[Chimera-users] Ribosomal RNA depiction
goddard at cgl.ucsf.edu
Fri Apr 13 11:38:04 PDT 2007
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
> 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
> 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?
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