Add Charges: Nonstandard name for heavy atom

[Elaine Meng]

The following bug report has been submitted:
Platform:        macOS-12.6.1-arm64-arm-64bit
ChimeraX Version: 1.6.dev202211100132 (2022-11-10 01:32:17 UTC)
Description
open 1ivs
delete /A,C

try to run Add Charge tool with defaults -- bad atom name (maybe the fault of the data)

Log:
> open /Users/meng/Desktop/startup.cxc

> alias reset view orient; view initial

> alias start tool show $1

> alias whereprefs info path user unversioned config

> alias captut open help:user/tutorials/binding-sites.html#cap-example

> alias previewts toolshed url https://cxtoolshed-
> preview.rbvi.ucsf.edu;toolshed reload available

> alias normalts toolshed url https://cxtoolshed.rbvi.ucsf.edu;toolshed reload
> available

> alias btut open
> https://www.cgl.ucsf.edu/home/meng/chimerax/vdocs/user/tutorials/binding-
> sites.html

> alias stut open https://www.rbvi.ucsf.edu/chimerax/data/conservation-
> coloring/conservation-coloring.html

> alias ltut open https://www.rbvi.ucsf.edu/chimerax/data/loop-modeling/loop-
> modeling.html; ui dockable false "Help Viewer"

executed startup.cxc  
UCSF ChimeraX version: 1.6.dev202211100132 (2022-11-10)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 4enl

4enl title:  
Crystal structure of holoenzyme refined At 1.9 angstroms resolution: trigonal-
bipyramidal geometry of the cation binding site [more info...]  
  
Chain information for 4enl #1  
---  
Chain | Description | UniProt  
A | ENOLASE | ENO1_YEAST  
  
Non-standard residues in 4enl #1  
---  
SO4 — sulfate ion  
ZN — zinc ion  
  
4enl mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> ui tool show "Add Charges"

> close

> open 4rna

Summary of feedback from opening 4rna fetched from pdb  
---  
notes | Fetching compressed mmCIF 4rna from
http://files.rcsb.org/download/4rna.cif  
Fetching CCD CSS from http://ligand-expo.rcsb.org/reports/C/CSS/CSS.cif  
  
4rna title:  
Crystal structure of PLpro from Middle East Respiratory Syndrome (MERS)
coronavirus [more info...]  
  
Chain information for 4rna #1  
---  
Chain | Description | UniProt  
A | papain-like protease | K4LC41_9BETC  
  
Non-standard residues in 4rna #1  
---  
PO4 — phosphate ion  
ZN — zinc ion  
  
4rna mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  

> open 1ivs

Summary of feedback from opening 1ivs fetched from pdb  
---  
notes | Fetching compressed mmCIF 1ivs from
http://files.rcsb.org/download/1ivs.cif  
Fetching CCD VAA from http://ligand-expo.rcsb.org/reports/V/VAA/VAA.cif  
  
1ivs title:  
Crystal structure of thermus thermophilus valyl-TRNA synthetase complexed with
TRNA(val) and valyl-adenylate analogue [more info...]  
  
Chain information for 1ivs #2  
---  
Chain | Description | UniProt  
A B | Valyl-tRNA synthetase | SYV_THETH  
C D | tRNA (Val) |  
  
Non-standard residues in 1ivs #2  
---  
VAA — N-[valinyl]-N'-[adenosyl]-diaminosufone  
  
1ivs mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> close

> open 1ivs

1ivs title:  
Crystal structure of thermus thermophilus valyl-TRNA synthetase complexed with
TRNA(val) and valyl-adenylate analogue [more info...]  
  
Chain information for 1ivs #1  
---  
Chain | Description | UniProt  
A B | Valyl-tRNA synthetase | SYV_THETH  
C D | tRNA (Val) |  
  
Non-standard residues in 1ivs #1  
---  
VAA — N-[valinyl]-N'-[adenosyl]-diaminosufone  
  
1ivs mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /A,B

> close

> open 1ivs

1ivs title:  
Crystal structure of thermus thermophilus valyl-TRNA synthetase complexed with
TRNA(val) and valyl-adenylate analogue [more info...]  
  
Chain information for 1ivs #1  
---  
Chain | Description | UniProt  
A B | Valyl-tRNA synthetase | SYV_THETH  
C D | tRNA (Val) |  
  
Non-standard residues in 1ivs #1  
---  
VAA — N-[valinyl]-N'-[adenosyl]-diaminosufone  
  
1ivs mmCIF Assemblies  
---  
1| author_defined_assembly  
2| author_defined_assembly  
  

> delete /A

> delete /C

> ui tool show "Add Charges"

> addh #!1

Summary of feedback from adding hydrogens to 1ivs #1  
---  
notes | Termini for 1ivs (#1) chain D determined from SEQRES records  
Termini for 1ivs (#1) chain B determined from SEQRES records  
Chain-initial residues that are actual N termini: /B MET 1  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /B GLY 862  
Chain-final residues that are not actual C termini:  
1081 hydrogen bonds  
7965 hydrogens added  
  
Closest equivalent command: addcharge & sel standardizeResidues
5BU,CSL,MSE,UMS  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 117, in add_standard_charges  
a.charge, a.gaff_type = heavy_charge_type_data[(a.residue.amber_name,
a.name.lower())]  
KeyError: ('RG', 'op3')  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/addh/tool.py", line 198, in add_h  
cb()  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 109, in <lambda>  
'callback': lambda f=self._finish_add_charge, r=residues: f(r)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/tool.py", line 142, in _finish_add_charge  
non_std = add_standard_charges(self.session, residues=residues, **params)  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 119, in add_standard_charges  
raise ChargeError("Nonstandard name for heavy atom %s" % a)  
chimerax.add_charge.charge.ChargeError: Nonstandard name for heavy atom /D G
901 OP3  
  
chimerax.add_charge.charge.ChargeError: Nonstandard name for heavy atom /D G
901 OP3  
  
File
"/Users/meng/Desktop/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/add_charge/charge.py", line 119, in add_standard_charges  
raise ChargeError("Nonstandard name for heavy atom %s" % a)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Pro
OpenGL vendor: Apple

Python: 3.9.11
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,1
      Chip: Apple M1 Pro
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 16 GB
      System Firmware Version: 8419.41.10
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.1 (21G217)
      Kernel Version: Darwin 21.6.0
      Time since boot: 39 minutes

Graphics/Displays:

    Apple M1 Pro:

      Chipset Model: Apple M1 Pro
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 16
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


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    appdirs: 1.4.4
    appnope: 0.1.3
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    certifi: 2021.10.8
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    ChimeraX-AddCharge: 1.5
    ChimeraX-AddH: 2.2.1
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    ChimeraX-AlignmentHdrs: 3.3
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    ChimeraX-Crystal: 1.0
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[pett]

Okay, I understand it. Chain D has a (non-standard) 5' terminal phosphate. Add charge is therefore trying to charge it as a non-terminal nucleic acid, but that doesn't work because of the third oxygen (OP3) on the phosphate, which it doesn't know the type/charge for. Need to discuss what to do about it.

[pett]

Tomorrow's daily build will handle phosphorylated 5' termini.