Hi Jason,

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


On Wed, May 19, 2010 at 10:39, Jason Vertrees <jason.vertrees@schrodinger.com> 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.


-- Jason

On Wed, May 19, 2010 at 12:22 AM, Nicolas Bock <nicolasbock@gmail.com> 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) Jason.Vertrees@schrodinger.com
(o) +1 (603) 374-7120