ISOLDE: various errors

[mks131@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/ubcg90c/Downloads/6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb

Chain information for 6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb
#1  
---  
Chain | Description  
A E | No description available  
B | No description available  
C G | No description available  
D H | No description available  
F | No description available  
I | No description available  
J | No description available  
  

> open /Users/ubcg90c/Downloads/P208_J2708_07_new.mrc

Opened P208_J2708_07_new.mrc, grid size 286,286,286, pixel 1.3, shown at level
0.182, step 2, values float32  

> ui tool show ISOLDE

> set selectionWidth 4

Chain information for 6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb  
---  
Chain | Description  
1.2/A 1.2/E | No description available  
1.2/B | No description available  
1.2/C 1.2/G | No description available  
1.2/D 1.2/H | No description available  
1.2/F | No description available  
1.2/I | No description available  
1.2/J | No description available  
  
Done loading forcefield  

> addh

Summary of feedback from adding hydrogens to
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb #1.2  
---  
warning | Not adding hydrogens to /J DC -71 P because it is missing heavy-atom
bond partners  
notes | No usable SEQRES records for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb (#1.2) chain A;
guessing termini instead  
No usable SEQRES records for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb (#1.2) chain B;
guessing termini instead  
No usable SEQRES records for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb (#1.2) chain C;
guessing termini instead  
No usable SEQRES records for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb (#1.2) chain D;
guessing termini instead  
No usable SEQRES records for
6ipu_align_Lin28b_extraDNAbuild_relativealign_J2708.pdb (#1.2) chain E;
guessing termini instead  
5 messages similar to the above omitted  
Chain-initial residues that are actual N termini: /A PRO 38, /B VAL 21, /C LYS
13, /D ARG 28, /E PRO 38, /F LYS 16, /G LYS 13, /H ARG 28, /I DA -72, /J DC
-71  
Chain-initial residues that are not actual N termini:  
Chain-final residues that are actual C termini: /A ALA 135, /B GLY 102, /D LYS
122, /F GLY 102, /H LYS 122, /I DG 71, /J DT 72  
Chain-final residues that are not actual C termini: /C LYS 119, /E ALA 135, /G
LYS 119  
1147 hydrogen bonds  
/C LYS 119 is not terminus, removing H atom from 'C'  
/E ALA 135 is not terminus, removing H atom from 'C'  
/G LYS 119 is not terminus, removing H atom from 'C'  
9742 hydrogens added  
  

> volume #1.1.1.1 level 0.4202

> volume #1.1.1.1 step 2

> volume #1.1.1.1 level 0.2826

> volume #1.1.1.1 step 1

Traceback (most recent call last):  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2569, in _xtal_step_backward  
self._xtal_mask_to_atoms(sel, focus=False)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2589, in _xtal_mask_to_atoms  
atoms, 0, context, cutoff, focus=focus)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/symmetry.py", line 982, in
isolate_and_cover_selection  
extra_padding=extra_padding)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 364, in cover_atoms  
zm.set_symmetry_map(atoms, transforms, transform_indices)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 119, in set_symmetry_map  
self.structure = self._unique_structure(atoms)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
TypeError: All atoms for zone mask must be from a single model!  
  
TypeError: All atoms for zone mask must be from a single model!  
  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/mask_handler.py", line 185, in
_unique_structure  
raise TypeError('All atoms for zone mask must be from a single model!')  
  
See log for complete Python traceback.  
  

> volume #1.1.1.1 level 0.06974

Traceback (most recent call last):  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2552, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2552, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2552, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  

> volume style surface

> volume show

> ui tool show "Volume Viewer"

> view #!1.2 clip false

> ui tool show ISOLDE

> set selectionWidth 4

Done loading forcefield  
Traceback (most recent call last):  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/isolde/isolde.py", line 2552, in _xtal_step_forward  
sel = sh.stepper.step_forward()  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 71, in step_forward  
return self._step(direction=self.FORWARD)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 81, in _step  
return self._step_generic(direction)  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
IndexError: index -5 is out of bounds for axis 0 with size 0  
  
File "/Users/ubcg90c/Library/Application Support/ChimeraX/1.1/site-
packages/chimerax/clipper/structurestepper.py", line 104, in _step_generic  
first_index = indices[-overlap]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-3.10.23
OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine
OpenGL vendor: ATI Technologies Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,1
      Processor Name: 8-Core Intel Core i9
      Processor Speed: 2.3 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache: 16 MB
      Hyper-Threading Technology: Enabled
      Memory: 32 GB
      Boot ROM Version: 1715.81.2.0.0 (iBridge: 19.16.10744.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.7 (19H1713)
      Kernel Version: Darwin 19.6.0
      Time since boot: 11 days 11:24

Graphics/Displays:

    Intel UHD Graphics 630:

      Chipset Model: Intel UHD Graphics 630
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3e9b
      Revision ID: 0x0002
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1

    AMD Radeon Pro 5500M:

      Chipset Model: AMD Radeon Pro 5500M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x8
      VRAM (Total): 4 GB
      Vendor: AMD (0x1002)
      Device ID: 0x7340
      Revision ID: 0x0040
      ROM Revision: 113-D3220E-190
      VBIOS Version: 113-D32206U1-019
      Option ROM Version: 113-D32206U1-019
      EFI Driver Version: 01.A1.190
      Automatic Graphics Switching: Supported
      gMux Version: 5.0.0
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 3072 x 1920 Retina
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.0
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-Clipper: 0.15.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    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: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-ISOLDE: 1.1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    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: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    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
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    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
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    ptyprocess: 0.6.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    versioneer: 0.20
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

[Eric Pettersen]

Reported by "Manoj"

[Tristan Croll]

The version you're working with is very old. Could you try updating to ChimeraX 1.3 and ISOLDE 1.3 and see if the problem persists?

[Tristan Croll]

Going to tentatively close this as fixed - haven't seen another instance of it reported.