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. http://www.cgl.ucsf.edu/home/goddard/temp/1s72-rna/1s72.html Tom David Konerding wrote:
On 4/12/07, *Thomas Goddard* <goddard@cgl.ucsf.edu <mailto:goddard@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