Opened 13 months ago

Closed 13 months ago

Last modified 13 months ago

#15955 closed defect (not a bug)

H-bonds: acc_phi_psi() number of arguments

Reported by: heather.noriega@… 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:        Windows-10-10.0.19045
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:/Users/Haten/OneDrive/Desktop/GROMACS_PEG/TEST4.1.pdb

Summary of feedback from opening
C:/Users/Haten/OneDrive/Desktop/GROMACS_PEG/TEST4.1.pdb  
---  
warning | Ignored bad PDB record found on line 3  
  
TEST4.1.pdb title:  
HER2_pmab_1K [more info...]  
  
Chain information for TEST4.1.pdb #1  
---  
Chain | Description  
A B | No description available  
E | No description available  
F G | No description available  
  
Non-standard residues in TEST4.1.pdb #1  
---  
BMA — (BMA)  
FUC — (FUC)  
MAN — (MAN)  
NAG — (NAG)  
UNK — (UNK)  
UNL — (UNL)  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 14160 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> close session

> open C:/Users/Haten/OneDrive/Desktop/GROMACS_PEG/TEST4.pdb

TEST4.pdb title:  
Crystal structure of HER2 binding IGG1-FC (fcab STAB19) [more info...]  
  
Chain information for TEST4.pdb #1  
---  
Chain | Description | UniProt  
A B | FCAB STAB19 | IGHG1_HUMAN 225-446  
E | No description available |   
F G | No description available |   
  
Non-standard residues in TEST4.pdb #1  
---  
BMA — β-D-mannopyranose  
FUC — α-L-fucopyranose  
MAN — α-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
UNK — (UNK)  
UNL — (UNL)  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 14160 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> ui mousemode right select

> ui mousemode right "bond rotation"

> torsion /H:1@O1,C1,N1,N2 166.00

> ui mousemode right select

> ui mousemode right "bond rotation"

> torsion /C:7@C4 /H:1@N2 /H:1@N1 /H:1@C1 98.01

> ui mousemode right select

> ui mousemode right "bond rotation"

> torsion /H:1@O1,C1,N1,N2 154.00

> torsion /H:1@C2,O2,C1,O1 7.95

> torsion /H:1@O1,C1,N1,N2 154.00

> ui mousemode right select

> ui mousemode right "bond rotation"

> torsion /C:7@O6,C6,C5,C4 89.08

> select

14474 atoms, 14930 bonds, 1855 residues, 1 model selected  

> save C:/Users/Haten/OneDrive/Desktop/GROMACS_PEG/TEST4.2.pdb selectedOnly
> true

> close session

> open C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.2.pdb format pdb

Summary of feedback from opening
C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.2.pdb  
---  
warning | Ignored bad PDB record found on line 3  
  
TEST4.2.pdb title:  
HER2_pmab_1K [more info...]  
  
Chain information for TEST4.2.pdb #1  
---  
Chain | Description  
A B | No description available  
E | No description available  
F G | No description available  
  
Non-standard residues in TEST4.2.pdb #1  
---  
BMA — (BMA)  
FUC — (FUC)  
MAN — (MAN)  
NAG — (NAG)  
UNK — (UNK)  
UNL — (UNL)  
  

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 14160 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> ui mousemode right "translate selected models"

> select ligand

314 atoms, 326 bonds, 16 residues, 1 model selected  

> select

14474 atoms, 14930 bonds, 1855 residues, 1 model selected  

> addh H

No structures specified  

> addh

Summary of feedback from adding hydrogens to TEST4.2.pdb #1  
---  
warnings | C-terminal /A GLY 448 O does not look like carboxylate oxygen; cannot complete teminus  
Unknown hybridization for atoms (O, NZ, N) of residue type LYS; not adding
hydrogens to them  
notes | No usable SEQRES records for TEST4.2.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for TEST4.2.pdb (#1) chain B; guessing termini
instead  
No usable SEQRES records for TEST4.2.pdb (#1) chain E; guessing termini
instead  
No usable SEQRES records for TEST4.2.pdb (#1) chain F; guessing termini
instead  
No usable SEQRES records for TEST4.2.pdb (#1) chain G; guessing termini
instead  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1, /E THR
130, /F ASP 1, /G ASP 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A GLY 448, /B GLY 448, /F CYS
214, /G CYS 214  
Chain-final residues that are not actual C termini: /E ALA 644  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
donor: /A GLN 344 N acceptor: /A GLY 343 O  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.pdb format pdb

TEST4.pdb title:  
Crystal structure of HER2 binding IGG1-FC (fcab STAB19) [more info...]  
  
Chain information for TEST4.pdb #1  
---  
Chain | Description | UniProt  
A B | FCAB STAB19 | IGHG1_HUMAN 225-446  
E | No description available |   
F G | No description available |   
  
Non-standard residues in TEST4.pdb #1  
---  
BMA — β-D-mannopyranose  
FUC — α-L-fucopyranose  
MAN — α-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
UNK — (UNK)  
UNL — (UNL)  
  

> close session

> open C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.2.pdb format pdb

Summary of feedback from opening
C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.2.pdb  
---  
warning | Ignored bad PDB record found on line 3  
  
TEST4.2.pdb title:  
HER2_pmab_1K [more info...]  
  
Chain information for TEST4.2.pdb #1  
---  
Chain | Description  
A B | No description available  
E | No description available  
F G | No description available  
  
Non-standard residues in TEST4.2.pdb #1  
---  
BMA — (BMA)  
FUC — (FUC)  
MAN — (MAN)  
NAG — (NAG)  
UNK — (UNK)  
UNL — (UNL)  
  

> close session

> open C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.2.pdb format pdb

Summary of feedback from opening
C:\Users\Haten\OneDrive\Desktop\GROMACS_PEG\TEST4.2.pdb  
---  
warning | Ignored bad PDB record found on line 3  
  
TEST4.2.pdb title:  
HER2_pmab_1K [more info...]  
  
Chain information for TEST4.2.pdb #1  
---  
Chain | Description  
A B | No description available  
E | No description available  
F G | No description available  
  
Non-standard residues in TEST4.2.pdb #1  
---  
BMA — β-D-mannopyranose  
FUC — α-L-fucopyranose  
MAN — α-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
UNK — (UNK)  
UNL — (UNL)  
  

> log metadata #1

Metadata for TEST4.2.pdb #1  
---  
Title | HER2_pmab_1K  
Non-standard residues | BMA — β-D-mannopyranose  
FUC — α-L-fucopyranose  
MAN — α-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose  
UNK — (UNK)  
UNL — (UNL)  
  
> select

14474 atoms, 14930 bonds, 1855 residues, 1 model selected  

> addh

Summary of feedback from adding hydrogens to TEST4.2.pdb #1  
---  
warnings | C-terminal /A GLY 448 O does not look like carboxylate oxygen; cannot complete teminus  
Unknown hybridization for atoms (O, NZ, N) of residue type LYS; not adding
hydrogens to them  
notes | Termini for TEST4.2.pdb (#1) chain A determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain B determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain E determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain F determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain G determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1, /F ASP
1, /G ASP 1  
Chain-initial residues that are not actual N termini: /E THR 130  
Chain-final residues that are actual C termini: /A GLY 448, /B GLY 448, /E ALA
644, /F CYS 214, /G CYS 214  
Chain-final residues that are not actual C termini:  
Missing OXT added to C-terminal residue /E ALA 644  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
donor: /A GLN 344 N acceptor: /A GLY 343 O  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> select clear

> preset cartoons/nucleotides ribbons/slabs

Using preset: Cartoons/Nucleotides / Ribbons/Slabs  
Changed 24250 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    ~worm
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> select

24841 atoms, 25297 bonds, 1855 residues, 1 model selected  

> save C:/Users/Haten/OneDrive/Desktop/GROMACS_PEG/TEST4.3.pdb selectedOnly
> true

> delete H

> save C:/Users/Haten/OneDrive/Desktop/GROMACS_PEG/TEST4.3.pdb selectedOnly
> true

> addh

Summary of feedback from adding hydrogens to TEST4.2.pdb #1  
---  
warnings | C-terminal /A GLY 448 O does not look like carboxylate oxygen; cannot complete teminus  
Unknown hybridization for atoms (O, NZ, N) of residue type LYS; not adding
hydrogens to them  
notes | Termini for TEST4.2.pdb (#1) chain A determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain B determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain E determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain F determined from SEQRES records  
Termini for TEST4.2.pdb (#1) chain G determined from SEQRES records  
Chain-initial residues that are actual N termini: /A GLU 1, /B GLU 1, /F ASP
1, /G ASP 1  
Chain-initial residues that are not actual N termini: /E THR 130  
Chain-final residues that are actual C termini: /A GLY 448, /B GLY 448, /E ALA
644, /F CYS 214, /G CYS 214  
Chain-final residues that are not actual C termini:  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
Skipping possible acceptor with bad geometry: /B PHE 172 O  
Wrong number of grandchild atoms for phi/psi acceptor /B PHE 172 O  
  
donor: /A GLN 344 N acceptor: /A GLY 343 O  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\cmd_line\tool.py", line 319, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\core\commands\cli.py", line 3213, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 77, in cmd_addh  
add_h_func(session, structures, template=template, in_isolation=in_isolation,
**prot_schemes)  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\cmd.py", line 184, in hbond_add_hydrogens  
add_hydrogens(session, atoms, type_info_for_atom, naming_schemas,
hydrogen_totals,  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\addh\hbond.py", line 259, in add_hydrogens  
hbonds = find_hbonds(session, s_list, dist_slop=rec_dist_slop,
angle_slop=rec_angle_slop)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
TypeError: acc_phi_psi() takes 8 positional arguments but 9 were given  
  
File "C:\Program Files\ChimeraX 1.8\bin\Lib\site-
packages\chimerax\hbonds\hbond.py", line 614, in find_hbonds  
if not geom_func(donor_atom, donor_hyds, *args):  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 497.17
OpenGL renderer: NVIDIA GeForce RTX 3060 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.cp1252
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: windows

Manufacturer: Micro-Star International Co., Ltd.
Model: GE76 Raider 11UE
OS: Microsoft Windows 10 Home (Build 19045)
Memory: 34,046,738,432
MaxProcessMemory: 137,438,953,344
CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    biopython: 1.83
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-crai: 0.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PhenixUI: 1.3.2
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-QScore: 1.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StarMap: 1.2.15
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-XMAS: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    comtypes: 1.4.1
    contourpy: 1.2.1
    cripser: 0.0.13
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    et-xmlfile: 1.1.0
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    fsspec: 2024.6.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    intel-openmp: 2021.4.0
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    mkl: 2021.4.0
    MolecularDynamicsViewer: 1.4
    mpmath: 1.3.0
    mrcfile: 1.5.0
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openpyxl: 3.1.4
    openvr: 1.26.701
    packaging: 24.1
    pandas: 2.2.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
    prompt-toolkit: 3.0.47
    psutil: 5.9.8
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    pyqtgraph: 0.13.7
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pywin32: 306
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    QtRangeSlider: 0.1.5
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    seaborn: 0.13.2
    Send2Trash: 1.8.3
    SEQCROW: 1.8.12
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
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    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
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    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
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    widgetsnbextension: 4.0.11
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Change History (5)

comment:1 by Eric Pettersen, 13 months ago

Component: Unassigned → Structure Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → H-bonds: acc_phi_psi() number of arguments

comment:2 by Eric Pettersen, 13 months ago

Resolution: → not a bug
Status: accepted → closed

Hi Heather,

This problem typically occurs when the bond connectivity in your structure is bad. For PDB files, the most frequently cause of bad connectivity is out-of-date CONECT records in the file. I would recommend deleting all LINK and CONECT records in your TEST4.2.pdb file and trying again.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by heather.noriega@…, 13 months ago 

Ok, thank you. I have a question. When I bond the glycan to the protein or the glycan to the ligand, should I use the bond sel reasonable true? Not false, correct? Or does it matter? The protein to glycan I am positive it is a covalent bond between NAG and ASN299, but the glycan to ligand I am unsure where they bond I know it is covalently bonded

Thank you,

Heather Noriega
PhD-Pharmaceutical Science candidate
Howard University
College of Pharmacy
heather.noriega@bison.howard.edu<mailto:heather.noriega@bison.howard.edu>
520-203-1883

________________________________
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Sent: Tuesday, September 17, 2024 12:25 PM
To: Noriega, Heather <heather.noriega@bison.howard.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: [Possible SPAM]: Re: [ChimeraX] #15955: H-bonds: acc_phi_psi() number of arguments

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#15955: H-bonds: acc_phi_psi() number of arguments
-----------------------------------------+--------------------
          Reporter:  heather.noriega@…   |      Owner:  pett
              Type:  defect              |     Status:  closed
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:  not a bug           |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+--------------------
Changes (by pett):

 * resolution:   => not a bug
 * status:  accepted => closed

Comment:

 Hi Heather,
         This problem typically occurs when the bond connectivity in your
 structure is bad.  For PDB files, the most frequently cause of bad
 connectivity is out-of-date CONECT records in the file.  I would recommend
 deleting all LINK and CONECT records in your TEST4.2.pdb file and trying
 again.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab
--
Ticket URL: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15955%23comment%3A2&data=05%7C02%7Cheather.noriega%40bison.howard.edu%7C7e8377b5e1c54166f5f108dcd73558ef%7C02ac0c07b75f46bf9b133630ba94bb69%7C0%7C0%7C638621871373764050%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=etgj1igcEpgQpc2wCFJzt57xzkp0eMOyLkHnHLwt08w%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15955#comment:2>>
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comment:4 by Eric Pettersen, 13 months ago

If the atoms are in normal covalent-bonding distance then I would use "reasonable true" (or omit it, since that's the default). Otherwise I would select just the two atoms I know need to be bonded and use "reasonable false".

--Eric

comment:5 by heather.noriega@…, 13 months ago 

Ok, perfect. Thank you.

Thank you,

Heather Noriega
PhD-Pharmaceutical Science candidate
Howard University
College of Pharmacy
heather.noriega@bison.howard.edu<mailto:heather.noriega@bison.howard.edu>
520-203-1883

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Tuesday, September 17, 2024 12:37 PM
To: Noriega, Heather <heather.noriega@bison.howard.edu>; pett@cgl.ucsf.edu <pett@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #15955: H-bonds: acc_phi_psi() number of arguments

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#15955: H-bonds: acc_phi_psi() number of arguments
-----------------------------------------+--------------------
          Reporter:  heather.noriega@…   |      Owner:  pett
              Type:  defect              |     Status:  closed
          Priority:  normal              |  Milestone:
         Component:  Structure Analysis  |    Version:
        Resolution:  not a bug           |   Keywords:
        Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
           Project:  ChimeraX            |
-----------------------------------------+--------------------
Comment (by pett):

 If the atoms are in normal covalent-bonding distance then I would use
 "reasonable true" (or omit it, since that's the default).  Otherwise I
 would select just the two atoms I know need to be bonded and use
 "reasonable false".

 --Eric
--
Ticket URL: <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F15955%23comment%3A4&data=05%7C02%7Cheather.noriega%40bison.howard.edu%7C96e848d2fdca4ebbe8b008dcd7370766%7C02ac0c07b75f46bf9b133630ba94bb69%7C0%7C0%7C638621878579384385%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=khI1bZZDazlPkIJplJkLkqZJIAfQ3oCI1VDvUfpASSk%3D&reserved=0<https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/15955#comment:4>>
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