[Chimera-users] changing atomic radii in Chimera

[Elaine Meng]

Hi Yu Guo,
(including chimera-users in the message since it is a general question that other people might be interested in)

You can change atomic radii as shown in sphere style with command “vdwdefine,” for example
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>

vdwdef -0.2 Ca
  (subtract from current size)
vdwdef 1.0 Ca
   (set size to specific value)
 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/vdwdefine.html>

Maybe the single O atoms (those without bonds) are in stick style, however, so you would also need to change them to sphere style to see a difference. Since the molecule also has O you wouldn’t want to use “O” in the commands or you would change them all.  Instead you could select them (Ctrl-click on atom) and then use “sel” in the command, e.g.

repr sphere sel
vdwdef 0.8 sel 

Actually, if you select the atom(s) another way is to use Selection Inspector (open by clicking green magnifying glass icon near the bottom right of the Chimera window) to change their display style and radius.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/inspection.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Dec 7, 2018, at 11:05 AM, Yu Guo <yg2 at kth.se> wrote:
> 
> The movie is fine now! I am now wondering how can I change the atomic radii in Chimera? I find Ca is much too big, and O is too small. See the attached movie.