<div dir="ltr"><div dir="ltr">Hi Andrea, <div><br></div><div>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?</div><div><br></div><div>They do have a line "any information or data you wish to keep confidential should be sent separately" in the bug report guide. </div><div><br></div><div>Many thanks,</div><div>Roden</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 9:36 PM Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div><div>Hi Roden,</div><div><br></div>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.<div><br></div><div><span style="white-space:pre-wrap"> </span>Tom</div><div><br><div><br><blockquote type="cite"><div>On Oct 25, 2021, at 11:29 AM, Roden Deng Luo <<a href="mailto:deng.luo@kaust.edu.sa" target="_blank">deng.luo@kaust.edu.sa</a>> wrote:</div><br><div><div dir="ltr">Hi Tom,<div><br></div><div>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. </div><div><br></div><div>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".</div><div><br></div><div><a href="https://urldefense.com/v3/__https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am__;!!Nmw4Hv0!kcq4sFF8Gr7jlb4rYFCXX92mN_4LF7NvtzMDXcdXva7oIjK1Od5zJWng0B9n2x4q_Zw$" target="_blank">https://edmond.mpdl.mpg.de/imeji/file/60/17/dc/32-bf46-4e34-b9ba-f02d2fe070b4/0/original/ae8b3e16a7a0f881f66b804ceac50b97.am?filename=190522a_STACK.labels.am</a></div><div><a href="https://urldefense.com/v3/__https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http:**Aedmond.mpdl.mpg.de*imeji*item*IoNX5MO0lyzezIwX__;Ly8vLy8!!Nmw4Hv0!kcq4sFF8Gr7jlb4rYFCXX92mN_4LF7NvtzMDXcdXva7oIjK1Od5zJWng0B9nuV8PogA$" target="_blank">https://edmond.mpdl.mpg.de/imeji/exportServlet?format=file&id=http://edmond.mpdl.mpg.de/imeji/item/IoNX5MO0lyzezIwX</a><br></div><div><br></div><div>Thanks,</div><div>Roden</div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Oct 25, 2021 at 8:37 PM Tom Goddard <<a href="mailto:goddard@sonic.net" target="_blank">goddard@sonic.net</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Hi Roden,<div><br></div><div>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)<div><br></div><div><span style="white-space:pre-wrap"> </span>ChimeraX.app/Contents/lib/python3.9/site-packages/chimerax/map_data/amira/amira_format.py<br><div><br></div><div>changing these lines</div><div><br></div><div><div> if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or</div><div> line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):</div><div> raise SyntaxError('First line of AmiraMesh file must start with '</div><div> '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '</div><div> 'instead got "%s"' % line[:256])</div></div><div><br></div><div>to</div><div><br></div><div><div># if not (line.startswith(b'# AmiraMesh BINARY-LITTLE-ENDIAN 2.1') or</div><div># line.startswith(b'# Avizo BINARY-LITTLE-ENDIAN 2.1')):</div><div># raise SyntaxError('First line of AmiraMesh file must start with '</div><div># '"# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", '</div><div># 'instead got "%s"' % line[:256])</div><div><br></div><div>so the version test will not be done.</div><div><br></div><div> Or you could use ChimeraX menu Help / Report a Bug... and attach a modest size Amira 3.0 file and I can try it.</div><div><br></div><div> 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.</div><div><br></div><div><span style="white-space:pre-wrap"> </span>Tom</div><div><br></div><div><br><blockquote type="cite"><div>On Oct 23, 2021, at 8:12 AM, Roden Deng Luo via ChimeraX-users <<a href="mailto:chimerax-users@cgl.ucsf.edu" target="_blank">chimerax-users@cgl.ucsf.edu</a>> wrote:</div><br><div><div dir="ltr">Dear ChimeraX Users,<div><br></div><div>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.</div><div><br></div><div><div style="margin:0px;white-space:pre-wrap">First line of AmiraMesh file must start with "# AmiraMesh BINARY-LITTLE-ENDIAN 2.1", instead got "b'# AmiraMesh BINARY-LITTLE-ENDIAN 3.0\n'"</div></div><div><br></div><div>Googling "AmiraMesh site:<a href="https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/pipermail/chimerax-users__;!!Nmw4Hv0!gswyBcLggCUszrrkzuG1NAh0dA6mXVnN-mOrDaZJKGhoRMCix2NZTs_HZ5w3Eiak_ks$" target="_blank">https://www.rbvi.ucsf.edu/pipermail/chimerax-users</a>" shows no result. Can anyone kindly help here? <br></div><div><br></div><div>Many thanks,</div><div>Roden</div><div><br></div><div><br></div></div>
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