Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#7750 closed defect (not a bug)

Tug: All atoms within a residue must be contiguous

Reported by: eackad@… Owned by: Tom Goddard
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-5.15.0-48-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
I wanted to move a water mol out of the way since it was inside a ligand so I tried the tug mode.

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/eddie/shareddata/namdoutput/p450/p450_pgm_allo_C1/p450_pgm_allo_level2_chimera_hy36.pdb
> format pdb

Chain information for p450_pgm_allo_level2_chimera_hy36.pdb #1  
---  
Chain | Description  
P | No description available  
  

> select all

146509 atoms, 113354 bonds, 33755 residues, 1 model selected  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel ball

Changed 39 atom styles  

> show sel atoms

> select zone :TRA 5

Selected 236 atoms  

> select zone :TRA 4

Selected 144 atoms  

> show sel atoms

> style sel stick

Changed 144 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 144 atom styles  

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> style sel stick

Changed 144 atom styles  

> style sel ball

Changed 144 atom styles  

> style sel stick

Changed 144 atom styles  

> select zone /O:53,142 4

Selected 28 atoms  

> show sel atoms

[Repeated 1 time(s)]

> select zone /O:53,142 4

Selected 28 atoms  

> show sel atoms

> select zone /O:53 4

Selected 28 atoms  

> show sel atoms

> style sel stick

Changed 28 atom styles  

> select /O:53

1 atom, 1 residue, 1 model selected  

> show sel atoms

> select all

146509 atoms, 113354 bonds, 33755 residues, 1 model selected  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> select zone :TRA 4

Selected 144 atoms  

> show sel atoms

> select zone /CO:53,142 4

Selected 483 atoms  

> select /CO:53,142 4

Expected a keyword  

> select /CO:53,142

268 atoms, 266 bonds, 2 residues, 1 model selected  

> show sel atoms

> close session

> open
> /home/eddie/shareddata/namdoutput/p450/p450_pgm_allo_C1/p450_pgm_allo_level3_hy36.pdb

Chain information for p450_pgm_allo_level3_hy36.pdb #1  
---  
Chain | Description  
P | No description available  
  

> select all

146510 atoms, 113360 bonds, 33754 residues, 1 model selected  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> select add zone :TRA 4 ; show sel atoms ;

Expected an objects specifier or a keyword  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> select zone :TRA 4

Selected 178 atoms  

> show sel atoms

> select zone /CO:53,142 4 show sel atoms ;sel /CO:53,142 4 ; show sel atoms

Expected an objects specifier or a keyword  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> select zone :TRA 4

Selected 178 atoms  

> show sel atoms

> select zone /CO:53,142 4

No atoms or surfaces specified  

> select zone /CO:53,142 4

No atoms or surfaces specified  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> select zone :TRA 4

Selected 178 atoms  

> show sel atoms

> select zone /O:53,142 4

Selected 506 atoms  

> show sel atoms

> select /O:53,142 4 ; show sel atoms

Expected a keyword  

> style sel stick

Changed 506 atom styles  

> hide sel atoms

> select :TRA

39 atoms, 42 bonds, 1 residue, 1 model selected  

> show sel atoms

> select zone :TRA 4

Selected 178 atoms  

> show sel atoms

> select zone /O:53,142 4

Selected 506 atoms  

> show sel atoms

> select /O:53,142

269 atoms, 266 bonds, 3 residues, 1 model selected  

> show sel atoms

> vr true

started SteamVR rendering  
VR mode select  
[Repeated 1 time(s)]VR mode translate selected models  

> view matrix models
> #1,0.99985,-0.017483,0.00088293,-0.17722,0.017489,0.99982,-0.0076857,0.31484,-0.00074836,0.0077,0.99997,0.057937

> view matrix models
> #1,0.99995,-0.0016497,0.0096747,0.020316,0.0016951,0.99999,-0.0046812,0.106,-0.0096669,0.0046974,0.99994,-0.076068

> view matrix models
> #1,0.99922,0.03815,0.010375,0.33932,-0.038704,0.99746,0.059842,-0.19892,-0.0080658,-0.060196,0.99815,-0.60397

> view matrix models
> #1,0.99882,0.03844,0.029816,0.38248,-0.040742,0.99589,0.080894,-0.090432,-0.026584,-0.082013,0.99628,-1.0687

VR mode move picked models  

> view matrix models
> #1,0.99957,0.025299,0.015126,0.19637,-0.026903,0.99271,0.11748,0.17181,-0.012044,-0.11784,0.99296,-0.91153

VR mode move scene  
VR mode translate selected atoms  
VR mode select  

> select @@serial_number=84181

1 atom, 1 residue, 1 model selected  
VR mode translate selected atoms  
VR mode select  

> select clear

> select @@serial_number=84182

1 atom, 1 residue, 1 model selected  

> select @@serial_number=84181

1 atom, 1 residue, 1 model selected  

> select clear

[Repeated 3 time(s)]

> select @@serial_number=84182

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  

> select clear

[Repeated 1 time(s)]

> select up

Nothing selected  

> select clear

> select up

Nothing selected  

> select /P:211@HD11

1 atom, 1 residue, 1 model selected  

> select @@serial_number=84182

1 atom, 1 residue, 1 model selected  

> select up

3 atoms, 2 bonds, 1 residue, 1 model selected  
VR mode translate selected models  

> view matrix models
> #1,0.99957,0.025299,0.015126,0.19637,-0.026903,0.99271,0.11748,0.17181,-0.012044,-0.11784,0.99296,-0.91153

> view matrix models
> #1,0.99979,0.013343,0.015631,0.092361,-0.015081,0.99302,0.11697,0.42637,-0.013961,-0.11719,0.99301,-0.88157

VR mode translate selected atoms  
VR mode select  

> select @@serial_number=65475

1 atom, 1 residue, 1 model selected  

> select @@serial_number=65476

1 atom, 1 residue, 1 model selected  

> select @@serial_number=65474

1 atom, 1 residue, 1 model selected  

> select @@serial_number=65476

1 atom, 1 residue, 1 model selected  
VR mode tug  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 802, in _next_frame  
self.process_controller_events()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 830, in process_controller_events  
self.process_controller_buttons()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 857, in process_controller_buttons  
hc.process_event(e)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 2691, in process_event  
self._dispatch_event(m, event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 2695, in _dispatch_event  
mode.pressed(hand_event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 3536, in pressed  
self._click(hand_button_event)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/vive/vr.py",
line 3545, in _click  
m.vr_press(e)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/tug/tugatoms.py", line 161, in vr_press  
self._pick_atom(pick)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/tug/tugatoms.py", line 86, in _pick_atom  
self._tugger = st = StructureTugger(a.structure)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/tug/tugatoms.py", line 248, in __init__  
self._create_openmm_system()  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/tug/tugatoms.py", line 420, in _create_openmm_system  
self._topology = openmm_topology(atoms, bonds)  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/tug/tugatoms.py", line 589, in openmm_topology  
atoms[i] = top.addAtom(aname[i], element, rmap[rid])  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/topology.py", line 190, in addAtom  
raise ValueError('All atoms within a residue must be contiguous')  
ValueError: All atoms within a residue must be contiguous  
  
Error processing trigger "new frame":  
ValueError: All atoms within a residue must be contiguous  
  
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/openmm/app/topology.py", line 190, in addAtom  
raise ValueError('All atoms within a residue must be contiguous')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 515.76
OpenGL renderer: NVIDIA GeForce RTX 2080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 22.04 jammy
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 Intel(R) Core(TM) i7-7700K CPU @ 4.20GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            62Gi       7.8Gi        30Gi       272Mi        24Gi        53Gi
	Swap:           31Gi          0B        31Gi

Graphics:
	03:00.0 VGA compatible controller [0300]: NVIDIA Corporation TU102 [GeForce RTX 2080 Ti] [10de:1e04] (rev a1)	
	Subsystem: PNY TU102 [GeForce RTX 2080 Ti] [196e:12af]	
	Kernel driver in use: nvidia

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    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
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (3)

comment:1 by pett, 3 years ago

Component: Unassigned → Structure Editing
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Tug: All atoms within a residue must be contiguous

comment:2 by Tom Goddard, 3 years ago

Resolution: → not a bug
Status: assigned → closed

The error message says "All atoms within a residue must be contiguous". So the PDB file you read in has atoms belonging to the same residue that are not contiguous. The PDB file does not have the atoms in proper order and this is a problem with the software that created the file.

File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/openmm/app/topology.py", line 190, in addAtom  
raise ValueError('All atoms within a residue must be contiguous')  
ValueError: All atoms within a residue must be contiguous

But beyond that there is no way interactive molecular dynamics is going to run fast enough on 150,000 atoms. This is not the way to move a water molecule. Select the water and use the "Move atoms" mouse mode in the Right Mouse tab of the toolbar to do that. Or just delete the water after selecting it with menu Actions / Atoms / delete or with the delete command.

in reply to:  3 ; comment:3 by eackad@…, 3 years ago 

Ok. Thank you. That makes sense.


_________________________________________________________
Edward Ackad, Ph.D<http://www.siue.edu/%7Eeackad>
Associate Professor of Physics
Computational Nanophotonics/Biophysics
Southern Illinois University Edwardsville
(618) 650-2390

________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Thursday, October 6, 2022 7:12 PM
Cc: Ackad, Edward <eackad@siue.edu>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>
Subject: Re: [ChimeraX] #7750: Tug: All atoms within a residue must be contiguous

#7750: Tug: All atoms within a residue must be contiguous
----------------------------------------+-------------------------
          Reporter:  eackad@…           |      Owner:  Tom Goddard
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  not a bug          |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+-------------------------
Changes (by Tom Goddard):

 * status:  assigned => closed
 * resolution:   => not a bug


Comment:

 The error message says "All atoms within a residue must be contiguous".
 So the PDB file you read in has atoms belonging to the same residue that
 are not contiguous.  The PDB file does not have the atoms in proper order
 and this is a problem with the software that created the file.

 {{{
 File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
 packages/openmm/app/topology.py", line 190, in addAtom
 raise ValueError('All atoms within a residue must be contiguous')
 ValueError: All atoms within a residue must be contiguous
 }}}

 But beyond that there is no way interactive molecular dynamics is going to
 run fast enough on 150,000 atoms.  This is not the way to move a water
 molecule.  Select the water and use the "Move atoms" mouse mode in the
 Right Mouse tab of the toolbar to do that.  Or just delete the water after
 selecting it with menu Actions / Atoms / delete or with the delete
 command.

--
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