Opened 19 months ago

Last modified 19 months ago

#14912 assigned defect

SEQCROW failure computing buried volume

Reported by: neryvillegas@… Owned by: Tony Schaefer
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:        Linux-5.15.0-91-generic-x86_64-with-glibc2.14
ChimeraX Version: 1.3.dev202105120156 (2021-05-12 01:56:35 UTC)
Description
I followed very carefully the SQROW tutorial but it failed when computing the Buried Volume

Log:
UCSF ChimeraX version: 1.3.dev202105120156 (2021-05-12)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /media/nery/5835F55C23BF5A65/research/rene/PAPER_2/rene/one_comp_mechanism/b3lyp/I/I.log

Opened I.log as a Gaussian output file  

> ui mousemode right "select fragment"

> ui tool show "Buried Volume"

> select clear

Traceback (most recent call last):  
File "/home/nery/.local/share/ChimeraX/1.3/site-
packages/SEQCROW/tools/percent_Vbur.py", line 651, in calc_vbur  
info = percent_vbur_cmd(  
File "/home/nery/.local/share/ChimeraX/1.3/site-
packages/SEQCROW/commands/percent_Vbur.py", line 187, in percent_vbur  
x, y, z, min_alt, max_alt, basis, _ = rescol.steric_map(  
File "/home/nery/.local/share/ChimeraX/1.3/site-
packages/AaronTools/geometry.py", line 2885, in steric_map  
w[pt_in_shape] = (xs - atom_coords[k][0]) ** 2 + (ys - atom_coords[k][1]) ** 2  
TypeError: NumPy boolean array indexing assignment requires a 0 or
1-dimensional input, input has 2 dimensions  
  
TypeError: NumPy boolean array indexing assignment requires a 0 or
1-dimensional input, input has 2 dimensions  
  
File "/home/nery/.local/share/ChimeraX/1.3/site-
packages/AaronTools/geometry.py", line 2885, in steric_map  
w[pt_in_shape] = (xs - atom_coords[k][0]) ** 2 + (ys - atom_coords[k][1]) ** 2  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 190, in <lambda>  
sb.clicked.connect(lambda e: self.submit())  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
fields.extend(file_list)  
TypeError: 'NoneType' object is not iterable  
  
TypeError: 'NoneType' object is not iterable  
  
File "/usr/lib/ucsf-chimerax-daily/lib/python3.8/site-
packages/chimerax/bug_reporter/bug_reporter_gui.py", line 237, in submit  
fields.extend(file_list)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 21.2.6
OpenGL renderer: Mesa Intel(R) UHD Graphics 630 (CFL GT2)
OpenGL vendor: Intel
Manufacturer: System manufacturer
Model: System Product Name
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 6 Intel(R) Core(TM) i5-9600K CPU @ 3.70GHz
Cache Size: 9216 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi        10Gi       1.2Gi       1.5Gi       3.6Gi       3.0Gi
	Swap:         2.0Gi       2.0Gi        17Mi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation UHD Graphics 630 (Desktop 9 Series) [8086:3e98] (rev 02)	
	DeviceName: Onboard - Video	
	Subsystem: ASUSTeK Computer Inc. UHD Graphics 630 (Desktop 9 Series) [1043:8694]
Locale: ('en_US', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 4.0.0
    ChimeraX-AddCharge: 1.1.1
    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: 1.19
    ChimeraX-AtomicLibrary: 3.2.1
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.3
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3.dev202105120156
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.2.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    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
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    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: 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: 1.1
    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-SelInspector: 1.0
    ChimeraX-SeqView: 2.4
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.5
    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: 1.9.2
    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: 0.4.4
    comtypes: 1.1.10
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.23
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.20
    imagecodecs: 2021.4.28
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.3
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 1.1.1
    matplotlib: 3.4.2
    msgpack: 1.0.2
    netCDF4: 1.5.6
    networkx: 2.5.1
    numexpr: 2.7.3
    numpy: 1.20.3
    numpydoc: 1.1.0
    openvr: 1.16.801
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.2.0
    pip: 21.1.1
    pkginfo: 1.7.0
    prompt-toolkit: 3.0.18
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.9.0
    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: 2.25.1
    scipy: 1.6.3
    Send2Trash: 1.5.0
    SEQCROW: 1.5.10
    setuptools: 56.2.0
    sfftk-rw: 0.6.7.dev1
    six: 1.16.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.3.0
    Sphinx: 4.0.1
    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: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.26.4
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.2
    wheel-filename: 1.3.0
File attachment: double_AlI.log

double_AlI.log​

Attachments (1)

double_AlI.log​ (6.5 MB ) - added by neryvillegas@… 19 months ago.
Added by email2trac

Change History (3)

by neryvillegas@…, 19 months ago

Attachment: double_AlI.log​ added

Added by email2trac

comment:1 by Eric Pettersen, 19 months ago

Cc: Tom Goddard added
Component: Unassigned → Third Party
Owner: set to Tony Schaefer
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → SEQCROW failure computing buried volume

Report by Nery Villegas using pre-1.3 ChimeraX

Also, failure in bug-reporter GUI.

comment:2 by Tony Schaefer, 19 months ago 

Nery,

It looks like there's a bug calculating steric maps with a square shape.
Are you able to calculate steric maps with a circle shape?

Note, I will be able to fix this, but the updated version of SEQCROW will
not be compatible with your version of ChimeraX. Please install at least
the full release of ChimeraX 1.3

Best,

Tony

On Mon, Apr 8, 2024 at 11:30 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

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