AddCharge: Hydrogen not bonded to exactly one other atom

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-6.8.0-45-generic-x86_64-with-glibc2.39
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 /media/alrsong/x/workspace/BaiduSyncdisk/ZJU/MHC-I/UHRF1_dock.pdb

Chain information for UHRF1_dock.pdb #1  
---  
Chain | Description  
A | No description available  
  

> ui tool show "Add Hydrogens"

> addh #!1

Summary of feedback from adding hydrogens to UHRF1_dock.pdb #1  
---  
warnings | Not adding hydrogens to /A LYS 500 CD because it is missing heavy-atom bond partners  
Not adding hydrogens to /A LYS 568 CG because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 570 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A PHE 573 CB because it is missing heavy-atom bond
partners  
Not adding hydrogens to /A LYS 595 CD because it is missing heavy-atom bond
partners  
2 messages similar to the above omitted  
Skipped 10 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for UHRF1_dock.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A PRO 414  
Chain-initial residues that are not actual N termini: /A CYS 497  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A HIS 619, /A GLY 483  
Skipping possible acceptor with bad geometry: /A GLU 613 OE2  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 OE2  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
5 messages similar to the above omitted  
162 hydrogen bonds  
Adding 'H' to /A CYS 497  
/A HIS 619 is not terminus, removing H atom from 'C'  
1082 hydrogens added  
  

> ui tool show ViewDockX

No suitable models found for ViewDockX  

> toolshed show

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/A LYS 500: phi -122.1, psi 155.2 trans  
/A LYS 568: phi -81.1, psi 123.3 trans  
/A LYS 570: phi -70.5, psi -30.8 trans  
/A PHE 573: phi -85.6, psi -167.4 trans  
/A LYS 595: phi -64.6, psi -40.5 trans  
/A LYS 599: phi -61.0, psi -44.5 trans  
/A LYS 600: phi -72.2, psi -35.3 trans  
/A GLU 613: phi -66.0, psi -32.7 trans  
/A HIS 619: phi -153.5, psi none trans  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
[Repeated 33 time(s)]

Skipped 34 atom(s) with bad connectivities; see log for details  

Applying LYS rotamer (chi angles: -58.7 -67.4 -174.2 -67.0) to /A LYS 500  
Applying LYS rotamer (chi angles: -173.7 178.4 -68.9 -68.5) to /A LYS 568  
Applying LYS rotamer (chi angles: -69.7 -179.1 -177.9 -64.9) to /A LYS 570  
Applying PHE rotamer (chi angles: -66.8 118.2) to /A PHE 573  
Applying LYS rotamer (chi angles: -68.3 -171.6 -72.2 -66.9) to /A LYS 595  
Applying LYS rotamer (chi angles: -68.3 -171.6 -72.2 -66.9) to /A LYS 599  
Applying LYS rotamer (chi angles: -177.4 77.6 -89.8 -82.1) to /A LYS 600  
Applying GLU rotamer (chi angles: -65.3 82.2 1.8) to /A GLU 613  
Applying HIS rotamer (chi angles: 65.4 -79.5) to /A HIS 619  
Summary of feedback from adding hydrogens to UHRF1_dock.pdb #1  
---  
warnings | Not adding hydrogens to /A GLU 613 CA because it is missing heavy-atom bond partners  
Skipped 7 atom(s) with bad connectivities; see log for details  
notes | No usable SEQRES records for UHRF1_dock.pdb (#1) chain A; guessing termini instead  
Chain-initial residues that are actual N termini: /A PRO 414  
Chain-initial residues that are not actual N termini: /A CYS 497  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A HIS 619, /A GLY 483  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
Skipping possible acceptor with bad geometry: /A GLU 613 O  
Wrong number of grandchild atoms for phi/psi acceptor /A GLU 613 O  
  
2 messages similar to the above omitted  
170 hydrogen bonds  
/A HIS 619 is not terminus, removing H atom from 'C'  
82 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 120, in add_charges  
self._finish_add_charge(residues)  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/tool.py", line 146, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 107, in add_standard_charges  
raise ChargeError("Hydrogen %s not bonded to exactly one other atom" % a)  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 613 H not bonded to
exactly one other atom  
  
chimerax.add_charge.charge.ChargeError: Hydrogen /A GLU 613 H not bonded to
exactly one other atom  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/add_charge/charge.py", line 107, in add_standard_charges  
raise ChargeError("Hydrogen %s not bonded to exactly one other atom" % a)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 535.183.01
OpenGL renderer: NVIDIA GeForce RTX 4090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: ASUS
Model: System Product Name
OS: Ubuntu 24.04 Noble Numbat
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 13th Gen Intel(R) Core(TM) i9-13900K
Cache Size: 36864 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           125Gi        10Gi       3.7Gi       458Mi       113Gi       115Gi
	Swap:          186Gi       1.5Mi       186Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation AD102 [GeForce RTX 4090] [10de:2684] (rev a1)	
	Subsystem: ASUSTeK Computer Inc. AD102 [GeForce RTX 4090] [1043:889c]	
	Kernel driver in use: nvidia

Installed Packages:
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    build: 1.2.1
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    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
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    ChimeraX-Crystal: 1.0
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    ChimeraX-ESMFold: 1.0
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    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
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    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
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    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
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    ChimeraX-STL: 1.0.1
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    ChimeraX-Struts: 1.0.1
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    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
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    ChimeraX-Topography: 1.0
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    ChimeraX-Tug: 1.0.1
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    ChimeraX-WavefrontOBJ: 1.0
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[Eric Pettersen]

Either mangled CONECT records or badly incomplete structure