Opened 3 years ago
Last modified 3 years ago
#7603 assigned defect
Problems opening MTX file
Reported by: | 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 , 3 years ago
Component: | Unassigned → Third Party |
---|---|
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Problems opening MTX file |
follow-up: 2 comment:2 by , 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:
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Reported by Kartik Manne