Re: [PyMOL] drawing of objects for illustration

[Nicolas B. <nic...@gm...>]

Hi Jason,

nice. I didn't know about the pseudoatoms, very cool.

nick


On Wed, May 19, 2010 at 10:39, Jason Vertrees <
jas...@sc...> wrote:

> Hi Nicolas,
>
> Cool idea.  First the "witihin" operator works on more than just
> single atoms.  So, how about something like this:
>
> # fetch a protein
> fetch 1oky, async=0
>
> # let's target _all_ atoms within 8 Angs of _all_ of
> # residue 55, not just one atom
> select target, all within 8 of i. 55
> color red, target
>
> cmd.center("i. 55")
> vPos = cmd.get_position()
>
> cmd.pseudoatom("identifier",pos= vPos);
> show_as spheres, identifier
> cmd.set("sphere_transparency", 0.5, "identifier")
> cmd.set("sphere_scale", 8, "identifier")
>
> In sum, use pseudoatom for and position it at vPos.
>
> Cheers,
>
> -- Jason
>
> On Wed, May 19, 2010 at 12:22 AM, Nicolas Bock <nic...@gm...>
> wrote:
> > Hello,
> >
> > I would like to do the following: I have a large protein loaded in pymol.
> I
> > would like to select all atoms within a radius around a point. I know
> about
> > "select within", however, this command requires the second selection to
> be
> > an atom. I would prefer if the center of the sphere is not necessarily
> > centered on an atom. Is this possible? In addition I would like to draw
> the
> > spherical selection region somewhat transparently, so that I can
> illustrate
> > what I have selected. Is that possible?
> >
> > Thanks already,
> >
> > nick
> >
> >
> >
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>
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) Jas...@sc...
> (o) +1 (603) 374-7120
>