[Chimera-users] Gold atoms

Lia Thompson justmelia1966 at gmail.com
Thu Apr 13 09:02:11 PDT 2017


On Thu, Apr 13, 2017 at 10:30 AM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Small correction: default ball scale factor is 0.25
>
> Elaine
>
> > On Apr 13, 2017, at 8:25 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> >
> > Dear Dominique,
> > Ball radius is ball scale factor multiplied by sphere radius, with
> default ball scale factor = 0.2.  The sphere radius is a VDW radius or
> ionic radius, see the page on “VDW radii” and links therein for the default
> values and how to change the values:
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwrad.html>
> >
> > As mentioned in that page, you can change the sphere radius of an atom
> to basically whatever you want with command “vdwdefine”, e.g.
> >
> > vdwdef +1 Au
> > vdwdef 2 Au
> >
> > …to set radius of element Au 1.0 Angstrom larger than current (relative)
> or to 2.0 Angstroms (absolute).  You could use other specifiers like atom
> name, residue number, etc. instead of the element symbol, but it sounded
> like element symbol might be convenient in your case.
> > <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>
> >
> > You can also change the ball scale factor for a whole model in the
> Selection Inspector or with command “setattr”.
> > I hope this helps,
> > Elaine
> > ----------
> > Elaine C. Meng, Ph.D.
> > UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> > Department of Pharmaceutical Chemistry
> > University of California, San Francisco
> >
> >> On Apr 12, 2017, at 10:57 PM, Dominique Matt <dmatt at unistra.fr> wrote:
> >>
> >> Dear Colleagues,
> >> I am an enthusiastic Chimera user.
> >> I recently got some structures of gold complexes and noticed that the
> when using the ball&stick or the sphere representation, gold atoms are too
> small, while palladium atoms are absolutely OK.
> >> What can I do to increase the size of the gold atoms ? Or could you
> correct this directly in the online program ?
> >>
> >> I thank you for your help
> >> Sincerely,
> >> Dominique MATT
> >> CNRS Research Director
> >
> >
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>
>
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