[Chimera-users] Ribosomal RNA depiction

[Thomas Goddard]

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 
Resurface
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


http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna.png

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,

http://www.cgl.ucsf.edu/chimera/ImageGallery/entries/stmvrna/1a34.png

	Tom

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