[Chimera-users] Ribosomal RNA depiction

Tom Goddard goddard at cgl.ucsf.edu
Fri Apr 13 11:38:04 PDT 2007

Hi Dave,

  The RNA display using surfaces for each base could be done easily in a 
Python script, but not with Chimera commands since those are not 
available for multiscale.  The result could be exported to POV-ray, or 
since Chimera now includes POV-ray the raytraced image can be directly 
produced in Chimera.

  I still think that a fat tubular ribbon with a single base atom shown 
as sphere gives a cleaner coarse view of RNA that indicates base 
orientations.  Here's a ribbon and sphere image, also a ribbon with 
surface bases, also an image with bases with NDB colors.



David Konerding wrote:
> On 4/12/07, *Thomas Goddard* <goddard at cgl.ucsf.edu 
> <mailto:goddard at cgl.ucsf.edu>> wrote:
>     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
> Tom-
> This looks nice.  I don't have a lot of time to look into the 
> implementation right now,
> but can steps 6-11 be done programmatically easily? 
> Will the resulting images export to povray?
> Dave

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