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<p>Just to clarify, for mmCIF files, currently ChimeraX can write
out the assembly position matrices, but only if they were present
when reading in the mmCIF file. Tom is proposing that the sym
command optionally add the new assembly position matrices to the
molecule's metadata so they will be written out.</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 9/8/22 14:28, Tom Goddard via
ChimeraX-users wrote:<br>
</div>
<blockquote type="cite"
cite="mid:793326BE-117B-4F62-8624-EE699588AF9D@sonic.net">
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Hi Pranav,
<div class=""><br class="">
</div>
<div class=""> ChimeraX currently does not write out the assembly
position matrices when saving mmCIF (.cif) or PDB (.pdb) format
files. But it probably could be added. We have that as a
feature request</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span><a
href="https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6538"
class="moz-txt-link-freetext" moz-do-not-send="true">https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/6538</a></div>
<div class=""><br class="">
</div>
<div class="">Here is how I'd envision that working. You use the
ChimeraX sym command to make symmetric copies of the asymmetric
unit, then you save in mmCIF format. It would write the mmCIF
tables pdbx_struct_assembly, pdbx_struct_assembly_gen,
pdbx_struct_oper_list to encode the positions of the symmetric
copies. I don't know of other software that reads these tables
except for ChimeraX. When you opened the written mmcif file in
ChimeraX you would be able to to reproduce the symmetry with a
command like "sym #1 assembly 1".</div>
<div class=""><br class="">
</div>
<div class=""> Is that what you had in mind?</div>
<div class=""><br class="">
</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div>
<div class=""><br class="">
<div><br class="">
<blockquote type="cite" class="">
<div class="">On Sep 8, 2022, at 5:44 AM, Pranav Shah via
ChimeraX-users <<a
href="mailto:chimerax-users@cgl.ucsf.edu"
class="moz-txt-link-freetext" moz-do-not-send="true">chimerax-users@cgl.ucsf.edu</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Hi Team,<br class="">
<br class="">
Is it possible to insert BIOMT like fields into the
asymmetric unit of<br class="">
a symmetric molecule when saving the coordinates as a
cif file?<br class="">
Best,<br class="">
Pranav<br class="">
--<br class="">
Pranav Shah<br class="">
Postdoctoral Research Fellow.<br class="">
<br class="">
Division of Structural Biology,<br class="">
Wellcome Trust Centre for Human Genetics,<br class="">
University of Oxford,<br class="">
Roosevelt Drive, Oxford OX3 7BN,<br class="">
UK<br class="">
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</blockquote>
</div>
<br class="">
</div>
<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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