Opened 7 months ago

Closed 7 months ago

#17098 closed defect (nonchimerax)

XPLOR file: Bad number format

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.8.0-52-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7.1 (2024-01-23)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/yashaswini/Desktop/density_map/random_ligand-grid2.xplor

Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 170, in read_float_lines  
values = [float(x) for x in fields]  
^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 170, in <listcomp>  
values = [float(x) for x in fields]  
^^^^^^^^  
ValueError: could not convert string to float: b'0 2366.0000'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/__main__.py", line 885, in init  
commands.run(sess, 'open %s' % StringArg.unparse(arg))  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 131, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2908, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 213, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 513, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 484, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/__init__.py", line 182, in open  
return open_map(session, path, format=_name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3621, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 3723, in open_grids  
v.update_drawings()  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 802, in update_drawings  
levels, colors = self.initial_surface_levels()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 603, in initial_surface_levels  
mstats = self.matrix_value_statistics()  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1734, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1769, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1252, in matrix  
m = self.region_matrix(r, read_matrix)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map/volume.py", line 1276, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/griddata.py", line 317, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/xplor/xplor_grid.py", line 40, in read_matrix  
matrix = self.density_map.matrix(progress)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/xplor/xplor_format.py", line 102, in matrix  
read_float_lines(f, data[c,:,:], line_format = (12,6))  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 173, in read_float_lines  
raise SyntaxError(msg)  
SyntaxError: Bad number format in
/home/yashaswini/Desktop/density_map/random_ligand-grid2.xplor, line  
b'358760.000001066668.00000940180.00000110218.00000 2366.00000 0.00000\n'  
  
SyntaxError: Bad number format in
/home/yashaswini/Desktop/density_map/random_ligand-grid2.xplor, line  
b'358760.000001066668.00000940180.00000110218.00000 2366.00000 0.00000\n'  
  
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/map_data/readarray.py", line 173, in read_float_lines  
raise SyntaxError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.3
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: Dell Inc.
Model: Inspiron 5406 2n1
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 11th Gen Intel(R) Core(TM) i7-1165G7 @ 2.80GHz
Cache Size: 12288 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:            15Gi        13Gi       315Mi       680Mi       1.5Gi       778Mi
	Swap:          232Gi        52Gi       180Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	DeviceName: Onboard - Video	
	Subsystem: Dell TigerLake-LP GT2 [Iris Xe Graphics] [1028:0a05]

Installed Packages:
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    appdirs: 1.4.4
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    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.2
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
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    ChimeraX-BlastProtein: 2.1.2
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    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
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    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
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    ChimeraX-Clipper: 0.22.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.1
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
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    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.7.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-LinuxSupport: 1.0.1
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6.1
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.14
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.3
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.1
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    distro: 1.7.0
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.2
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
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    Jinja2: 3.1.2
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    packaging: 23.2
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    parso: 0.8.3
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    pip: 23.0
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    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
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    pyopenxr: 1.0.2801
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    wcwidth: 0.2.13
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    wheel: 0.38.4
    wheel-filename: 1.4.1
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Change History (2)

comment:1 by Eric Pettersen, 7 months ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → XPLOR file: Bad number format

comment:2 by Tom Goddard, 7 months ago

Resolution: → nonchimerax
Status: assigned → closed

Bad input file. Has no spaces between some of the numbers.

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