[Chimera-users] Relevant interacting amino acids between molecules

Ogunniyan, Abisola aabisoye-ogunniyan4879 at mytu.tuskegee.edu
Tue Apr 15 18:04:00 PDT 2014

Dear Elaine,

Thank you for the prompt response.
I will go through the tutorials and I am sure it will be of great help.

Thank you.

Best Regards,

Abisola Abisoye-Ogunniyan

On Tue, Apr 15, 2014 at 5:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Abisola,
> You can use the "Find Clashes/Contacts" tool or just a simple distance
> cutoff to find all the amino acid residues in one protein that are close to
> another molecule, which could be a small ligand, or another protein, DNA,
> etc.
> There is an example of using "FindHBond" and "Find Clashes/Contacts" to
> identify amino acids interacting with a ligand molecule in the "Structure
> Analysis and Comparison" tutorial:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
> >
> It would be very similar to find the H-bonds and contacts between amino
> acids and some other kind of molecule (such as another protein), you would
> just need to select that other molecule instead of the ligand molecule.  I
> think it will be clearer if you try that tutorial.
> Or, for simple cutoff you can first select one molecule and then use menu:
> Select... Zone to also select the nearby residues.  Once they are selected,
> you can do other stuff with the Actions menu like labeling them, or getting
> a list of them as in the tutorial mentioned above. How to select:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>
> There is a more advanced example of using findclash (the command version
> of Find Clashes/Contacts) to color the atoms involved in a protein-protein
> interaction in the "Opened Interface" image tutorial:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/openbook.html>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Apr 15, 2014, at 2:34 PM, Ogunniyan, Abisola wrote:
> > Hi,
> > My name is Abisola Abisoye-Ogunniyan, a first year Biology Graduate
> student in Tuskegee University. I got to learn about the use of Chimera in
> my Biochemistry Class.
> > I have been having difficulty in trying to determine the relevant
> interacting amino acids between molecules.
> > Please, I will really appreciate it if this is made clearer to me.
> > Thank You.
> > Best Regards,
> > Abisola Abisoye-Ogunniyan.
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