[chimerax-users] Exporting DNA Molecules from Chimera X

[Greg Couch]

Hi Matthew,

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.

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.

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.

     -- Greg

On 4/13/2021 7:50 AM, AQUILINA Matthew wrote:
> Dear ChimeraX users,
>
> I’ve recently started using ChimeraX to produce rendered 3D models of 
> DNA nanostructures.  I do this through the following process:
>
>   * Prepare nanostructure as a PDB file.
>   * Import this into ChimeraX.
>   * Arrange visualization settings such as nucleotide representation
>     shape, width etc.
>   * Export .x3d file into Blender for downstream processing.
>
>
> 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.
>
> 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.
>
> Many thanks for your help!
>
> Best wishes,
>
> Matthew Aquilina
> --
> *Matthew Aquilina*
> *Precision Medicine PhD Student*
> College of Medicine and Veterinary Medicine & School of Engineering | 
> University of Edinburgh
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