[Chimera-users] how to change the atom type in chimera

[Elaine Meng]

Hi Hina,
Sorry, Chimera does not show double bonds with two lines, but you can show aromatic rings with a circle or disk.  For example, command:

aromatic circle

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/aromatic.html>

You can label atoms with atom types, for example menu "Actions... Label... IDATM type"

You can change atom type, for example with command setattr:

setattr a idatmType Car sel

(to change the selected atom(s) to aromatic carbon)

<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

The label will not change automatically, you would have to label again to see the change.

Here are the atom types:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

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 Dec 12, 2011, at 9:09 PM, Hina wrote:

> Dear All,
> Can you kindly let me know how to change or edit atom typing in chimera and how to visualize the ligands in the form that double bond single bonds aromatic centers are clearly seen.