Opened 3 years ago

Closed 3 years ago

#7168 closed defect (fixed)

ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan

Reported by: dkuntz@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Using Isolde to fit Ramachandran outliers.
Went through quite a few and then died

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Volumes/dkuntz/KCTD5/9Jun2022/phenix/Autosharpen_30/fitbtm_iscrashtime.pdb
> format pdb

Summary of feedback from opening
/Volumes/dkuntz/KCTD5/9Jun2022/phenix/Autosharpen_30/fitbtm_iscrashtime.pdb  
---  
warnings | Ignored bad PDB record found on line 1981  
ATOM 1736 N LEU B 48 ,),(-.*,,),(-.*,,),(-.*, 1.00 10.87 N  
  
Ignored bad PDB record found on line 1982  
ATOM 1737 CA LEU B 48 ,),(-.*,,),(-.*,,),(-.*, 1.00 10.87 C  
  
Ignored bad PDB record found on line 1983  
ATOM 1738 C LEU B 48 ,),(-.*,,),(-.*,,),(-.*, 1.00 10.87 C  
  
Ignored bad PDB record found on line 1984  
ATOM 1739 O LEU B 48 ,),(-.*,,),(-.*,,),(-.*, 1.00 10.87 O  
  
Ignored bad PDB record found on line 1985  
ATOM 1740 CB LEU B 48 ,),(-.*,,),(-.*,,),(-.*, 1.00 10.87 C  
  
168 messages similar to the above omitted  
Start residue of secondary structure not found: HELIX 13 13 PRO B 96 HIS B 108
1 13  
Start residue of secondary structure not found: HELIX 15 15 VAL B 122 TYR B
129 1 8  
  
Chain information for fitbtm_iscrashtime.pdb #1  
---  
Chain | Description  
A C D E | No description available  
B | No description available  
F G K L O | No description available  
  

> close #1

> open
> /Volumes/dkuntz/KCTD5/9Jun2022/phenix/RealSpaceRefine_31/4jan_merged_penta_chainfits-
> with-H-coot-1_real_space_refined_031.pdb

Chain information for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb #1  
---  
Chain | Description  
A B C D E | No description available  
F G K L O | No description available  
  

> open
> /Volumes/dkuntz/KCTD5/9Jun2022/phenix/Autosharpen_30/1043_3.2A_sharpened_map.ccp4
> format ccp4

Opened 1043_3.2A_sharpened_map.ccp4 as #2, grid size 324,324,324, pixel 1.03,
shown at level 2.97, step 2, values float32  

> volume #2 level 3.876

> addh H

Summary of feedback from adding hydrogens to 4jan_merged_penta_chainfits-with-
H-coot-1_real_space_refined_031.pdb #1  
---  
notes | No usable SEQRES records for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb (#1) chain A; guessing termini instead  
No usable SEQRES records for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb (#1) chain B; guessing termini instead  
No usable SEQRES records for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb (#1) chain C; guessing termini instead  
No usable SEQRES records for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb (#1) chain D; guessing termini instead  
No usable SEQRES records for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb (#1) chain E; guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A TRP 45, /B TRP 45, /C TRP
45, /D TRP 45, /E TRP 45, /F THR 24, /G THR 24, /K THR 24, /L THR 24, /O THR
24  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ASP 146, /B ASP 146, /C
ASP 146, /D ASP 146, /E ASP 146, /F GLY 325, /G GLY 325, /K GLY 325, /L GLY
325, /O GLY 325  
1533 hydrogen bonds  
/A ASP 146 is not terminus, removing H atom from 'C'  
/B ASP 146 is not terminus, removing H atom from 'C'  
/C ASP 146 is not terminus, removing H atom from 'C'  
/D ASP 146 is not terminus, removing H atom from 'C'  
/E ASP 146 is not terminus, removing H atom from 'C'  
5 messages similar to the above omitted  
8 hydrogens added  
  

> hide HC

> clipper associate #2 toModel #1

Opened 1043_3.2A_sharpened_map.ccp4 as #1.1.1.1, grid size 324,324,324, pixel
1.03, shown at level 12.2, step 1, values float32  
Chain information for 4jan_merged_penta_chainfits-with-H-
coot-1_real_space_refined_031.pdb  
---  
Chain | Description  
1.2/A 1.2/B 1.2/C 1.2/D 1.2/E | No description available  
1.2/F 1.2/G 1.2/K 1.2/L 1.2/O | No description available  
  

> isolde start

> set selectionWidth 4

ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 211 residues in model #1.2 to IUPAC-IUB
standards.  
Done loading forcefield  

> save
> /Volumes/dkuntz/KCTD5/9Jun2022/phenix/RealSpaceRefine_31/is1_beginning.pdb

Populating font family aliases took 610 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  
ISOLDE: paused sim  
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  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  

> save /Volumes/dkuntz/KCTD5/9Jun2022/phenix/RealSpaceRefine_31/is2.pdb

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
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  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
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  

> save /Volumes/dkuntz/KCTD5/9Jun2022/phenix/RealSpaceRefine_31/is3.pdb

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
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  
ISOLDE: started sim  
ISOLDE: paused sim  
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  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
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  
ISOLDE: started sim  
ISOLDE: paused sim  
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  

> save /Volumes/dkuntz/KCTD5/9Jun2022/phenix/RealSpaceRefine_31/is4.pdb

ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: Corrected atom nomenclature of 2 residues in model #1.2 to IUPAC-IUB
standards.  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...  
ISOLDE: stopped sim  
ISOLDE: started sim  
ISOLDE: paused sim  
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  
ISOLDE: started sim  
ISOLDE: paused sim  
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  
ISOLDE: started sim  
Traceback (most recent call last):  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/triggerset.py", line 134, in invoke  
return self._func(self._name, data)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1687, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords  
f(self._c_pointer, n, pointer(coords))  
RuntimeError: Particle coordinate is nan  
  
Error processing trigger "new frame":  
RuntimeError: Particle coordinate is nan  
  
File
"/opt/sbgrid/i386-mac/chimerax/1.3/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 305, in coords  
f(self._c_pointer, n, pointer(coords))  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac21,1
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 8 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.1 (21C52)
      Kernel Version: Darwin 21.2.0
      Time since boot: 4 days 2:47

Graphics/Displays:

    Apple G13G:

      Chipset Model: Apple G13G
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        iMac:
          Display Type: Built-In Retina LCD
          Resolution: Retina 4.5K (4480 x 2520)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: ('en_CA', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    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: 2.2.2
    ChimeraX-Clipper: 0.17.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    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: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    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-ISOLDE: 1.3
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    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: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    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: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    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: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
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    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
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    jedi: 0.18.0
    Jinja2: 3.0.1
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    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
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    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (6)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Reporter: changed from chimerax-bug-report@… to dkuntz@…
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan

in reply to:  2 ; comment:2 by Tristan Croll, 3 years ago 

This is a very rare phenomenon these days, but since it can still happen occasionally I really should do something about catching it gracefully (or, better, preventing it). In molecular dynamics, when a very large force is encountered it will cause one or more atoms to fly off at a very high rate. ISOLDE checks for high-velocity atoms every 10 time steps (5 times per coordinate update that you see) and if it sees one automatically triggers a brief energy minimisation followed by reinitialisation of velocities. So to get this error an atom has to experience a force so high that it flies out past the maximum possible single-precision coordinate (about 10^38 nm) within that 10 time step window. Usually the culprit is a mobile atom trapped in a badly-clashing geometry against a fixed one... as much as possible I encourage people to first run a brief simulation of the entire model before digging into the details, to relax out these potentially-problematic sites.
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From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 24 June 2022 17:35
Cc: dkuntz@uhnresearch.ca <dkuntz@uhnresearch.ca>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #7168: ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan (was: ChimeraX bug report submission)

#7168: ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan
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          Reporter:  dkuntz@…     |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------
Changes (by pett):

 * status:  new => assigned
 * reporter:  chimerax-bug-report@… => dkuntz@…
 * cc: Tom Goddard (added)
 * component:  Unassigned => Third Party
 * project:   => ChimeraX
 * platform:   => all
 * owner:  (none) => Tristan Croll


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comment:3 by Tom Goddard, 3 years ago

This seems like a deficiency of OpenMM that has come up so many times that it would be nice if it were addressed in OpenMM as a long term solution. I think that solution is that OpenMM raises an error when it generates a NaN coordinate. Instead it seems it currently just hands the NaN back as if nothing is wrong.

in reply to:  4 ; comment:4 by Tristan Croll, 3 years ago 

That error is actually thrown by OpenMM - ISOLDE just isn't catching it gracefully at the moment.
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From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: 24 June 2022 19:11
Cc: dkuntz@uhnresearch.ca <dkuntz@uhnresearch.ca>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; Tristan Croll <tic20@cam.ac.uk>
Subject: Re: [ChimeraX] #7168: ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan

#7168: ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan
----------------------------------+---------------------------
          Reporter:  dkuntz@…     |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by Tom Goddard):

 This seems like a deficiency of OpenMM that has come up so many times that
 it would be nice if it were addressed in OpenMM as a long term solution.
 I think that solution is that OpenMM raises an error when it generates a
 NaN coordinate.  Instead it seems it currently just hands the NaN back as
 if nothing is wrong.

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Ticket URL: <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.rbvi.ucsf.edu%2Ftrac%2FChimeraX%2Fticket%2F7168%23comment%3A3&amp;data=05%7C01%7Ctic20%40universityofcambridgecloud.onmicrosoft.com%7Cb9406d5d63f54fbcf99708da560cfd81%7C49a50445bdfa4b79ade3547b4f3986e9%7C0%7C0%7C637916911045765879%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&amp;sdata=fej%2FbIC1xOC9x6MtCYZwY1zrfUm75y0mXB5QLyQ2F6M%3D&amp;reserved=0>
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in reply to:  5 ; comment:5 by Doug.Kuntz@…, 3 years ago 

Thanks for looking into this. I have just taken to saving much more frequently since this has happened relatively often.
Have a great weekend.

Doug
________________________________
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
Sent: Friday, June 24, 2022 2:11 PM
Cc: Kuntz, Doug <Doug.Kuntz@uhnresearch.ca>; goddard@cgl.ucsf.edu <goddard@cgl.ucsf.edu>; tic20@cam.ac.uk <tic20@cam.ac.uk>
Subject: [External] Re: [ChimeraX] #7168: ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan

#7168: ISOLDE/OpenMM: fitting Ramachandran outliers: Particle coordinate is nan
----------------------------------+---------------------------
          Reporter:  dkuntz@…     |      Owner:  Tristan Croll
              Type:  defect       |     Status:  assigned
          Priority:  normal       |  Milestone:
         Component:  Third Party  |    Version:
        Resolution:               |   Keywords:
        Blocked By:               |   Blocking:
Notify when closed:               |   Platform:  all
           Project:  ChimeraX     |
----------------------------------+---------------------------

Comment (by Tom Goddard):

 This seems like a deficiency of OpenMM that has come up so many times that
 it would be nice if it were addressed in OpenMM as a long term solution.
 I think that solution is that OpenMM raises an error when it generates a
 NaN coordinate.  Instead it seems it currently just hands the NaN back as
 if nothing is wrong.

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comment:6 by Tristan Croll, 3 years ago

Resolution: → fixed
Status: assigned → closed

This should become *almost* impossible in ISOLDE 1.6 (when it comes out) - it now uses soft-core nonbonded potentials which remove the singularities (~infinite forces) when the distance between two atoms goes to zero. Probably still technically possible to trigger, but you'd have to try *really* hard.

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