[Chimera-users] Changes in protein stability

Elaine Meng meng at cgl.ucsf.edu
Fri Dec 21 12:02:27 PST 2018

Hi Kloe,
There are many tutorials, including “Getting Started” for new users, “Structure Analysis and Comparison” for examples of finding H-bonds and clashes, etc.

For general information of what’s available, you can look at the User’s Guide, which lists all the tools and commands with short descriptions of each:

Open tools from the Chimera Tools menu, for example:

Tools… Structure Analysis… FindHBond
Tools… Structure Analysis… Find Clashes/Contacts
Tools… Structure Editing… Minimize Structure

Not everything is included in some tutorial, but if you click the Help button on each tool it will show the full description of that tool and its options.
I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Dec 21, 2018, at 11:31 AM, Xhoela Bame <xhoelabame at yahoo.com> wrote:
> Thank you for the reply! 
> I do not need many specifities. I only need to imagine what could be the change. 
> Can I please have any more information or any website where I can learn the steps to perform local minimization/ count steric clashes/H bonding in Chimera?
> I do not know where to start from.
>  I would highly appreciate any clue.
> Thank you! 
> Kloe
> On Friday, December 21, 2018, 9:59 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Kloe,
> Chimera does not calculate free energies or thermodynamic stabilities, sorry.  This generally requires much more extensive modeling, such as long dynamics simulations with a dedicated package like AMBER, Gromacs, etc.  Other, more empirical programs (i.e. easier to use and shorter calculations) also exist for estimating the effects on stability of mutations, but I don’t have specific knowledge or recommendations in that area.
> What you can do with Chimera is simple first-order assessments of amino acid mutations or modifications of ligands, by simply counting up H-bonds and steric clashes, or performing small local minimizations, and using your own chemical intuition. I hope this clarifies the situation,
> Elaine

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