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<p>Hi Matthew,</p>
<p>For drawing speed, ChimeraX puts all of the nucleotide depictions
into huge set of triangles per-model. It would be fairly easy to
add a XML comment or X3D metadata that listed which triangles
correspond to which set of atoms. Would that work for you? With
that information, you could write a program to split the huge
triangle list into multiple X3D objects and label them
appropriately. And then import the post-processed X3D file into
Blender.</p>
<p>Can Blender select by color? If so, you could uniquely color the
nucleotides by type in ChimeraX, and select them that way in
Blender for post-processing.<br>
</p>
<p>I've added an enhancement ticket for having separate X3D objects
per-nucleotide, so you'll be notified if it is implemented.
Unfortunately, that is not a short term solution.<br>
</p>
<p> -- Greg<br>
</p>
<div class="moz-cite-prefix">On 4/13/2021 7:50 AM, AQUILINA Matthew
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:D14CD5A8-1532-41B2-A624-968F51E1B693@ed.ac.uk">
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Dear ChimeraX users,</div>
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<br class="">
</div>
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode:
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I’ve recently started using ChimeraX to produce rendered 3D
models of DNA nanostructures. I do this through the following
process:</div>
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<br class="">
</div>
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode:
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<ul class="MailOutline">
<li class="">Prepare nanostructure as a PDB file.</li>
<li class="">Import this into ChimeraX.</li>
<li class="">Arrange visualization settings such as nucleotide
representation shape, width etc.</li>
<li class="">Export .x3d file into Blender for downstream
processing.</li>
</ul>
<div class=""><br class="">
</div>
<div class="">However, there is one issue - the 3D models
exported by ChimeraX aren’t grouped into individual objects
per nucleotide, so I am not able to easily select nucleotides
and colour them in according to their type (A, T, G or C).
With the older version of Chimera, these nucleotides are
exported as individual objects, but then are given identical
names with randomized IDs. This means that setting the
nucleotide types is a long manual process of clicking on each
resulting nucleotide and naming them individually.</div>
<div class=""><br class="">
</div>
<div class="">Does anyone know of a way to export a 3D model of
a DNA structure which also exports the IDs of each nucleotide?
This would greatly speed up the process for me to produce and
render a DNA structure.</div>
<div class=""><br class="">
</div>
<div class="">Many thanks for your help!</div>
</div>
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<br class="">
</div>
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Best wishes,</div>
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode:
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<br class="">
</div>
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode:
space; line-break: after-white-space;" class="">
Matthew Aquilina<br class="">
<div class="">
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class="">
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<a class="" moz-do-not-send="true"><span
style="color: black;" class="">--</span></a></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size:
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class="">
<b class=""><span style="color: rgb(0, 70, 49);"
class="">Matthew Aquilina</span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size:
11pt; font-family: Calibri, sans-serif;"
class="">
<b class=""><span style="color: rgb(0, 70, 49);"
class="">Precision Medicine PhD Student</span></b></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size:
11pt; font-family: Calibri, sans-serif;"
class="">
College of Medicine and Veterinary Medicine
& School of Engineering | University of
Edinburgh</div>
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11pt; font-family: Calibri, sans-serif;"
class="">
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