[chimerax-users] Open AmiraMesh 3.0 in ChimeraX

[Tom Goddard]

Hi Roden,

The ChimeraX reader is for AmiraMesh format 2.1 and you are trying to read a version 3.0 file.  I don't know if those are compatible.  You can test by making ChimeraX not check the Amira file version by editing the following file  (location for Mac, ChimeraX 1.3 daily build shown)

	ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/map_data/amira/amira_format.py

changing these lines

    if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or
            line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):
      raise SyntaxError('First line of AmiraMesh file must start with '
                        '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '
                        'instead got "%s"' % line[:256])

to

#    if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or
#            line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):
#      raise SyntaxError('First line of AmiraMesh file must start with '
#                        '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '
#                        'instead got "%s"' % line[:256])

so the version test will not be done.

  Or you could use ChimeraX menu Help / Report a Bug... and attach a modest size Amira 3.0 file and I can try it.

  Or you could make a copy of your Amira file and edit the first line so instead of saying it is version 3.0 it says it is version 2.1.

	Tom


> On Oct 23, 2021, at 8:12 AM, Roden Deng Luo via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX Users,
> 
> I have an AmiraMesh .am file exported from Amira 3D 2021.1 (Build date: 2021-06-21 13:21:22, SHA id: 213bd1......13c73e). When I load it into ChimeraX 1.2.5 or ChimeraX 1.3.dev202110231141, ChimeraX tells me the following error.
> 
> First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'"
> 
> Googling "AmiraMesh site:https://www.rbvi.ucsf.edu/pipermail/chimerax-users <https://www.rbvi.ucsf.edu/pipermail/chimerax-users>" shows no result. Can anyone kindly help here? 
> 
> Many thanks,
> Roden
> 
> 
> 
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