatment-13Paminoacyl-pose-aII/after-we-discovery-
> theChirality-errorOn6TA-usingPoseII/Non-Modified-From-Leo-To-Ewe-
> post6TAchiralityFIxing-FINALnoH.pdb.pdb

Chain information for Non-Modified-From-Leo-To-Ewe-post6TAchiralityFIxing-
FINALnoH.pdb.pdb #1  
---  
Chain | Description  
1 | No description available  
2 | No description available  
3 | No description available  
A | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
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L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
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e | No description available  
f | No description available  
g | No description available  
i | No description available  
j | No description available  
k | No description available  
l | No description available  
n | No description available  
  

> hide

> ribbon

> view #1/2:1244

No objects specified.  

> view #1/5

> isolde start

> set selectionWidth 4

> addh

Summary of feedback from adding hydrogens to Non-Modified-From-Leo-To-Ewe-
post6TAchiralityFIxing-FINALnoH.pdb.pdb #1  
---  
warnings | Not adding hydrogens to /1 A 2 P because it is missing heavy-atom
bond partners  
Not adding hydrogens to /2 A 1242 P because it is missing heavy-atom bond
partners  
Not adding hydrogens to /3 A 47 P because it is missing heavy-atom bond
partners  
Unknown hybridization for atom (O) of residue type 13P; not adding hydrogens
to it  
/2 A 1242 O4' has bad number of bonds (4)  
notes | No usable SEQRES records for Non-Modified-From-Leo-To-Ewe-
post6TAchiralityFIxing-FINALnoH.pdb.pdb (#1) chain 1; guessing termini instead  
No usable SEQRES records for Non-Modified-From-Leo-To-Ewe-
post6TAchiralityFIxing-FINALnoH.pdb.pdb (#1) chain 2; guessing termini instead  
No usable SEQRES records for Non-Modified-From-Leo-To-Ewe-
post6TAchiralityFIxing-FINALnoH.pdb.pdb (#1) chain 3; guessing termini instead  
No usable SEQRES records for Non-Modified-From-Leo-To-Ewe-
post6TAchiralityFIxing-FINALnoH.pdb.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for Non-Modified-From-Leo-To-Ewe-
post6TAchiralityFIxing-FINALnoH.pdb.pdb (#1) chain C; guessing termini instead  
35 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A CYS 6, /C GLY 3, /D LYS
19, /E GLY 30, /F MET 1, /G MET 1, /H THR 29, /I MET 1, /J SER 5, /K GLY 2, /L
MET 1, /M MET 1, /N MET 1, /O GLY 9, /P GLY 2, /Q SER 16, /R VAL 4, /S PRO 6,
/T MET 1, /U PRO 6, /V VAL 4, /W ALA 16, /X MET 1, /Y VAL 2, /Z MET 1, /a ASP
3, /b THR 2, /c MET 1, /d ARG 5, /e GLN 4, /f LYS 82, /g THR 2, /i VAL 76, /j
GLY 8, /k LYS 4, /l MET 1, /n ARG 41  
Chain-initial residues that are not actual N termini: /I THR 171, /I ARG 178,
/Z TYR 27  
Chain-final residues that are actual C termini: /C GLU 209, /G GLY 263, /H ARG
219, /I LEU 237, /J LEU 194, /K GLY 207, /L GLY 188, /M ARG 98, /N PHE 158, /O
LYS 132, /P ALA 151, /Q LEU 151, /S ARG 146, /V LYS 144, /W ALA 119, /Y PHE
130, /c HIS 84, /f LYS 152, /g ILE 314, /i SER 133, /j ILE 115, /k ASP 598, /l
LYS 25  
Chain-final residues that are not actual C termini: /A VAL 271, /D GLY 233, /E
THR 255, /F LYS 227, /I PRO 169, /I ILE 176, /R PRO 143, /T MET 126, /U LYS
150, /X PHE 83, /Z ARG 142, /Z LYS 25, /a GLY 128, /b ARG 100, /d LEU 68, /e
ASP 56, /n GLY 115  
donor: /2 A 1242 O2' acceptor: /2 A 1242 N3  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/cmd_line/tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 62, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/addh/cmd.py", line 169, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/addh/hbond.py", line 249, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 10 were given  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/hbonds/hbond.py", line 603, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 470.141.03
OpenGL renderer: Quadro K4200/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Dell Inc.
Model: Precision Tower 5810
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 12 Intel(R) Xeon(R) CPU E5-1650 v3 @ 3.50GHz
Cache Size: 15360 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            31Gi       8.6Gi       5.6Gi       209Mi        17Gi        21Gi
	Swap:          2.0Gi       1.0Mi       2.0Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation GK104GL [Quadro K4200] [10de:11b4] (rev a1)	
	Subsystem: NVIDIA Corporation GK104GL [Quadro K4200] [10de:1096]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-Clipper: 0.18.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.4
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → hbonds: acc_phi_psi() takes 8 positional arguments but 10 were given

comment:2 by Eric Pettersen, 3 years ago

Status: accepted → feedback

Hi Leonardo,

Without access to your PDB file, all I can say fro certain is that there is something problematic with residue 1242 in chain 2 -- probably missing atoms and/or bonds.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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