Re: [PyMOL] How to color in a different way different helix types?

[Jason V. <jas...@sc...>]

Hi Adam,

You could script this using the angle command with specific selections.

Cheers,

-- Jason

On Wed, Apr 6, 2011 at 11:49 AM, H. Adam Steinberg <ad...@st...> wrote:
> Jason (or someone else),
> Is there way in pymol to look for the following angle in a structure φ=-49o
> and ψ=-26o ? Which is the definition of a 310 helix. And yes we'd have to
> search for a few degrees plus of minus of those angles. They should all
> appear in tight turns and last for about 3 or 4 amino acids (I don't think
> there wouldn't be any cartoon helix shown).
> I don't think there are any pdbs yet that contain pi helices (because of the
> loose packing and steric hindrance of the side chains), does anyone know of
> any?
> Thanks
> Adam
> On Apr 6, 2011, at 8:16 AM, Jason Vertrees wrote:
>
> Hi Ramiro,
>
> PyMOL doesn't differentiate helices, so it cannot color them
> differently.  If you had the residue labels from some other program
> you could read them in and then color by type.
>
> Cheers,
>
> -- Jason
>
> On Wed, Apr 6, 2011 at 5:22 AM, Ramiro Téllez Sanz <urc...@gm...>
> wrote:
>
> Hi and thanks for reading this.
>
> I have googled for a way to achieve what I want and have gone through
>
> the wiki, to no avail.
>
> I would like to color in a different way the different helix types:
>
> alpha, pi and 310. When you open, for instance, 1pyg into Jmol, you get
>
> distinct colors for each type by default. But if the same pdb file is
>
> open with PyMOL all helices are treated the same way. Can't PyMOL
>
> distinguish helix types?
>
> Thanks in advance,
>
> Ramiro Téllez Sanz
>
> Dept. Physical Chemistry
>
> University of Almeria
>
> Spain
>
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> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
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>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) Jas...@sc...
(o) +1 (603) 374-7120