[Chimera-users] Gold atoms

Elaine Meng meng at cgl.ucsf.edu
Thu Apr 13 08:25:01 PDT 2017


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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