Opened 4 years ago
Closed 4 years ago
#4644 closed defect (fixed)
AddCharge: Ng+ charges
Reported by: | Eric Pettersen | Owned by: | Eric Pettersen |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Structure Editing | Version: | |
Keywords: | Cc: | ||
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
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 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 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 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.3 comtypes: 1.1.7 cxservices: 1.0 cycler: 0.10.0 Cython: 0.29.21 decorator: 4.4.2 distlib: 0.3.1 docutils: 0.16 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 2.10.0 html2text: 2020.1.16 idna: 2.10 ihm: 0.17 imagecodecs: 2020.5.30 imagesize: 1.2.0 ipykernel: 5.3.4 ipython: 7.18.1 ipython-genutils: 0.2.0 jedi: 0.17.2 Jinja2: 2.11.2 jupyter-client: 6.1.7 jupyter-core: 4.7.1 kiwisolver: 1.3.1 line-profiler: 2.1.2 lxml: 4.6.2 lz4: 3.1.0 MarkupSafe: 1.1.1 matplotlib: 3.3.2 msgpack: 1.0.0 netCDF4: 1.5.4 networkx: 2.5 numexpr: 2.7.3 numpy: 1.19.2 numpydoc: 1.1.0 openvr: 1.14.1501 packaging: 20.9 ParmEd: 3.2.0 parso: 0.7.1 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 7.2.0 pip: 21.0.1 pkginfo: 1.5.0.1 prompt-toolkit: 3.0.16 psutil: 5.7.2 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.0.0 Pygments: 2.7.1 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 2.4.7 PyQt5: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine: 5.15.2 python-dateutil: 2.8.1 pytz: 2021.1 PyYAML: 5.4.1 pyzmq: 22.0.3 qtconsole: 4.7.7 QtPy: 1.9.0 RandomWords: 0.3.0 requests: 2.24.0 scipy: 1.5.2 Send2Trash: 1.5.0 SEQCROW: 0.25.2 setuptools: 50.3.2 sfftk-rw: 0.6.7.dev1 six: 1.15.0 snowballstemmer: 2.1.0 sortedcontainers: 2.2.2 Sphinx: 3.2.1 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 1.0.3 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.4 suds-jurko: 0.6 tables: 3.6.1 tifffile: 2020.9.3 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.0.5 urllib3: 1.25.11 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.36.0 wheel-filename: 1.3.0
Change History (3)
comment:1 by , 4 years ago
Component: | Unassigned → Structure Editing |
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Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → AddCharge: 'r0' is not defined |
comment:2 by , 4 years ago
Summary: | AddCharge: 'r0' is not defined → AddCharge: Ng+ charges |
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comment:3 by , 4 years ago
Resolution: | → fixed |
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Status: | accepted → closed |
Changed and simplified the charge estimation code for guanidinium groups.
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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.