Opened 4 months ago

Closed 4 months ago

#17973 closed defect (can't reproduce)

Add Charge: non-standard residue list is empty

Reported by: chimerax-bug-report@… Owned by: pett
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:        Linux-3.10.0-1160.108.1.el7.x86_64-x86_64-with-glibc2.38
ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

> set selectionWidth 4

Done loading forcefield  
UCSF ChimeraX version: 1.8 (2024-06-10)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> isolde set simFidelityMode Highest/Slowest

ISOLDE: setting sim fidelity mode to Highest/Slowest  
nonbonded_cutoff_distance = 1.700000  
use_gbsa = True  
gbsa_cutoff = 2.000000  

> isolde tutorial

> open
> /mnt/work1/Cesar_Juan_nanowires/Modeling/Tfer2153_fiber/J215_flipped.mrc
> format mrc

Opened J215_flipped.mrc as #1, grid size 986,986,986, pixel 0.366, shown at
step 1, values float32  

> volume #1 region 0,0,0,985,985,985 step 4

[Repeated 1 time(s)]

> volume #1 change image level -4.497e-06,0 level 0.01191,0.8 level 0.08756,1

> volume #1 step 1

> volume #1 level 0.03616

> open
> /mnt/work1/Cesar_Juan_nanowires/Modeling/Tfer2153_fiber/job071-HEC_reordered-
> coot-12.pdb

Summary of feedback from opening
/mnt/work1/Cesar_Juan_nanowires/Modeling/Tfer2153_fiber/job071-HEC_reordered-
coot-12.pdb  
---  
warnings | Cannot find LINK/SSBOND residue HEC (401 )  
Cannot find LINK/SSBOND residue HEC (401 )  
Cannot find LINK/SSBOND residue HEC (301 )  
Cannot find LINK/SSBOND residue HEC (101 )  
Cannot find LINK/SSBOND residue HEC (101 )  
45 messages similar to the above omitted  
  
Chain information for job071-HEC_reordered-coot-12.pdb #2  
---  
Chain | Description  
Aa | No description available  
Ab | No description available  
Ac | No description available  
Ad | No description available  
Ae | No description available  
Af | No description available  
Ag | No description available  
  

> select add #1

3 models selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,-0.97912,0.1889,0.075147,308.85,-0.17907,-0.97636,0.12105,367.26,0.096236,0.10506,0.9898,-34.465

> view matrix models
> #1,-0.94865,0.30894,0.068042,282.97,-0.29564,-0.94235,0.15676,375.7,0.11255,0.12859,0.98529,-40.84

> view matrix models
> #1,-0.92112,0.38653,0.046125,267.95,-0.38019,-0.91875,0.10654,395.7,0.083556,0.080597,0.99324,-28.383

> view matrix models
> #1,-0.9952,-0.086431,0.045949,366.7,0.088469,-0.99509,0.044358,336.24,0.04189,0.04821,0.99796,-15.881

> select add #1

3 models selected  

> select add #1

3 models selected  

> select add #1

3 models selected  

> select add #1

3 models selected  

> select add #2

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 6 models selected  

> select add #1.1

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 6 models selected  

> select subtract #1.2

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 5 models selected  

> select add #1.1

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 5 models selected  

> select add #1

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 6 models selected  

> select subtract #1.2

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 5 models selected  

> lighting full

> lighting shadows false

> select subtract #2

2 models selected  

> ui tool show "Fit in Map"

> fitmap #2 inMap #1

Fit molecule job071-HEC_reordered-coot-12.pdb (#2) to map J215_flipped.mrc
(#1) using 20250 atoms  
average map value = 0.03638, steps = 240  
shifted from previous position = 1.35  
rotated from previous position = 5.43 degrees  
atoms outside contour = 10005, contour level = 0.036163  
  
Position of job071-HEC_reordered-coot-12.pdb (#2) relative to J215_flipped.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.99990710 0.01191742 0.00661511 357.69550031  
-0.01189428 -0.99992304 0.00352587 361.85158644  
0.00665662 0.00344686 0.99997190 -2.54670738  
Axis -0.00331807 -0.00174326 -0.99999298  
Axis point 179.92907006 179.86328585 0.00000000  
Rotation angle (degrees) 179.31782411  
Shift along axis 0.72902841  
  

> style ball

Changed 20250 atom styles  

> show atoms

[Repeated 1 time(s)]

> view matrix models
> #1,-0.19219,0.98018,-0.047975,46.408,-0.98096,-0.19327,-0.018992,395.5,-0.027888,0.043412,0.99867,-2.5743

> undo

> select add #1

3 models selected  

> select subtract #1.2

2 models selected  

> select add #1.1

2 models selected  

> select add #1.1

2 models selected  

> ui mousemode right select

> select clear

> fitmap #2 inMap #1

Fit molecule job071-HEC_reordered-coot-12.pdb (#2) to map J215_flipped.mrc
(#1) using 20250 atoms  
average map value = 0.03638, steps = 24  
shifted from previous position = 0.00632  
rotated from previous position = 0.0165 degrees  
atoms outside contour = 10007, contour level = 0.036163  
  
Position of job071-HEC_reordered-coot-12.pdb (#2) relative to J215_flipped.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.99991061 0.01163016 0.00659534 357.75018266  
-0.01160696 -0.99992635 0.00354480 361.79955942  
0.00663608 0.00346793 0.99997197 -2.54125871  
Axis -0.00330799 -0.00175325 -0.99999299  
Axis point 179.93024618 179.86281516 0.00000000  
Rotation angle (degrees) 179.33428576  
Shift along axis 0.72347977  
  

> volume #1 level 0.02346

> fitmap #2 inMap #1

Fit molecule job071-HEC_reordered-coot-12.pdb (#2) to map J215_flipped.mrc
(#1) using 20250 atoms  
average map value = 0.03638, steps = 28  
shifted from previous position = 0.00714  
rotated from previous position = 0.0118 degrees  
atoms outside contour = 5667, contour level = 0.023461  
  
Position of job071-HEC_reordered-coot-12.pdb (#2) relative to J215_flipped.mrc
(#1) coordinates:  
Matrix rotation and translation  
-0.99991295 0.01142588 0.00659906 357.78537158  
-0.01140288 -0.99992881 0.00351299 361.76925415  
0.00663873 0.00343744 0.99997205 -2.54332344  
Axis -0.00330958 -0.00173768 -0.99999301  
Axis point 179.92928913 179.86580782 0.00000000  
Rotation angle (degrees) 179.34598540  
Shift along axis 0.73054804  
  

> set bgColor gray

> view

[Repeated 1 time(s)]

> volume style mesh

> volume #1 color #99c1f1

> volume #1 color #1a5fb4

> volume #1 color #62a0ea

> select /Aa

2719 atoms, 2787 bonds, 3 pseudobonds, 372 residues, 2 models selected  

> view sel

Drag select of 1 J215_flipped.mrc , 1 atoms, 1 bonds  

> select subtract #1.2

1 atom, 1 bond, 1 residue, 2 models selected  

> select add #2

20250 atoms, 20794 bonds, 176 pseudobonds, 2448 residues, 4 models selected  

> select subtract #2

1 model selected  

> ui tool show "Change Chain IDs"

> ui tool show "Dock Prep"

Starting dock prep  
Deleting solvent  
Deleting non-metal-complex ions  
Deleting non-current alt locs  
Filling out missing side chains  
/Aa PRO 372: phi -60.7, psi none trans  
/Ab PRO 372: phi -20.0, psi none trans  
/Ac LEU 371: phi -44.5, psi none trans  
/Ad PRO 372: phi -56.0, psi none trans  
/Ae PRO 372: phi -86.2, psi none trans  
/Af HIS 346: phi -68.5, psi none trans  
/Ag PRO 372: phi 160.8, psi none trans  
Applying PRO rotamer (chi angles: 27.0 -34.6) to /Aa PRO 372  
Applying PRO rotamer (chi angles: -25.1 36.3) to /Ab PRO 372  
Applying LEU rotamer (chi angles: 58.2 -73.6) to /Ac LEU 371  
Applying PRO rotamer (chi angles: 27.0 -34.6) to /Ad PRO 372  
Applying PRO rotamer (chi angles: -25.1 36.3) to /Ae PRO 372  
Applying HIS rotamer (chi angles: -66.0 85.6) to /Af HIS 346  
Applying PRO rotamer (chi angles: 27.0 -34.6) to /Ag PRO 372  
Summary of feedback from adding hydrogens to job071-HEC_reordered-coot-12.pdb
#2  
---  
notes | No usable SEQRES records for job071-HEC_reordered-coot-12.pdb (#2) chain Aa; guessing termini instead  
No usable SEQRES records for job071-HEC_reordered-coot-12.pdb (#2) chain Ab;
guessing termini instead  
No usable SEQRES records for job071-HEC_reordered-coot-12.pdb (#2) chain Ac;
guessing termini instead  
No usable SEQRES records for job071-HEC_reordered-coot-12.pdb (#2) chain Ad;
guessing termini instead  
No usable SEQRES records for job071-HEC_reordered-coot-12.pdb (#2) chain Ae;
guessing termini instead  
2 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /Aa ALA 1, /Ab ALA 1, /Ac
ASP 4, /Ad ASP 24, /Ae ALA 1, /Af ALA 1, /Ag ALA 1  
Chain-initial residues that are not actual N termini: /Aa GLY 271, /Aa ASN
364, /Ac THR 63, /Ac HIS 223, /Ac LYS 249, /Ac LEU 274, /Ac PRO 278, /Ac VAL
307, /Ac PRO 311, /Ad LEU 59, /Ad GLY 125, /Ad MET 174, /Ad HIS 223, /Ad LYS
249, /Ad VAL 262, /Ad GLN 315, /Ad ALA 369, /Ae ASN 332, /Ae GLY 358, /Af VAL
225, /Af LYS 249, /Af GLY 310, /Af ASP 322, /Ag ALA 169, /Ag ILE 187, /Ag HIS
223, /Ag ASP 253, /Ag GLY 266, /Ag GLY 271, /Ag CYS 365  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /Aa PRO 372, /Aa ASP 269,
/Aa PRO 270, /Ab PRO 372, /Ac LEU 371, /Ac GLY 61, /Ac ALA 212, /Ac SER 244,
/Ac ALA 272, /Ac GLY 276, /Ac ALA 304, /Ac SER 309, /Ad PRO 372, /Ad THR 38,
/Ad ALA 119, /Ad SER 171, /Ad ALA 220, /Ad ILE 246, /Ad VAL 260, /Ad CYS 313,
/Ad GLY 367, /Ae PRO 372, /Ae ALA 330, /Ae GLU 356, /Af HIS 346, /Af GLY 212,
/Af PHE 245, /Af ALA 285, /Af PRO 320, /Ag PRO 372, /Ag VAL 167, /Ag ASN 185,
/Ag HIS 217, /Ag PHE 245, /Ag THR 264, /Ag ASP 269, /Ag THR 343  
1429 hydrogen bonds  
Adding 'H' to /Aa GLY 271  
Adding 'H' to /Aa ASN 364  
Adding 'H' to /Ac THR 63  
Adding 'H' to /Ac HIS 223  
Adding 'H' to /Ac LYS 249  
23 messages similar to the above omitted  
/Aa PRO 372 is not terminus, removing H atom from 'C'  
/Ab PRO 372 is not terminus, removing H atom from 'C'  
/Ac LEU 371 is not terminus, removing H atom from 'C'  
/Ad PRO 372 is not terminus, removing H atom from 'C'  
/Ae PRO 372 is not terminus, removing H atom from 'C'  
2 messages similar to the above omitted  
16550 hydrogens added  
  
Closest equivalent command: addcharge standardizeResidues none  
Using Amber 20 recommended default charges and atom types for standard
residues  
Traceback (most recent call last):  
File "/app/lib/python3.11/site-packages/chimerax/add_charge/tool.py", line
120, in add_charges  
self._finish_add_charge(residues)  
File "/app/lib/python3.11/site-packages/chimerax/add_charge/tool.py", line
151, in _finish_add_charge  
AddNonstandardChargesTool(self.session, "Add Non-Standard Charges", non_std,  
File "/app/lib/python3.11/site-packages/chimerax/add_charge/tool.py", line
200, in __init__  
enc = estimate_net_charge(residues[0].atoms)  
~~~~~~~~^^^  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/app/lib/python3.11/site-packages/chimerax/add_charge/tool.py", line
200, in __init__  
enc = estimate_net_charge(residues[0].atoms)  
~~~~~~~~^^^  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 520.61.05
OpenGL renderer: NVIDIA GeForce GTX TITAN X/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=gnome-classic
XDG_SESSION_DESKTOP=gnome-classic
XDG_CURRENT_DESKTOP=GNOME-Classic:GNOME
DISPLAY=:99.0
Manufacturer: Silicon Mechanics
Model: Rackform R2504.v6
OS: Freedesktop SDK 23.08 Flatpak runtime
Architecture: 64bit ELF
Virtual Machine: detection failed
CPU: 48 Intel(R) Xeon(R) CPU E5-2650 v4 @ 2.20GHz
Cache Size: 30720 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           251Gi        14Gi       235Gi       294Mi       2.4Gi       237Gi
	Swap:          4.0Gi       311Mi       3.7Gi

Graphics:
	02:00.0 VGA compatible controller [0300]: NVIDIA Corporation GM200 [GeForce GTX TITAN X] [10de:17c2] (rev a1)	
	Subsystem: NVIDIA Corporation Device [10de:1132]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2024.6.2
    cftime: 1.6.4
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.7
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.57.1
    ChimeraX-AtomicLibrary: 14.0.6
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.7
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-Clipper: 0.23.1
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.8
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.4
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    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: 1.8
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.10
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.1
    ChimeraX-MedicalToolbar: 1.0.3
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.17
    ChimeraX-ModelPanel: 1.5
    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: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.5
    ChimeraX-PDB: 2.7.5
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.0.15
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.5
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    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: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.3
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    distro: 1.9.0
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.53.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.3
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.11
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 24.1
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.2
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    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
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    sphinx-autodoc-typehints: 2.0.1
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
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    tinyarray: 1.2.4
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    urllib3: 2.2.1
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Change History (2)

comment:1 by pett, 4 months ago

Component: Unassigned → Structure Editing
Owner: set to pett
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Add Charge: non-standard residue list is empty

comment:2 by pett, 4 months ago

Resolution: → can't reproduce
Status: accepted → closed

Eyeballing the code, I don't see how this could happen. Need the data.

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