AddCharge: Ng+ charges

[Eric Pettersen]

The following bug report has been submitted:
Platform:        macOS-10.15.7-x86_64-i386-64bit
ChimeraX Version: 1.3.dev202105130135 (2021-05-13 01:35:20 UTC)
Description
coul surf #1.3

Log:
UCSF ChimeraX version: 1.3.dev202105130135 (2021-05-13)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Unable to load numpy_formathandler accelerator from OpenGL_accelerate  

> open 1a0m format mmcif fromDatabase pdb

1a0m title:  
1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...]  
  
Chain information for 1a0m #1  
---  
Chain | Description  
A B | α-conotoxin [TYR15]-epi  
  
Non-standard residues in 1a0m #1  
---  
NH2 — amino group  
  

> surface

> ui tool show "Side View"

> coulombic

The following heavy (non-hydrogen) atoms are missing, which may result in
inaccurate electrostatics:  
/A ARG 7 NH2  
/A ARG 7 CD  
/A ARG 7 CZ  
/A ARG 7 NH1  
/A ARG 7 NE  
/A ARG 7 CG  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for 1a0m_A SES surface #1.1: minimum, -9.82, mean -1.86,
maximum 8.57  
Coulombic values for 1a0m_B SES surface #1.2: minimum, -9.76, mean -0.71,
maximum 8.53  

> close

> open 6ztq format mmcif fromDatabase pdb

6ztq title:  
Cryo-EM structure of respiratory complex I from Mus musculus inhibited by
piericidin A at 3.0 A [more info...]  
  
Chain information for 6ztq #1  
---  
Chain | Description  
A | NADH-ubiquinone oxidoreductase chain 3  
B | NADH dehydrogenase [ubiquinone] iron-sulfur protein 7, mitochondrial  
C | NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial  
D | NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial  
E | NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial  
F | NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial  
G | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial  
H | NADH-ubiquinone oxidoreductase chain 1  
I | NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial  
J | NADH-ubiquinone oxidoreductase chain 6  
K | NADH-ubiquinone oxidoreductase chain 4L  
L | NADH-ubiquinone oxidoreductase chain 5  
M | NADH-ubiquinone oxidoreductase chain 4  
N | NADH-ubiquinone oxidoreductase chain 2  
O | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 10, mitochondrial  
P | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 9, mitochondrial  
Q | NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, mitochondrial  
R | NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial  
S | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 2  
T U | Acyl carrier protein, mitochondrial  
V | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 5  
W | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 6  
X | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 8  
Y | MCG5603  
Z | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 13  
a | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 1  
b | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 3  
c | NADH dehydrogenase [ubiquinone] 1 subunit C1, mitochondrial  
d | NADH dehydrogenase [ubiquinone] 1 subunit C2  
e | NADH dehydrogenase [ubiquinone] iron-sulfur protein 5  
f | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 1  
g | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 11, mitochondrial  
h | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 5, mitochondrial  
i | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 6  
j | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 2, mitochondrial  
k | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 3  
l | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 8, mitochondrial  
m | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 4  
n | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 9  
o | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 7  
p | NADH dehydrogenase [ubiquinone] 1 β subcomplex subunit 10  
q | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 12  
r | NADH dehydrogenase [ubiquinone] 1 α subcomplex subunit 7  
s | NADH dehydrogenase [ubiquinone] flavoprotein 3, mitochondrial  
  
Non-standard residues in 6ztq #1  
---  
3PE — 1,2-diacyl-Sn-glycero-3-phosphoethanolamine (3-Sn-
phosphatidylethanolamine)  
ATP — adenosine-5'-triphosphate  
CDL — cardiolipin (diphosphatidyl glycerol; bis-(1,2-diacyl-Sn-
glycero-3-phospho)-1',3'-Sn-glycerol)  
EHZ — ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-
butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate  
FES — FE2/S2 (inorganic) cluster  
FMN — flavin mononucleotide (riboflavin monophosphate)  
HQH — Piericidin A  
NDP — nadph dihydro-nicotinamide-adenine-dinucleotide phosphate  
PC1 — 1,2-diacyl-Sn-glycero-3-phosphocholine (3-Sn-phosphatidylcholine)  
SF4 — iron/sulfur cluster  
ZN — zinc ion  
  

> help surf

> surface enclose #1

> help coul

> coulombic surfaces #1.3

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/A GLU 115  
/B ARG 189  
/D ARG 430  
/H MET 318  
/I ARG 178  
/K CYS 98  
/M MET 459  
/O LYS 320  
/P TYR 342  
/Q LYS 133  
/U GLU 88  
/V ILE 115  
/W PRO 130  
/X VAL 171  
/Y VAL 142  
/Z THR 143  
/b LEU 83  
/d ARG 120  
/e PRO 105  
/f LYS 56  
/h ASN 143  
/m TYR 128  
/r LEU 112  

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue AYA (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpync1coim/ante.in.mol2 -fi
mol2 -o
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpync1coim/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(AYA) ``  
(AYA) `Welcome to antechamber 20.0: molecular input file processor.`  
(AYA) ``  
(AYA) `Info: Finished reading file
(/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpync1coim/ante.in.mol2);
atoms read (22), bonds read (21).`  
(AYA) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(AYA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(AYA) ``  
(AYA) ``  
(AYA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(AYA) `Info: Total number of electrons: 78; net charge: 0`  
(AYA) ``  
(AYA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(AYA) ``  
(AYA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(AYA) ``  
(AYA) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(AYA) ``  
Charges for residue AYA determined  
Assigning partial charges to residue AME (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmp7_wmsi6o/ante.in.mol2 -fi
mol2 -o
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmp7_wmsi6o/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(AME) ``  
(AME) `Welcome to antechamber 20.0: molecular input file processor.`  
(AME) ``  
(AME) `Info: Finished reading file
(/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmp7_wmsi6o/ante.in.mol2);
atoms read (29), bonds read (28).`  
(AME) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(AME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(AME) ``  
(AME) ``  
(AME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(AME) `Info: Total number of electrons: 110; net charge: 0`  
(AME) ``  
(AME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(AME) ``  
(AME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(AME) ``  
(AME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(AME) ``  
Charges for residue AME determined  
Assigning partial charges to residue FME (net charge +0) with am1-bcc method  
Running ANTECHAMBER command:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpai4fdumx/ante.in.mol2 -fi
mol2 -o
/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpai4fdumx/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n  
(FME) ``  
(FME) `Welcome to antechamber 20.0: molecular input file processor.`  
(FME) ``  
(FME) `Info: Finished reading file
(/var/folders/p6/r5049lvm8xj99q001s6g8l_00000gn/T/tmpai4fdumx/ante.in.mol2);
atoms read (26), bonds read (25).`  
(FME) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(FME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/bondtype -j
part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(FME) ``  
(FME) ``  
(FME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(FME) `Info: Total number of electrons: 102; net charge: 0`  
(FME) ``  
(FME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`  
(FME) ``  
(FME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(FME) ``  
(FME) `Running:
/Users/pett/src/chimerax/ChimeraX.app/Contents/bin/amber20/bin/atomtype -f ac
-p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(FME) ``  
Charges for residue FME determined  
Assigning partial charges to residue 2MR (net charge +0) with am1-bcc method  
Traceback (most recent call last):  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/cmd_line/tool.py", line 280, in execute  
cmd.run(cmd_text)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2854, in run  
result = ci.function(session, **kw_args)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/cmd.py", line 90, in cmd_coulombic  
assign_charges(session, needs_assignment, his_scheme, charge_method,  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/coulombic/coulombic.py", line 90, in assign_charges  
add_charges(session, charged_residues, method=charge_method, status=status,  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 26, in add_charges  
add_nonstandard_res_charges(session, res_list,
estimate_net_charge(res_list[0].atoms),  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 341, in
add_nonstandard_res_charges  
_nonstd_charge(session, tautomer_residues, net_charge, method, status)  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 545, in _nonstd_charge  
" for radical species using AM1-BCC method" % (r0.name, electrons,
total_net_charge))  
NameError: name 'r0' is not defined  
  
NameError: name 'r0' is not defined  
  
File
"/Users/pett/src/chimerax/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/add_charge/charge.py", line 545, in _nonstd_charge  
" for radical species using AM1-BCC method" % (r0.name, electrons,
total_net_charge))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-14.7.12
OpenGL renderer: Intel(R) Iris(TM) Pro Graphics 6200
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2.8 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 4 MB
      Memory: 16 GB
      Boot ROM Version: 426.0.0.0.0
      SMC Version (system): 2.32f21

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H524)
      Kernel Version: Darwin 19.6.0
      Time since boot: 8:44

Graphics/Displays:

    Intel Iris Pro Graphics 6200:

      Chipset Model: Intel Iris Pro Graphics 6200
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1622
      Revision ID: 0x000a
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AltlocExplorer: 1.0
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.20.1
    ChimeraX-AtomicLibrary: 3.2.1
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202105130135
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.3
    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-GaudiViewX: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.3
    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: 1.2
    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
    ChimeraX-ModelPanel: 1.1
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    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6
    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: 1.9.3
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
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[Eric Pettersen]

Fixed the r0 problem, which was trying to report that 2MR (example: 3MEU) an arginine analog was charge 0 when it should be charge 1. This is because or the _ng_charge routine treating the terminal Ng+s like the in-chain one (i.e. charge 0) because they're connected to other heavy atoms.

[Eric Pettersen]

Changed and simplified the charge estimation code for guanidinium groups.