Opened 2 years ago
Closed 22 months ago
#10022 closed enhancement (fixed)
RFE: coulombic option to force charge recalculation
Reported by: | Tristan Croll | Owned by: | Eric Pettersen |
---|---|---|---|
Priority: | low | Milestone: | |
Component: | Surface/Binding Analysis | Version: | |
Keywords: | Cc: | Elaine Meng | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: Windows-10-10.0.22621 ChimeraX Version: 1.7.dev202309180647 (2023-09-18 06:47:42 UTC) Description If I use the "coulombic" command to calculate the charges on a ligand, then delete a proton and repeat the command, it simply re-uses the existing charges rather than recognising the molecule has changed. I don't see an option to force recalculation. Log: UCSF ChimeraX version: 1.7.dev202309180647 (2023-09-18) © 2016-2023 Regents of the University of California. All rights reserved. > open "C:/Users/Tristan > Croll/Documents/Structures/terazosin/4o33/4o33_rebuild.cxs" Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 1,1,1, pixel 0.515,0.512,0.519, shown at level 0.429, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 1,1,1, pixel 0.515,0.512,0.519, shown at level -0.172,0.172, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_13 as #1.1.1.4, grid size 1,1,1, pixel 0.515,0.512,0.519, shown at level 0.21, step 1, values float32 Opened (LIVE) MDFF potential as #1.1.1.5, grid size 1,1,1, pixel 0.515,0.512,0.519, shown at level 0.565, step 1, values float32 Restoring stepper: 4o33 Launching live xmap mgr took 2.0299994945526123 seconds. Log from Fri Dec 2 09:55:05 2022 > isolde shorthand Initialising ISOLDE-specific command aliases: Alias Equivalent full command ------------------------------------------------- st isolde step {arguments} aw isolde add water {arguments} awsf isolde add water {arguments} sim false al isolde add ligand {arguments} aa isolde add aa $1 sel {arguments} ht isolde mod his sel {arguments} so setattr sel atoms occupancy {arguments} ab isolde adjust bfactors {arguments} ss isolde sim start sel rt isolde release torsions sel {arguments} rd isolde release distances sel {arguments} ra rd; rt pf isolde pepflip sel cf isolde cisflip sel cbb color bfactor {arguments} cbo color byattr occupancy {arguments} cbc color {arguments} bychain; color {arguments} byhet cs clipper set contourSensitivity {arguments} UCSF ChimeraX version: 1.6.dev202211300249 (2022-11-30) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 4o33 structureFactors true Summary of feedback from opening 4o33 fetched from pdb --- notes | Fetching compressed mmCIF 4o33 from http://files.rcsb.org/download/4o33.cif Fetching CCD TZN from http://ligand-expo.rcsb.org/reports/T/TZN/TZN.cif Fetching CCD 3PG from http://ligand-expo.rcsb.org/reports/3/3PG/3PG.cif Fetching compressed 4o33 structure factors from http://files.rcsb.org/download/4o33-sf.cif Resolution: 2.105118128819088 Reflection data provided as intensities. Performing French & Wilson scaling to convert to amplitudes... Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 40,38,38, pixel 0.644,0.683,0.649, shown at level 0.716, step 1, values float32 Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 40,38,38, pixel 0.644,0.683,0.649, shown at level -0.172,0.172, step 1, values float32 Opened (LIVE) 2mFo-DFc_smooth_13 as #1.1.1.4, grid size 40,38,38, pixel 0.644,0.683,0.649, shown at level 0.224, step 1, values float32 4o33 title: Crystal Structure of human PGK1 3PG and terazosin(TZN) ternary complex [more info...] Chain information for 4o33 --- Chain | Description | UniProt 1.2/A | Phosphoglycerate kinase 1 | PGK1_HUMAN Non-standard residues in 4o33 #1.2 --- 3PG — 3-phosphoglyceric acid TZN — [4-(4-amino-6,7-dimethoxyquinazolin-2-yl)piperazin-1-yl][(2R)-tetrahydrofuran-2-yl]methanone (Terazosin) > addh Summary of feedback from adding hydrogens to 4o33 #1.2 --- notes | Termini for 4o33 (#1.2) chain A determined from SEQRES records Chain-initial residues that are actual N termini: /A MET 0 Chain-initial residues that are not actual N termini: Chain-final residues that are actual C termini: /A ILE 416 Chain-final residues that are not actual C termini: Missing OXT added to C-terminal residue /A ILE 416 1160 hydrogen bonds 3820 hydrogens added > isolde start > set selectionWidth 4 ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 15 residues in model #1.2 to IUPAC-IUB standards. Opened (LIVE) MDFF potential as #1.1.1.5, grid size 40,38,38, pixel 0.644,0.683,0.649, shown at level 0.565, step 1, values float32 Loading residue template for 3PG from internal database Loading residue template for TZN from internal database > view :TZN > select #1 7320 atoms, 7063 bonds, 727 residues, 26 models selected > isolde sim start sel ISOLDE: started sim > isolde sim pause > isolde sim resume > isolde sim pause > st [Repeated 2 time(s)] > isolde sim resume > st [Repeated 22 time(s)] > isolde sim pause > st [Repeated 5 time(s)] > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > st [Repeated 3 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 1 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 52 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 11 time(s)] > isolde sim resume > st > isolde sim pause > st [Repeated 86 time(s)] > isolde sim resume > isolde sim pause > isolde sim resume > isolde sim pause > st > isolde sim resume > isolde sim pause > st [Repeated 1 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 1 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 6 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 10 time(s)] > isolde sim resume > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 3 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > delete sel > al CL > select #1 7318 atoms, 7061 bonds, 727 residues, 31 models selected > isolde sim start sel ISOLDE: started sim > select clear > select up 7318 atoms, 7061 bonds, 727 residues, 1 model selected > select down 1 atom, 1 residue, 1 model selected > ab 10 > isolde sim stop discardTo start reverting to start Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > delete sel > aw > isolde sim start sel ISOLDE: started sim > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1 7320 atoms, 7063 bonds, 727 residues, 31 models selected > isolde sim start sel ISOLDE: started sim > select clear > st > isolde sim pause > st [Repeated 24 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 5 time(s)] > isolde sim resume > st > isolde sim pause > st [Repeated 2 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 14 time(s)] > isolde sim resume > isolde sim pause > st > isolde sim resume > isolde sim pause > st [Repeated 24 time(s)] > isolde sim resume > isolde sim pause > st > isolde sim resume > isolde sim pause > st [Repeated 1 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 10 time(s)] > isolde sim resume > st > isolde sim pause > st [Repeated 15 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 14 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 34 time(s)] > isolde sim resume > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim pause > st [Repeated 1 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 33 time(s)] > isolde sim resume > isolde sim pause > st [Repeated 8 time(s)] > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > view :TZN > select #1 7320 atoms, 7063 bonds, 727 residues, 31 models selected > isolde sim start sel ISOLDE: started sim > select clear > isolde sim pause > select :HOH 924 atoms, 616 bonds, 308 residues, 1 model selected > so 0 Assigning occupancy attribute to 924 items > so 1 Assigning occupancy attribute to 924 items > select clear > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: Corrected atom nomenclature of 1 residues in model #1.2 to IUPAC-IUB standards. ISOLDE: stopped sim > delete sel > select up 3 atoms, 2 bonds, 1 residue, 1 model selected > delete sel > select up 22 atoms, 21 bonds, 1 residue, 1 model selected > select up 46 atoms, 45 bonds, 4 residues, 1 model selected > isolde sim start sel ISOLDE: started sim > select clear > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > awsf [Repeated 1 time(s)] > isolde sim start sel ISOLDE: started sim > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1 7320 atoms, 7063 bonds, 727 residues, 31 models selected > isolde sim start sel ISOLDE: started sim > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > select #1 7320 atoms, 7063 bonds, 727 residues, 31 models selected > isolde sim start sel ISOLDE: started sim > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > ui tool show Shell > isolde sim start sel ISOLDE: started sim > select clear > view :TZN [Repeated 1 time(s)] > isolde sim pause > isolde sim resume > isolde pepflip sel Flipping the peptide bond for 1 residues > isolde sim stop Updating bulk solvent parameters... ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side chains... ISOLDE: stopped sim > save 4o33_rebuild.pdb #1 > save 4o33_rebuild.cxs Taking snapshot of stepper: 4o33 ——— End of log from Fri Dec 2 09:55:05 2022 ——— opened ChimeraX session > select /A:501@NAI 1 atom, 1 residue, 1 model selected > ui tool show "Build Structure" > build modify /A:501@NAI H 1 name H1 resName UNL > select /A:501@N3 1 atom, 1 residue, 1 model selected > build modify /A:501@N3 N 3 geometry trigonal > select /A:501@C5 1 atom, 1 residue, 1 model selected > select up 52 atoms, 55 bonds, 1 residue, 1 model selected > show sel > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue UNL (net charge +1) with am1-bcc method Running ANTECHAMBER command: C:/Program Files/ChimeraX- daily/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i C:\Users\TRISTA~1\AppData\Local\Temp\tmphavyi_6g\ante.in.mol2 -fi mol2 -o C:\Users\TRISTA~1\AppData\Local\Temp\tmphavyi_6g\ante.out.mol2 -fo mol2 -c bcc -nc 1 -j 5 -s 2 -dr n (UNL) `` (UNL) `Welcome to antechamber 20.0: molecular input file processor.` (UNL) `` (UNL) `Info: Finished reading file (C:\Users\TRISTA~1\AppData\Local\Temp\tmphavyi_6g\ante.in.mol2); atoms read (52), bonds read (55).` (UNL) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/bondtype" -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `Info: Total number of electrons: 198; net charge: 1` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/sqm" -O -i sqm.in -o sqm.out` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/am1bcc" -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p "C:/Program Files/ChimeraX-daily/bin/amber20/dat/antechamber/BCCPARM.DAT" -s 2 -j 1` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` (UNL) `Running: "C:/Program Files/ChimeraX-daily/bin/amber20/bin/atomtype" -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC` (UNL) `bash.exe: warning: could not find /tmp, please create!` (UNL) `` Charges for residue UNL determined Coulombic values for 4o33_A SES surface #1.2.7: minimum, -1.49, mean 2.52, maximum 6.21 > usage coul coulombic [atoms] [surfaces a surfaces specifier] [gpadding a number] [map true or false] [gspacing a number] [hisScheme hisScheme] [offset a number] [palette a colormap] [range range] [distDep true or false] [dielectric a number] [chargeMethod chargeMethod] [key true or false] — Color surfaces by coulombic potential atoms: an atoms specifier or nothing hisScheme: one of HID, HIE, or HIP range: some numbers or full chargeMethod: one of am1-bcc or gasteiger > hide #!1.2.7 models > ui tool show Shell 0.01s - Debugger warning: It seems that frozen modules are being used, which may 0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off 0.00s - to python to disable frozen modules. 0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation. > select /A:501@N1 1 atom, 1 residue, 1 model selected > select /A:501@H3 1 atom, 1 residue, 1 model selected > select /A:501@N3 1 atom, 1 residue, 1 model selected > select /A:501@H3 1 atom, 1 residue, 1 model selected > delete sel > select /A:501@C2 1 atom, 1 residue, 1 model selected > select up 51 atoms, 54 bonds, 1 residue, 2 models selected > coulombic sel Coulombic values for 4o33_A SES surface #1.2.7: minimum, -1.91, mean 1.59, maximum 3.68 > usage coul coulombic [atoms] [surfaces a surfaces specifier] [gpadding a number] [map true or false] [gspacing a number] [hisScheme hisScheme] [offset a number] [palette a colormap] [range range] [distDep true or false] [dielectric a number] [chargeMethod chargeMethod] [key true or false] — Color surfaces by coulombic potential atoms: an atoms specifier or nothing hisScheme: one of HID, HIE, or HIP range: some numbers or full chargeMethod: one of am1-bcc or gasteiger > hide #1.2.7 models > select /A:501@N1 1 atom, 1 residue, 1 model selected > coulombic sel chargeMethod am1-bcc Coulombic values for 4o33_A SES surface #1.2.7: minimum, -7.20, mean -7.11, maximum -7.06 > select up 51 atoms, 54 bonds, 1 residue, 2 models selected > coulombic sel chargeMethod am1-bcc Coulombic values for 4o33_A SES surface #1.2.7: minimum, -1.91, mean 1.59, maximum 3.68 > coulombic sel chargeMethod gasteiger Coulombic values for 4o33_A SES surface #1.2.7: minimum, -1.91, mean 1.59, maximum 3.68 > coulombic sel chargeMethod am1-bcc Coulombic values for 4o33_A SES surface #1.2.7: minimum, -1.91, mean 1.59, maximum 3.68 OpenGL version: 3.3.0 NVIDIA 529.08 OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2 OpenGL vendor: NVIDIA Corporation Python: 3.11.2 Locale: en_GB.cp1252 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: windows Manufacturer: HP Model: HP ZBook Studio 15.6 inch G8 Mobile Workstation PC OS: Microsoft Windows 11 Pro (Build 22621) Memory: 34,007,068,672 MaxProcessMemory: 137,438,953,344 CPU: 16 11th Gen Intel(R) Core(TM) i7-11800H @ 2.30GHz OSLanguage: en-GB Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 asttokens: 2.4.0 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2023.7.22 cftime: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.47.2 ChimeraX-AtomicLibrary: 10.0.8 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.3 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.1 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.4 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202309180647 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.2 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-ISOLDE: 1.7.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.12 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9.1 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.2 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.31.5 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.2 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.4 comtypes: 1.1.14 contourpy: 1.1.1 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 et-xmlfile: 1.1.0 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.42.1 funcparserlib: 1.0.1 glfw: 2.6.2 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.6 numpy: 1.25.1 openpyxl: 3.1.2 openvr: 1.23.701 packaging: 23.1 pandas: 2.0.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 psutil: 5.9.5 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pywin32: 305 pyzmq: 25.1.1 qtconsole: 5.4.3 QtPy: 2.4.0 QtRangeSlider: 0.1.5 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 seaborn: 0.12.2 Send2Trash: 1.8.2 SEQCROW: 1.7.3 setuptools: 67.4.0 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.2 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.3 traitlets: 5.9.0 typing-extensions: 4.8.0 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 WMI: 1.5.1
Change History (5)
comment:1 by , 2 years ago
Component: | Unassigned → Surface/Binding Analysis |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → accepted |
Summary: | ChimeraX bug report submission → Deleting protons does not affect coulombic |
comment:2 by , 2 years ago
Resolution: | → not a bug |
---|---|
Status: | accepted → closed |
comment:3 by , 2 years ago
Yes, I figured that was what was going on - my workaround was to just delete and re-add hydrogens. Thought I should report it anyway because the behaviour is initially quite confusing. :) On Thu, Oct 19, 2023 at 5:32 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > > >
comment:4 by , 2 years ago
Priority: | normal → low |
---|---|
Resolution: | not a bug |
Status: | closed → reopened |
Summary: | Deleting protons does not affect coulombic → RFE: coulombic option to force charge recalculation |
Type: | defect → enhancement |
Nonetheless, there probably should be an option for these rare use cases.
comment:5 by , 22 months ago
Cc: | added |
---|---|
Resolution: | → fixed |
Status: | reopened → closed |
Okay, in tomorrow's build the coulombic command will accept a reassignCharges keyword for this rare case of a deletion-only modification. The name of the keyword subject to Elaine's blessing. You would have to change atom types too in order to get the effect you desire I believe.
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Hi Tristan,
--Eric