[chimerax-users] Open AmiraMesh 3.0 in ChimeraX

[Tom Goddard]

Hi Roden,

I think you can attach a 64 Mbyte file to a ChimeraX bug report (menu Help / Report a Bug...).  I would be interested in looking at the file to see how different it is from the 2.1 version files.

	Tom


> On Oct 25, 2021, at 11:29 AM, Roden Deng Luo <deng.luo at kaust.edu.sa> wrote:
> 
> Hi Tom,
> 
> Thanks very much! After changing the first line to 2.1, it tells me "Did not find "define Lattice" mesh size line". So I guess there are some "fundamental" changes. 
> 
> The only .am file I have now is quite large in terms of debugging (64MB). I found two examples by googling "AmiraMesh BINARY-LITTLE-ENDIAN "3.0"". They give me "Did not find "Lattice { float ... }" line" after fooling ChimeraX. In case I get a smaller one or I got to know the way to crop only a small section and export a smaller one. I will let you know. I will also go through "Report a Bug".
> 
> https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am <https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am>
> https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX <https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX>
> 
> Thanks,
> Roden
> 
> 
> On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <goddard at sonic.net <mailto:goddard at sonic.net>> wrote:
> 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 <mailto: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://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-users__;!!Nmw4Hv0!gswyBcLggCUszrrkzuG1NAh0dA6mXVnN-mOrDaZJKGhoRMCix2NZTs_HZ5w3Eiak_ks$>" shows no result. Can anyone kindly help here? 
>> 
>> Many thanks,
>> Roden
>> 
>> 
>> 
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