Opened 2 years ago
Closed 23 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 , 23 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