[chimerax-users] Exporting DNA Molecules from Chimera X

[AQUILINA Matthew]

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
Profile<https://www.ed.ac.uk/profile/matthew-aquilina> | LinkedIn<https://www.linkedin.com/in/matthewaq/> | Twitter<https://twitter.com/matt_aqui>

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