Opened 3 years ago

Last modified 3 years ago

#7603 assigned defect

Problems opening MTX file

Reported by: kmanne@… 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:        Linux-3.10.0-1160.31.1.el7.x86_64-x86_64-with-redhat-7.9-Maipo
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/Refine_10/TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb

Chain information for TSLP_46640_AMG7p8_ALS502_20220902_refine_10.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> set bgColor white

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz
> structure#1

'structure#1' has no suffix  

> open
> /home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz
> structureModel #1

Summary of feedback from opening
/home/kmanne/Documents/TSLP/TSLP+46640/ALS_502_20220902/XDS_AMG7p8_1/pointless.mtz  
---  
notes | Discarding unrecognised/unsupported data array
/HKL_base/HKL_base/M_ISYM Y  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/BATCH B  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/FRACTIONCALC
R  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/XDET R  
Discarding unrecognised/unsupported data array /HKL_base/HKL_base/YDET R  
2 messages similar to the above omitted  
Reflection data provided as intensities. Performing French & Wilson scaling to
convert to amplitudes...  
Failed on HKL = ( -30, 0, 1)  
N_bins: 60 Imean: -0.2748146101960023 I: -16.93000030517578 sigI:
29.34000015258789 eobs_sq: 30.802584136813227 sig_eobs_sq: -53.38144164107964  
  
Traceback (most recent call last):  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 275, in execute  
cmd.run(cmd_text)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "/home/kmanne/Documents/Software/chimerax-1.1/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/__init__.py", line 228, in open  
return open_structure_factors(session, data, **kw)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/cmd.py", line 32, in open_structure_factors  
xmapset = mmgr.add_xmapset_from_file(path, oversampling_rate=over_sampling)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/map_mgr.py", line 306, in add_xmapset_from_file  
return XmapSet(self, mtzdata)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 189, in __init__  
fill_with_fcalc, exclude_missing_reflections)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/maps/xmapset.py", line 245, in init_maps  
fsigf_data = french_wilson_analytical(fsigf.data)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 110, in
french_wilson_analytical  
e_xpct = _expected_E_FW_cen(eobs_sq, sig_eobs_sq)  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
ValueError: math domain error  
  
ValueError: math domain error  
  
File "/home/kmanne/.local/share/ChimeraX/1.1/site-
packages/chimerax/clipper/reflection_tools/french_wilson.py", line 281, in
_expected_E_FW_cen  
e_xpct = sqrt(sig_eobs_sq /pi)*pcd_ratio  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 390.143
OpenGL renderer: Quadro 5000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Hewlett-Packard
Model: HP Z600 Workstation
OS: Red Hat Enterprise Linux Workstation 7.9 Maipo
Architecture: 64bit ELF
CPU: 8 Intel(R) Xeon(R) CPU           E5640  @ 2.67GHz
Cache Size: 12288 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:            15G        7.9G        1.2G        290M        6.5G        7.0G
	Swap:          7.9G        558M        7.3G

Graphics:
	0f:00.0 VGA compatible controller [0300]: NVIDIA Corporation GF100GL [Quadro 5000] [10de:06d9] (rev a3)	
	Subsystem: Hewlett-Packard Company Device [103c:0770]	
	Kernel driver in use: nvidia
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
    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
    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-LinuxSupport: 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-Phenix: 0.3
    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
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    distro: 1.5.0
    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: 0.16
    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
    MolecularDynamicsViewer: 1.1
    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
    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
    psutil: 5.7.0
    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
    Send2Trash: 1.8.0
    SEQCROW: 0.25.2
    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
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Third Party
Owner: set to Tristan Croll
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Problems opening MTX file

Reported by Kartik Manne

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

First thing: you should *definitely* update to ChimeraX and ISOLDE 1.4. A
huge number of changes and improvements since 1.1. That being said, in 1.4
you’ll probably still hit that error IF your MTZ doesn’t also contain
F/sigF data. The failure happens in French&Wilson conversion from I/sigI to
F/sigF if there is a resolution band where the average |F| drops below zero
(i.e. your data is *really* weak at your resolution cutoff). I have to get
my head around the strategies used to address this scenario, but in the
meantime the best workaround is to use e.g. Phenix to make the conversion
first.

On Thu, 15 Sep 2022 at 13:40, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:
Note: See TracTickets for help on using tickets.