[Chimera-users] Add hydrogens to get -NH2 group

Eric Pettersen pett at cgl.ucsf.edu
Fri Dec 2 15:06:14 PST 2005

Hi Dan,
	Chimera assumes that sp3 nitrogens bonded only to sp3 carbons and/or  
hydrogens are positively charged at physiological pH.  That means  
that their idatmType attribute is "N3+".  If you actually do want to  
use the neutral species, you need to get the idatmType changed to  
"N3" before adding hydrogens.  Here is some Python code that will  
change all selected nitrogens' idatmType to "N3":

--- start code ---
import chimera
for a in chimera.selection.currentAtoms():
	if a.element.name != "N":
	a.idatmType = "N3"
--- end code ---

You could either type that code into the IDLE interpreter (Tools- 
 >General Controls->IDLE) or put it in a .py file and open that file  
with File...Open or with Chimera's command line.


                         Eric Pettersen
                         UCSF Computer Graphics Lab
                         pett at cgl.ucsf.edu

On Dec 2, 2005, at 6:53 AM, Daniel Svozil wrote:

> Hi all,
> if I use addH tool on the C-N, I would expect to get C-NH2, but I get
> C-NH3 instead. How should I proceed to get C-NH2 correctly?
> Thanks
>    Dan
> -- 
> Daniel Svozil, PhD
> Institute of Organic Chemistry and Biochemistry
> Center for Biomolecules and Complex Molecular Systems
> http://www.molecular.cz/~svozil
> Czech Republic
> phone: +420-220 410 312
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users

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