Truncated APBS *.dx file

[minghao.chen@…]

The following bug report has been submitted:
Platform:        macOS-10.14.6-x86_64-i386-64bit
ChimeraX Version: 1.2.5 (2021-05-24 04:13:57 UTC)
Description
An error happened when I loaded a .dx file prepared by APBS.
I did the same thing on my colleague's computer but it worked fine. 

Thank you for your help.
Best regards,

Log:
UCSF ChimeraX version: 1.2.5 (2021-05-24)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 2ff6 format mmcif fromDatabase pdb

2ff6 title:  
Crystal structure of Gelsolin domain 1:ciboulot domain 2 hybrid in complex
with actin [more info...]  
  
Chain information for 2ff6 #1  
---  
Chain | Description  
A | Actin, α skeletal muscle  
G | Gelsolin  
H | CG4944-PC, isoform C  
  
Non-standard residues in 2ff6 #1  
---  
ATP — adenosine-5'-triphosphate  
CA — calcium ion  
  

> open /Users/mchen/Downloads/4gj03b8qjs-pot.dx

Traceback (most recent call last):  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 261, in event  
_open_dropped_file(self.session, event.file())  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/ui/gui.py", line 1812, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/core/commands/cli.py", line 2852, in run  
result = ci.function(session, **kw_args)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 166, in provider_open  
models, status = collated_open(session, None, paths, data_format, _add_models,
log_errors,  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/open_command/cmd.py", line 421, in collated_open  
return func(*func_args, **func_kw)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/__init__.py", line 148, in open  
return open_map(session, path, format=_name, **kw)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 3589, in open_map  
smodels, smsg = open_grids(session, sgrids, name, **kw)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 3683, in open_grids  
v.update_drawings()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 777, in update_drawings  
levels, colors = self.initial_surface_levels()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 578, in initial_surface_levels  
mstats = self.matrix_value_statistics()  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 1708, in matrix_value_statistics  
matrices = self.displayed_matrices(read_matrix)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 1743, in displayed_matrices  
matrices.append(self.matrix(read_matrix))  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 1228, in matrix  
m = self.region_matrix(r, read_matrix)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map/volume.py", line 1252, in region_matrix  
m = d.matrix(origin, size, step, progress, from_cache_only)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/griddata.py", line 302, in matrix  
m = self.read_matrix(ijk_origin, ijk_size, ijk_step, progress)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/apbs/apbs_grid.py", line 39, in read_matrix  
matrix = self.apbs_data.matrix(progress)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/apbs/apbs_format.py", line 124, in matrix  
data = read_text_floats(self.path, self.data_offset, self.grid_size,  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/readarray.py", line 121, in read_text_floats  
read_float_lines(f, array, line_format, progress)  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/readarray.py", line 149, in read_float_lines  
raise SyntaxError(msg)  
File "<string>", line None  
SyntaxError: Too few data values in /Users/mchen/Downloads/4gj03b8qjs-pot.dx,
found 4662590, expecting 5002753  
  
File "", line None  
SyntaxError: Too few data values in /Users/mchen/Downloads/4gj03b8qjs-pot.dx,
found 4662590, expecting 5002753  
  
File
"/Volumes/ChimeraXInstaller/ChimeraX-1.2.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/site-
packages/chimerax/map_data/readarray.py", line 149, in read_float_lines  
raise SyntaxError(msg)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 NVIDIA-12.0.24 355.11.10.50.10.103
OpenGL renderer: NVIDIA GeForce GTX 780M OpenGL Engine
OpenGL vendor: NVIDIA CorporationHardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac14,2
      Processor Name: Intel Core i7
      Processor Speed: 3.5 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 8 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 430.0.0.0.0
      SMC Version (system): 2.15f7

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G8022)
      Kernel Version: Darwin 18.7.0
      Time since boot: 20 minutes

Graphics/Displays:

    NVIDIA GeForce GTX 780M:

      Chipset Model: NVIDIA GeForce GTX 780M
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 4 GB
      Vendor: NVIDIA (0x10de)
      Device ID: 0x119e
      Revision ID: 0x00a2
      ROM Revision: 3782
      Metal: Supported, feature set macOS GPUFamily1 v4
      Displays:
        iMac:
          Display Type: LCD
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort
        EV2416W:
          Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array)
          UI Looks like: 1920 x 1200
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Display Serial Number: 74898044
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.5.0
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0.1
    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: 1.13.2
    ChimeraX-AtomicLibrary: 3.1.3
    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: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.5
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.3
    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: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    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: 1.2.1
    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: 1.0.1
    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-SeqView: 2.3
    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: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    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: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.6
    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: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.9
    distlib: 0.3.1
    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: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 2.0.1
    matplotlib: 3.3.2
    matplotlib-inline: 0.1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    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: 2.24.0
    scipy: 1.5.2
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
File attachment: IMG_9180.HEIC

IMG_9180.HEIC​

[minghao.chen@…]

Added by email2trac

[Tom Goddard]

The error message says

SyntaxError: Too few data values in /Users/mchen/Downloads/4gj03b8qjs-pot.dx, found 4662590, expecting 5002753

In other words the file is truncated or corrupted in some other way. I suggest you recopy the file from the other machine and verify that the file is the same size after you have copied it.

[Minghao.Chen@…]

Thanks for your comment.
It seems like a bug of APBS. The ChimeraX is fine.
I’ll contact the developer of APBS.

Thanks for your helps again.

-------------------------------------------------
Dr. Minghao Chen
Max Planck Institute Molecular Physiology
Department of Structural Biochemistry
Otto Hahn Str. 11
44227 Dortmund, Germany

Tel: (+49)(231)133-2311
minghao.chen@mpi-dortmund.mpg.de<mailto:minghao.chen@mpi-dortmund.mpg.de>
-------------------------------------------------

On 8. Jun 2021, at 18:43, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#4743: DX file works on some machines but not others
-------------------------------------+-------------------------
         Reporter:  minghao.chen@…  |      Owner:  Tom Goddard
             Type:  defect          |     Status:  closed
         Priority:  normal          |  Milestone:
        Component:  Volume Data     |    Version:
       Resolution:  not a bug       |   Keywords:
       Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
          Project:  ChimeraX        |
-------------------------------------+-------------------------
Changes (by Tom Goddard):

* status:  assigned => closed
* resolution:   => not a bug


Comment:

The error message says

SyntaxError: Too few data values in /Users/mchen/Downloads/4gj03b8qjs-
pot.dx, found 4662590, expecting 5002753

In other words the file is truncated or corrupted in some other way.  I
suggest you recopy the file from the other machine and verify that the
file is the same size after you have copied it.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4743#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[goddard@…]

If APBS outputs a truncated *.dx file then it would not open in ChimeraX on one machine but not open on another machine.  That suggests the problem was in copying the file to the computer where it did not work.  I don't think it is very likely that APBS wrote a truncated file.

[Minghao.Chen@…]

Dear Mr. Goddard,

Thank you for your comment!
I found this problem is dependent on the pdb. For in stance, I had the same problem with 2ff6, 4pkh, and 4z94, but APBS/Chimera works properly with 7nzk.

Enclosed please find the error .dx file, which was generated from 4z94 via the APBS online server.

Best regards,

Minghao
-------------------------------------------------
Dr. Minghao Chen
Max Planck Institute Molecular Physiology
Department of Structural Biochemistry
Otto Hahn Str. 11
44227 Dortmund, Germany

Tel: (+49)(231)133-2311
minghao.chen@mpi-dortmund.mpg.de<mailto:minghao.chen@mpi-dortmund.mpg.de>
-------------------------------------------------

On 10. Jun 2021, at 18:42, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#4743: DX file works on some machines but not others
-------------------------------------+-------------------------
         Reporter:  minghao.chen@…  |      Owner:  Tom Goddard
             Type:  defect          |     Status:  closed
         Priority:  normal          |  Milestone:
        Component:  Volume Data     |    Version:
       Resolution:  not a bug       |   Keywords:
       Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
          Project:  ChimeraX        |
-------------------------------------+-------------------------

Comment (by goddard@…):

{{{
If APBS outputs a truncated *.dx file then it would not open in ChimeraX
on one machine but not open on another machine.  That suggests the problem
was in copying the file to the computer where it did not work.  I don't
think it is very likely that APBS wrote a truncated file.

}}}

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4743#comment:4>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

hxbgzlkih6-pot.dx​

[Minghao.Chen@…]

Added by email2trac

[Tom Goddard]

The hxbgzlkih6-pot.dx file you attached is truncated as the ChimeraX error message indicates. The header of the file gives its size as 193 by 161 by 225 grid points, so a total o 6991525 (= 193 * 161 *225) are needed and the file only contains 4682199 values and it ends with an obviously truncated numeric value that does not have 2 digits for the exponent in scientific notation.

It could be the APBS server truncated the file. Or it could be your web browser or whatever software downloaded the file truncated it, or it could be you don't have enough disk space so it got truncated.

In any case the problem has nothing to do with ChimeraX.

# Data from 3.0
#
# POTENTIAL (kT/e)
#
object 1 class gridpositions counts 193 161 225
...
-2.056444e+00 -2.042640e+00 -2.028863e+00
-2.015110e+00 -2.001376e+00 -1.987660e+00
-1.973960e+00 -1.960275e+00 -1.946604e+0

[Minghao.Chen@…]

Thanks for your comment. ChimeraX on my computer can also open the old dx files which I created months ago, so I agree it’s a problem of the APBS server.

I’m reported this error to Elaine and Nathan. Hopefully they can figure out the problem soon.
The email is attached below:

--------------------
Hello all,
I can report exactly the same problem as Minghao, so now I also suspect it might be a change in the server.

I just now used the APBS webserver default options to run PDB2PQR and then APBS on 4z94, then tried to open the resulting dx file in Chimera and ChimeraX, with the error occurring around 2/3 of the way through the expected values.  This is not an extremely large structure, so its size shouldn't be a problem.

My ancient copy of MacPymol also gives an error reading the map.

I have used the ABPS webserver in the past to make dx files that work in Chimera/ChimeraX, so I suspect something has changed in how the data are written.

Elaine
-----
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



On 14. Jun 2021, at 19:20, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#4743: DX file works on some machines but not others
-------------------------------------+-------------------------
         Reporter:  minghao.chen@…  |      Owner:  Tom Goddard
             Type:  defect          |     Status:  closed
         Priority:  normal          |  Milestone:
        Component:  Volume Data     |    Version:
       Resolution:  not a bug       |   Keywords:
       Blocked By:                  |   Blocking:
Notify when closed:                  |   Platform:  all
          Project:  ChimeraX        |
-------------------------------------+-------------------------

Comment (by Tom Goddard):

The hxbgzlkih6-pot.dx file you attached is truncated as the ChimeraX error
message indicates.  The header of the file gives its size as 193 by 161 by
225 grid points, so a total o 6991525 (= 193 * 161 *225) are needed and
the file only contains 4682199 values and it ends with an obviously
truncated numeric value that does not have 2 digits for the exponent in
scientific notation.

It could be the APBS server truncated the file.  Or it could be your web
browser or whatever software downloaded the file truncated it, or it could
be you don't have enough disk space so it got truncated.

In any case the problem has nothing to do with ChimeraX.

# Data from 3.0
#
# POTENTIAL (kT/e)
#
object 1 class gridpositions counts 193 161 225
...
-2.056444e+00 -2.042640e+00 -2.028863e+00
-2.015110e+00 -2.001376e+00 -1.987660e+00
-1.973960e+00 -1.960275e+00 -1.946604e+0

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/4743#comment:6>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

[Tom Goddard]

I would suggest Minghao report to the APBS developers exactly the test case that Elaine described so they have all the information to reproduce the bug themselves. There is nothing ChimeraX can do about a truncated file.

[Elaine Meng]

This was a bug with their APBS web service at ​https://server.poissonboltzmann.org/ ... we and others reported the problem, see ​https://github.com/Electrostatics/pdb2pqr/issues/199

... and today they fixed the problem, and I tested it, seems to work now.

On Jun 16, 2021, at 3:42 PM, Offor, Elvis <elvis.offor@…> wrote:
Hi Elaine,
Thanks for reporting this issue. The behavior you experienced was a memory-related issue related to our deployment, where memory was depleted while the output files were mid-write.

A patch has been deployed to resolve this behavior. You should be able to confirm this through another attempt of the calculation via the website. Apologies for the trouble, and thanks again for reporting it.
Elvis

Date: June 16, 2021 at 5:55:02 PM PDT
Hi Elvis,
Thank you!! I did two spot checks of your web services just now, 4z94 and my old standby 3eeb chain A, using both PDB2PQR and APBS (all default options only). The jobs completed quickly and I could open the DX maps in ChimeraX without problems, use them for coloring, etc.
[...]