Re: [PyMOL] Cartoon backbone nitrogens

[Tsjerk W. <ts...@gm...>]

Hi Jon,

I think you're out of luck. The color of cartoon representation is
controlled only by the CAs, which is also used to trace the cartoon.
Probably using spheres is still the best option. Just make sure that
you set both cartoon_smooth_loops and cartoon_flat_sheets to 0, so
that these trace the backbone better. The nitrogens will then be on
the line, though a bit to the side. Also play a bit with the
sphere_scale... E.g.,

set cartoon_smooth_loops,0
set cartoon_flat_sheets,0
set sphere_scale,0.4

Hope it helps,

Tsjerk

On Fri, Mar 5, 2010 at 4:56 PM, J. Fleming <jon...@ho...> wrote:
> Hi all,
>
>   Is there a good method to display backbone nitrogens while in cartoon
> mode?  I tried using spheres on the backbone nitrogen positions but it
> doesn't look right.  Sticks also looked strange as the transition from
> cartoon to sticks was broken.  Perhaps there is a way to color just the
> cartoon backbone nitrogen blue?
>
> I'm open to any ideas.  Thanks,
> Jon
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist