Re: [chimerax-users] Open AmiraMesh 3.0 in ChimeraX

Hi Andrea, I am encountering the below error in ChimeraX. Would it be okay that I share the 64MB .am file you sent to me earlier with Tom, the developer of ChimeraX? They do have a line "any information or data you wish to keep confidential should be sent separately" in the bug report guide. Many thanks, Roden On Mon, Oct 25, 2021 at 9:36 PM Tom Goddard wrote:

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 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-f02d2fe070b... https://urldefense.com/v3/__https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/3...

https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX https://urldefense.com/v3/__https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http:**Aedmond.mpdl.mpg.de*imeji*item*IoNX5MO0lyzezIwX__;Ly8vLy8!!Nmw4Hv0!kcq4sFF8Gr7jlb4rYFCXX92mN_4LF7NvtzMDXcdXva7oIjK1Od5zJWng0B9nuV8PogA$

Thanks, Roden

On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard 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@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-use..." shows no result. Can anyone kindly help here?

Many thanks, Roden

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