Opened 5 years ago

Closed 5 years ago

#4065 closed defect (fixed)

Opening .nc file: No module named 'Scientific'

Reported by: ammirabileelena@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc: Greg Couch, Eric Pettersen
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-20.2.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1.1 (2020-10-07)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> nmwiz

Unknown command: nmwiz  

> nmwizexit

Unknown command: nmwizexit  

> open /Users/elenaammirabile/cpu-gpu-mode1.nc

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 533, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1754, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 140, in provider_open  
opener_info.open, (session, paths, name), provider_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 141, in open  
return open_map(session, path, format=_name, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3536, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/fileformats.py", line 162, in open_file  
data.extend(open_func(p, **okw))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/__init__.py", line 24, in open  
return read_netcdf(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_grid.py", line 51, in read_netcdf  
d = NetCDF_Data(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
ModuleNotFoundError: No module named 'Scientific'  
  
ModuleNotFoundError: No module named 'Scientific'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
  
See log for complete Python traceback.  
  

> open /Users/elenaammirabile/cpu-gpu-mode1.nc

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 533, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1754, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 140, in provider_open  
opener_info.open, (session, paths, name), provider_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 141, in open  
return open_map(session, path, format=_name, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3536, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/fileformats.py", line 162, in open_file  
data.extend(open_func(p, **okw))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/__init__.py", line 24, in open  
return read_netcdf(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_grid.py", line 51, in read_netcdf  
d = NetCDF_Data(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
ModuleNotFoundError: No module named 'Scientific'  
  
ModuleNotFoundError: No module named 'Scientific'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
  
See log for complete Python traceback.  
  

> open /Users/elenaammirabile/cpu-gpu-mode1.nc

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 533, in dropEvent  
_open_dropped_file(self.session, p)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1754, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 140, in provider_open  
opener_info.open, (session, paths, name), provider_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 141, in open  
return open_map(session, path, format=_name, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3536, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/fileformats.py", line 162, in open_file  
data.extend(open_func(p, **okw))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/__init__.py", line 24, in open  
return read_netcdf(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_grid.py", line 51, in read_netcdf  
d = NetCDF_Data(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
ModuleNotFoundError: No module named 'Scientific'  
  
ModuleNotFoundError: No module named 'Scientific'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
  
See log for complete Python traceback.  
  

> open /Users/elenaammirabile/cpu-gpu-mode1.nc

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 238, in event  
_open_dropped_file(self.session, event.file())  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1754, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/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
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 140, in provider_open  
opener_info.open, (session, paths, name), provider_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/open_command/cmd.py", line 389, in collated_open  
return func(*func_args, **func_kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/__init__.py", line 141, in open  
return open_map(session, path, format=_name, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3536, in open_map  
grids = open_file(path, file_type = format, log = session.logger, **kw)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/fileformats.py", line 162, in open_file  
data.extend(open_func(p, **okw))  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/__init__.py", line 24, in open  
return read_netcdf(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_grid.py", line 51, in read_netcdf  
d = NetCDF_Data(path)  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
ModuleNotFoundError: No module named 'Scientific'  
  
ModuleNotFoundError: No module named 'Scientific'  
  
File
"/Applications/ChimeraX-1.1.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map_data/netcdf/netcdf_format.py", line 36, in __init__  
from Scientific.IO import NetCDF  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.1.7
OpenGL renderer: Intel(R) HD Graphics 6000
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Air
      Model Identifier: MacBookAir7,2
      Processor Name: Dual-Core Intel Core i5
      Processor Speed: 1,6 GHz
      Number of Processors: 1
      Total Number of Cores: 2
      L2 Cache (per Core): 256 KB
      L3 Cache: 3 MB
      Hyper-Threading Technology: Enabled
      Memory: 4 GB
      System Firmware Version: 425.0.0.0.0
      SMC Version (system): 2.27f2

Software:

    System Software Overview:

      System Version: macOS 11.1 (20C69)
      Kernel Version: Darwin 20.2.0
      Time since boot: 22:37

Graphics/Displays:

    Intel HD Graphics 6000:

      Chipset Model: Intel HD Graphics 6000
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x1626
      Revision ID: 0x0009
      Metal Family: Supported, Metal GPUFamily macOS 1
      Displays:
        Color LCD:
          Display Type: LCD
          Resolution: 1440 x 900 (Widescreen eXtended Graphics Array Plus)
          UI Looks like: 1440 x 900
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal

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
    appnope: 0.1.0
    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-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1.1
    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-Label: 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-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
    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
    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
    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 (9)

comment:1 by Eric Pettersen, 5 years ago

Cc: Greg Couch added
Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Reporter: changed from ammirabileelen@… to ammirabileelena@…
Status: new → assigned
Summary: ChimeraX bug report submission → Opening .nc file: No module named 'Scientific'

Reported by Elena Ammirabile

comment:2 by Tom Goddard, 5 years ago

Chimera reads netcdf but ChimeraX does not. It is a bug that ChimeraX listed netcdf as readable -- it does not have the netcdf library needed to read that data. I'll take a look if the hdf5 library ChimeraX uses can read the netcdf.

comment:3 by Tom Goddard, 5 years ago

Cc: Eric Pettersen added

A quick look at what Python modules can read netcdf turns up a few options. The most widely used solution is the PyPi netcdf4 package

​https://pypi.org/project/netCDF4/

It is 4 Mbytes compressed, and I am not thrilled about increasing the ChimeraX distribution size for this obscure file format. We already have h5py and PyTables reading hdf5 which netcdf is based on. Another option is h5netcdf

​https://pypi.org/project/h5netcdf/

that simply uses h5py which we already include. It is a tiny 30 Kbytes, all python. Size is no problem, but we don't want to use an API that won't be supported in the future. Another possibility is that PyTables may be able to read netcdf directly. Information on the web about this is scant.

comment:4 by Tom Goddard, 5 years ago

Eric, are you reading netcdf for molecular dynamics trajectories in ChimeraX?

comment:5 by Eric Pettersen, 5 years ago

Yes, with the same extension: .nc. One of us should probably use the new 'is_default' attribute.

--Eric

in reply to:  6 ; comment:6 by goddard@…, 5 years ago 

Where is this MD netcdf reading code (what bundle) and what netcdf library is it using -- I am looking for how to read netcdf volume data, whether there is a copy of netcdf in ChimeraX already.

comment:7 by Eric Pettersen, 5 years ago

md_crds.read_coords.read_coords(), the format_name == "amber" clause.

in reply to:  8 ; comment:8 by goddard@…, 5 years ago 

I see I missed that ChimeraX already includes the Python netcdf4 PyPi package.  Somehow I missed it when I looked in app_requirements.txt earlier today.

comment:9 by Tom Goddard, 5 years ago

Resolution: → fixed
Status: assigned → closed

Fixed netcdf map reader. It was never ported from Chimera 1 and was trying to use the Scientific.NetCDF Python module which is not in ChimeraX. I made it use the netCDF4 PyPi module which was already in ChimeraX for reading Amber MD trajectories. I've only tested this on one multichannel light microscopy netcdf file I have so it may run into trouble with other files.

The default file reader for NetCDF is Amber MD so you have to choose the format to be "NetCDF map" in the file open dialog, or use command "open mymap.nc format netcdfmap" to specify the format.

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