defattr via 'open'

[jeandidier.marechal@…]

The following bug report has been submitted:
Platform:        Darwin-19.6.0-x86_64-i386-64bit
ChimeraX Version: 1.1.1 (2020-10-07 08:32:49 UTC)
Description
Dear all, 

I am moving attribute practices form chimera to chimeraX and apparently something is wrong (likey I do something wrong). I use mac and the command I try to execute is:

open /Users/jeandi/Downloads/attributes.defattr format defattr

That returns
Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild', 'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf', 'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images', 'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf', 'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir', 'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf', 'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm', 'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch', 'xplor', or 'xtc'

Thanks a lot for any help,

Kind regards,
jD

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
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  

> open 4zzd format mmcif fromDatabase pdb

4zzd title:  
Crystal structure of multidrug resistance regulator LMRR bound to riboflavin
[more info...]  
  
Chain information for 4zzd #1  
---  
Chain | Description  
A | transcriptional regulator, padr-like family  
  
Non-standard residues in 4zzd #1  
---  
RBF — riboflavin (riboflavine; vitamin B2)  
  
4zzd mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
  
Successfully installed ChimeraX-AddH-2.1.3 ChimeraX-HKCage-1.3  
Installed ChimeraX-AddH (2.1.3)  
Installed ChimeraX-HKCage (1.3)  

> open /Users/jeandi/Downloads/attributes.defattr

Unrecognized file suffix '.defattr'  

> open /Users/jeandi/Downloads/wwHydrophobicity.txt

Unrecognized file suffix '.txt'  

> open defattr /Users/jeandi/Downloads/wwHydrophobicity.txt

'defattr' has no suffix  

> open formats defattr /Users/jeandi/Downloads/wwHydrophobicity.txt

Expected fewer arguments  

> open /Users/jeandi/Downloads/wwHydrophobicity.txt format defattr

Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild',
'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled
python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf',
'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images',
'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf',
'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir',
'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf',
'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm',
'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch',
'xplor', or 'xtc'  

> open /Users/jeandi/Downloads/wwHydrophobicity.txt

Unrecognized file suffix '.txt'  

> open /Users/jeandi/Downloads/attributes.defattr format defattr

Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild',
'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled
python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf',
'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images',
'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf',
'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir',
'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf',
'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm',
'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch',
'xplor', or 'xtc'  

> open /Users/jeandi/Downloads/attributes.defattr format defattr log true

Invalid "format" argument: Should be one of 'aln', 'amira', 'apbs', 'bild',
'brix', 'ccd', 'ccp4', 'cellpack', 'cmap', 'cmd', 'collada', 'compiled
python', 'cube', 'dcd', 'delphi', 'dicom', 'dock', 'dsn6', 'dv', 'emanhdf',
'fasta', 'fsc', 'gltf', 'gopenmol', 'hdf', 'hssp', 'html', 'ihm', 'images',
'imagic', 'imod', 'imodmap', 'ims', 'macmolplt', 'markers', 'mmcif', 'mmtf',
'mol2', 'mrc', 'msf', 'netcdf', 'obj', 'pdb', 'pdbqt', 'pfam', 'pif', 'pir',
'positions', 'priism', 'profec', 'pseudobonds', 'python', 'rsf', 'sdf',
'segger', 'session', 'sff', 'situs', 'smiles', 'spider', 'stl', 'stockholm',
'storm', 'swc', 'tom_em', 'trr', 'uhbd', 'uniprot', 'vtk', 'web fetch',
'xplor', or 'xtc'  

> open /Users/jeandi/Downloads/attributes.defattr log true

Unrecognized file suffix '.defattr'  




OpenGL version: 4.1 INTEL-14.7.8
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.147.4.0.0 (iBridge: 17.16.16610.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.15.6 (19G2021)
      Kernel Version: Darwin 19.6.0
      Time since boot: 5 days 23:21

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        LED:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version: 7,55

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
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    ChimeraX-ConnectStructure: 2.0
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    ChimeraX-Core: 1.1.1
    ChimeraX-CoreFormats: 1.0
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    ChimeraX-FunctionKey: 1.0
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    ChimeraX-Hbonds: 2.0
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    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
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[pett]

Hi JD!

You aren't doing anything wrong per se, but the ability to read defattr files with the "open" command is only in the daily build. So you can either use the daily build, or you can continue to use the 1.1.1 release but you would have to use the 'defattr' command to read the file instead of 'open'.

--Eric