[Chimera-users] visualizing formal charges

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 24 15:27:12 PST 2020

In the rare case where a PDB lists the formal charges in columns 79-80 of the ATOM record (as per: wwPDB Format version 3.3: Coordinate Section <http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM>; [and very few entries have that info]), then the atoms in Chimera will have a “formalCharge” attribute that you can label by,


	Eric Pettersen
	UCSF Computer Graphics Lab

> On Feb 24, 2020, at 3:20 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 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 
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