Opened 22 months ago

Closed 22 months ago

#10426 closed defect (fixed)

ISOLDE: Particle coordinate is nan

Reported by: chimerax-bug-report@… Owned by: Tristan Croll
Priority: normal Milestone:
Component: Third Party Version:
Keywords: Cc:
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: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  
Successfully installed
'ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl'  
Looking in indexes: https://pypi.org/simple,
https://cxtoolshed.rbvi.ucsf.edu/pypi/  
Processing
/Users/eta/Library/Caches/ChimeraX/1.2/installers/ChimeraX_ISOLDE-1.2.2-cp38-cp38-macosx_10_13_x86_64.whl  
Requirement already satisfied: ChimeraX-Arrays~=1.0.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-Core~=1.2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (1.2.5)  
Requirement already satisfied: ChimeraX-Clipper~=0.16.0 in
/Users/eta/Library/Application Support/ChimeraX/1.2/site-packages (from
ChimeraX-ISOLDE==1.2.2) (0.16.1)  
Requirement already satisfied: ChimeraX-AtomicLibrary~=3.1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (3.1.3)  
Requirement already satisfied: ChimeraX-Atomic~=1.13.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ISOLDE==1.2.2) (1.13.2)  
Requirement already satisfied: ChimeraX-Nucleotides~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0.1)  
Requirement already satisfied: ChimeraX-PDB~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.4.1)  
Requirement already satisfied: ChimeraX-ConnectStructure~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Geometry~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-Graphics~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-mmCIF~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.3)  
Requirement already satisfied: ChimeraX-AtomSearchLibrary~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-ConnectStructure~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-PDBLibrary~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0.1)  
Requirement already satisfied: ChimeraX-OpenCommand~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.5)  
Requirement already satisfied: ChimeraX-SaveCommand~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.4)  
Requirement already satisfied: ChimeraX-DataFormats~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-mmCIF~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-IO~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-DataFormats~=1.0->ChimeraX-mmCIF~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.1)  
Requirement already satisfied: ChimeraX-UI~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.7.6)  
Requirement already satisfied: ChimeraX-Surface~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (1.0)  
Requirement already satisfied: ChimeraX-Map~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.0.2)  
Requirement already satisfied: ChimeraX-MapData~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-StdCommands~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-
Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.3.1)  
Requirement already satisfied: ChimeraX-MapFilter~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MapSeries~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-MouseModes~=1.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-Map~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (1.1)  
Requirement already satisfied: ChimeraX-MapFit~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-MapSeries~=2.0->ChimeraX-Map~=1.0->ChimeraX-
Surface~=1.0->ChimeraX-Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-
ISOLDE==1.2.2) (2.0)  
Requirement already satisfied: ChimeraX-Dssp~=2.0 in
/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages (from ChimeraX-StdCommands~=1.0->ChimeraX-Surface~=1.0->ChimeraX-
Nucleotides~=2.0->ChimeraX-Atomic~=1.13.0->ChimeraX-ISOLDE==1.2.2) (2.0)  
ChimeraX-ISOLDE is already installed with the same version as the provided
wheel. Use --force-reinstall to force an installation of the wheel.  
  

WARNING: You are using pip version 21.0.1; however, version 23.3.2 is
available.  
You should consider upgrading via the
'/Applications/ChimeraX-1.2.5.app/Contents/MacOS/ChimeraX -m pip install
--upgrade pip' command.  
  

> open "/Users/eta/Library/Application Support/ChimeraX/1.2/site-
> packages/chimerax/isolde/demo_data/3io0/before.pdb" format pdb

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  

> open "/Users/eta/Dropbox (Graduate
> Center)/Gardne_Lab/DS/phyR/amx23115/A4e/phenix/Refine_10/PhyR_DS_refine_10.mtz"
> "/Users/eta/Dropbox (Graduate
> Center)/Gardne_Lab/DS/phyR/amx23115/A4e/phenix/Refine_10/PhyR_DS_refine_10.pdb"

Must specify a structure model to associate with crystallographic data  

> close session

> open "/Users/eta/Dropbox (Graduate
> Center)/Gardne_Lab/DS/phyR/amx23115/A4e/phenix/Refine_10/PhyR_DS_refine_10.pdb"

Chain information for PhyR_DS_refine_10.pdb #1  
---  
Chain | Description  
A C D | No description available  
B | No description available  
  

> open "/Users/eta/Dropbox (Graduate
> Center)/Gardne_Lab/DS/phyR/amx23115/A4e/phenix/Refine_10/PhyR_DS_refine_10.mtz"

Must specify a structure model to associate with crystallographic data  

> isolde start

> set selectionWidth 4

Chain information for PhyR_DS_refine_10.pdb  
---  
Chain | Description  
1.2/A 1.2/C 1.2/D | No description available  
1.2/B | No description available  
  
Done loading forcefield  
Opened (LIVE) 2mFo-DFc as #1.1.1.2, grid size 46,36,36, pixel
0.668,0.692,0.681, shown at level 0.281, step 1, values float32  
Opened (LIVE) mFo-DFc as #1.1.1.3, grid size 46,36,36, pixel
0.668,0.692,0.681, shown at level -0.113,0.113, step 1, values float32  
Opened (LIVE) 2mFo-DFc_sharp_23 as #1.1.1.4, grid size 46,36,36, pixel
0.668,0.692,0.681, shown at level 0.575, step 1, values float32  
Opened (STATIC) (Model-structure-factors-(all-solvent-and-scales-included))
F-model, PHIF-model as #1.1.1.5, grid size 46,36,36, pixel 0.668,0.692,0.681,
shown at level -0.473,0.473, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT, PH2FOFCWT as #1.1.1.6,
grid size 46,36,36, pixel 0.668,0.692,0.681, shown at level 0.258, step 1,
values float32  
Opened (STATIC) (Fourier-map-coefficients) 2FOFCWT_no_fill, PH2FOFCWT_no_fill
as #1.1.1.7, grid size 46,36,36, pixel 0.668,0.692,0.681, shown at level
0.238, step 1, values float32  
Opened (STATIC) (Fourier-map-coefficients) FOFCWT, PHFOFCWT as #1.1.1.8, grid
size 46,36,36, pixel 0.668,0.692,0.681, shown at level -0.205,0.205, step 1,
values float32  
Opened (LIVE) MDFF potential as #1.1.1.9, grid size 46,36,36, pixel
0.668,0.692,0.681, shown at level 0.307, step 1, values float32  

> isolde set

> set bgColor grey

> ui mousemode right zoom

> isolde start

> addh

Summary of feedback from adding hydrogens to PhyR_DS_refine_10.pdb #1.2  
---  
warning | Not adding hydrogens to /A PHE 174 CB because it is missing heavy-
atom bond partners  
notes | No usable SEQRES records for PhyR_DS_refine_10.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for PhyR_DS_refine_10.pdb (#1.2) chain B; guessing
termini instead  
No usable SEQRES records for PhyR_DS_refine_10.pdb (#1.2) chain C; guessing
termini instead  
No usable SEQRES records for PhyR_DS_refine_10.pdb (#1.2) chain D; guessing
termini instead  
Chain-initial residues that are actual N termini: /A ALA 10, /B ALA 7, /C ALA
10, /D ALA 10  
Chain-initial residues that are not actual N termini: /A GLU 53, /A LEU 91, /A
ASN 205, /B GLU 53, /B LEU 91, /B ASN 205, /C GLU 53, /C LEU 91, /C ASN 205,
/D GLU 53, /D LEU 91, /D ASN 205  
Chain-final residues that are actual C termini:  
Chain-final residues that are not actual C termini: /A ALA 258, /A ALA 43, /A
ARG 67, /A ILE 192, /B ALA 258, /B ALA 43, /B ARG 67, /B ILE 192, /C ALA 258,
/C ALA 43, /C ARG 67, /C ILE 192, /D ALA 258, /D ALA 43, /D ARG 67, /D ILE 192  
997 hydrogen bonds  
Adding 'H' to /A GLU 53  
Adding 'H' to /A LEU 91  
Adding 'H' to /A ASN 205  
Adding 'H' to /B GLU 53  
Adding 'H' to /B LEU 91  
7 messages similar to the above omitted  
/A ALA 258 is not terminus, removing H atom from 'C'  
/B ALA 258 is not terminus, removing H atom from 'C'  
/C ALA 258 is not terminus, removing H atom from 'C'  
/D ALA 258 is not terminus, removing H atom from 'C'  
6886 hydrogens added  
  

> ui mousemode right tug

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 34 (ALA). The set of atoms matches ALA, but the
bonds are different.  
Error with ignoreExternalBonds=True was  
No template found for residue 133 (PHE). The set of atoms is similar to ALA,
but it is missing 3 hydrogen atoms.  

> select clear

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 34 (ALA). The set of atoms matches ALA, but the
bonds are different.  
Error with ignoreExternalBonds=True was  
No template found for residue 133 (PHE). The set of atoms is similar to ALA,
but it is missing 3 hydrogen atoms.  

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 34 (ALA). The set of atoms matches ALA, but the
bonds are different.  
Error with ignoreExternalBonds=True was  
No template found for residue 133 (PHE). The set of atoms is similar to ALA,
but it is missing 3 hydrogen atoms.  

> ui mousemode right tug

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 34 (ALA). The set of atoms matches ALA, but the
bonds are different.  
Error with ignoreExternalBonds=True was  
No template found for residue 133 (PHE). The set of atoms is similar to ALA,
but it is missing 3 hydrogen atoms.  

Missing atoms or parameterization needed by force field.  
All heavy atoms and hydrogens with standard names are required.  
  
Error with ignoreExternalBonds=False was  
No template found for residue 34 (ALA). The set of atoms matches ALA, but the
bonds are different.  
Error with ignoreExternalBonds=True was  
No template found for residue 133 (PHE). The set of atoms is similar to ALA,
but it is missing 3 hydrogen atoms.  

> isolde start

> isolde sim

Missing or invalid "cmd" argument: Expected one of 'checkpoint', 'pause',
'revert', 'start', or 'stop'  

> isolde sim start

Map is too large for fast cubic interpolation on the GPU! Switching to slower,
more memory-efficient implementation.  

Populating font family aliases took 230 ms. Replace uses of missing font
family "Carlito" with one that exists to avoid this cost.  

ISOLDE: started sim  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/triggerset.py", line 130, in invoke  
return self._func(self._name, data)  
File "/Users/eta/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/delayed_reaction.py", line 81, in callback  
self.ff(*self.ff_args)  
File "/Users/eta/Library/Application Support/ChimeraX/1.2/site-
packages/chimerax/isolde/openmm/openmm_interface.py", line 1673, in
_update_coordinates_and_repeat  
self.atoms.coords = th.coords  
File "/Users/eta/Library/Application Support/ChimeraX/1.2/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 "/Users/eta/Library/Application Support/ChimeraX/1.2/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 - 83.1
OpenGL renderer: Apple M2
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: Mac
      Model Identifier: Mac14,2
      Model Number: Z160000B7LL/A
      Chip: Unknown
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 8422.141.2
      OS Loader Version: 8422.141.2

Software:

    System Software Overview:

      System Version: macOS 13.5 (22G74)
      Kernel Version: Darwin 22.6.0
      Time since boot: 2 days, 21 hours, 26 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 8
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina Display
          Resolution: 2560 x 1664 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, '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: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.1
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2.1
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    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: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.1
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 23.3.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by pett, 22 months ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → ISOLDE: Particle coordinate is nan

Reporter provided the name "Eta Isiorho" but no email address.

comment:2 by Tristan Croll, 22 months ago

Resolution: → fixed
Status: assigned → closed

Ancient version. That sort of explosion should be *almost* impossible in current ISOLDE versions.

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