[Chimera-users] Swapping aminoacid to a non-standard residue

Elaine Meng meng at cgl.ucsf.edu
Tue Sep 23 10:07:39 PDT 2014

Hello Rui Almeida,
Just now I used the SwissSidechain plugin to Chimera to swap an amino acid to NIY, and then I could minimize (which adds hydrogens and charges first) without problems.

The Chimera Rotamers tool and "swapaa" command only include standard amino acids, whereas the SwissSideChain plugin includes many nonstandard amino acids.  Plugin download and instructions here:

After installation, it is available as a GUI similar to Rotamers (menu: Tools… Structure Editing… SwissSidechain) and command "swapnaa" as described in that page.

However, it should also be OK to add the nitro group yourself by building it in Chimera.  My guess is maybe the atom types were not correct.  In my swapped NIY that didn't have any problems with charge calculation (I tried both AM1-BCC and Gasteiger options in addcharge), the atom types of the nitro group were Ntr, O2-, O2-.  

You can label the selected atoms by atom type with menu: Actions… Label… IDATM type.  There are several ways to change atom type, e.g. with "setattr" command, for example if you selected the atom first: 

setattr a idatmType Ntr sel

The label won't update automatically; you'd have to label again to see the change.
I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Sep 23, 2014, at 9:38 AM, Rui Almeida <rui.almeida at fct.unl.pt> wrote:

> Hello all
> I am trying to change one aminoacid on a PDB file to a nonstandard residue: TYR to nitrotyroine (PDB ligand code: NIY). I tried modifying the structure of the existing aminoacid in the coordinate file to include an NO2 group in the meta position (Structure Editing --> Build Structure --> Modify Structure...), but ANTECHAMBER cannot assign the correct charges afterwards. Command "swapaa" was also ineffective. Is there anyway to modify the residue and assign the correct charges?
> Thank you in advance,
> Rui Almeida.

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