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 Eric Pettersen, 2 years ago

Component: Unassigned → Surface/Binding Analysis
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Deleting protons does not affect coulombic

comment:2 by Eric Pettersen, 2 years ago

Resolution: → not a bug
Status: accepted → closed

Hi Tristan,

If coulombic sees that all relevant atoms have a 'charge' attribute, it will use those attribute values. In your case, you would have to run addcharge "by hand" before running coulombic again.

--Eric

comment:3 by Tristan Croll, 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 Eric Pettersen, 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 Eric Pettersen, 23 months ago

Cc: Elaine Meng 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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