Re: [PyMOL] Displaying sticks on RNA bases only

[Thomas H. <tho...@sc...>]

Hi Maria,

The following shows filled rings and sticks for the nucleosides:

set cartoon_ring_finder, 1
set cartoon_ring_mode, 3
as cartoon

To not show filled rings for the nucleobases, you can hide cartoon for the sidechain selection, and show sticks instead (the sidechain selection keyword was introduced in PyMOL 1.7.0):

hide cartoon, sidechain
show sticks, sidechain extend 1

See also:
http://pymolwiki.org/index.php/Overview_of_nucleic_acid_cartoons

Hope that helps.

Cheers,
  Thomas

On 20 Jan 2016, at 10:10, COSTA Maria <mar...@i2...> wrote:

> Hello,
> 
> I am using Pymol to visualize nucleic acid structures ( I'm a new user) and I would like to be able to display the functional groups of bases A, G, T/U, C with sticks while using the cartoon mode : cartoon_ring_finder, 1 or 2 for the ribose_phosphate backbone of the molecule. Can you please tell me how to achieve that ? 
> For the moment the only thing I found was to display the 'cartoon' and the 'stick' modes at the same time to get the sticks corresponding to the functional groups of the bases but then I also visualize all the sticks of the riboses and phosphates which makes my drawings 'overloaded'. I hope I was clear enough. 
> 
> Many thanks in advance for your answers,
> 
> Maria
> 
> CNRS
> France

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.