[Chimera-users] Ribosomal RNA depiction

Thomas Goddard goddard at cgl.ucsf.edu
Thu Apr 12 10:01:50 PDT 2007

Hi Jean-Francois,

   Here are some tips for showing coarse RNA depictions.

   I too had lots of different colors for the ribosome rna bases using 
the nucleic acid blobs tool but I changed them.  Here was my procedure.

1. open 1s72
2. select chain 0 (menu Select / Chain / 0)
3. invert selection to select all proteins (menu Select / Invert)
4. delete all the proteins (menu Actions / Atoms+Bonds / Delete
5. open reschains.py
6. open multiscale (menu Tools / Higher-order Structure / Multiscale Models)
7. select multiscale multimer type None and press Make models.
8. press multiscale select All button, change resolution to 2, press 
9. ctrl-click on backbone to select it
10. invert selection (menu Select / Invert)
11. click multiscale color button and set color of all bases


Nicer simplified depictions can be made using ribbons with a single side 
chain atom as a sphere.  The ribbon style editor (Tools / Depictions / 
Ribbon Style Editor) can fatten up the ribbon.  Or for fancier bases 
shown as slabs use the Nucleotides tool (Tools / Depiction / 
Nucleotides), for example,



jean-francois menetret wrote:
> Hi Tom,
> the new reschains.py works well; but how did you specify the color 
> scheme in 1s72_rna.png using "multiscalemodel" option ? I am getting so 
> many different colours (see attached jpeg)
> Jean-François Ménétret,  PhD
> Boston University School of Medicine

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