[Chimera-users] visualizing formal charges

[Elaine Meng]

Hi Tasneem,
Sorry, I can’t think of a way to directly label by formal charge, other than by creating these labels manually yourself.  If you add hydrogens, you may be able to infer the formal charge just by looking at the hydrogens, or if you label by atom type, you may be able to infer the formal charge based on the knowledge of which types represent formal charge.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

Commands to label by atom type: 

labelopt info idatmType
la O | N

(that middle thing is a vertical bar, not a capital letter I or lowercase letter l)

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/labelopt.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#atprops>

If you know the formal charge and you just want to create labels illustrating this for a figure, you can manually add them as 2D Labels, or by changing the text in the regular (“3D” labels) using the “setattr” command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/setattr.html>

E.g. 

open 1gcn
disp
setattr a label "-“ :asp,glu at od1
setattr a label “+” :lys at nz

For 2D Labels (that don’t move when you move the structure) see:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/2dlabels/2dlabels.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 Feb 24, 2020, at 1:45 PM, Tasneem Vaid <tasneem1188 at gmail.com> wrote:
> 
> Hi everyone,
> I want to see the formal charges on the ligand as well as the receptor. Is there a way to get that in Chimera? 
> There is an option of setting charges under ‘label’, but that gives partial charges and not formal.
> Thanks,
> Tasneem