[Chimera-users] Amino acid substitution with Chimera

Elaine Meng meng at cgl.ucsf.edu
Wed May 19 16:38:32 PDT 2010

Hi Hayeon,
You would use the Rotamers tool or the command swapaa.

For more details, please see this previous post, "mutating residues":

Please note, however, that Chimera will only change the side chain.  It can try to use the conformation of that one sidechain that has the least clashes with the rest of the structure, but it will not predict how the backbone and other residues might change after the mutation.

However, from observing the change, you can make first-order predictions such as whether the new side chain can form a hydrogen bond or whether it is likely to disrupt packing.

After the change, you can perform a simple minimization (see Tools... Structure Editing... Minimize Structure), but that will only go to the closest local minimum and will not sample the different conformations that might be possible.  In my opinion, minimization is not useful in this situation.

To make a more detailed prediction, it would be necessary to use some other program, such as a homology modeling program or a simulation package like AMBER.

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 May 19, 2010, at 11:38 AM, Hayeon Kwak wrote:

> Hi,
> I am currently working on a homology-modelled protein.
> How do I mutate a certain amino acid with Chimera?
> For example, if I wanted to mutate 55N into 55K to look at how the structure changes, what would I do?
> Any help would be appreciated.
> Thank you.

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