Now it’s time to pimp your RNA 3D

Do you remember this post? Of course you do ;-). With the new daily build (Oct 3rd, 2013), a new option has appeared (“Edit -> Colors -> Color 3D”) allowing you to synchronize the colors between the 2D and the 3D scenes. As an example, i have opened the sample file 1ehz.pdb and i have assigned the following qualitative values (available as a sample file named tRNA_domains.txt):

tRNA_domains

By selecting “Edit -> Colors -> Color 3D”, i’m now able to produce easily such result:

pimp3D

You can see that i have slightly improved the way to define the molecular positions in the data file. A qualitative or quantitative value can be linked to:

  • a single position: 7
  • a range of contiguous positions: 7-14
  • several ranges of contiguous positions: 7-14,22-27,56-58

No spaces are allowed in the definition of the molecular positions.

If  your RNA structure is large, i suggest you to select subdomains before to launch the synchronization. Otherwise, Chimera could get stuck. Here is an example of quantitative data assigned to a large ribosomal RNA:

pimp3D_2

pimp3D_3

Enjoy your data mapped on the tertiary structure.

Using the consensus structural mask, you can now more easily identify the helices in a tertiary structure:

pimp3D_4

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