[Chimera-users] Chimera

[Elaine Meng]

> On Dec 16, 2018, at 6:05 AM, Xhoela Bame <xhoelabame at yahoo.com> wrote:
> 
> Hello,
> 
> I hope this message finds you well.
> 
> I had posed a question in chimera website but maybe it did not come to you.
> 
> I am studying ligand interaction with a protein and there are pi pi interaction. I am not sure on what is the principle I have to use to show that there is this type of interaction and illustrate that with chimera.
> 
> Also, when showing H bonds, I want to show residue side chain as well in the picture as open structures. Any suggestion on that?
> 
> I am quite new in using chimera and I would be extremely helpful if you would help me on these questions.
> 
> Best,
> Ann

Hello,
In the future, please send questions to chimera-users at cgl.ucsf.edu rather than to me directly, and put something useful about the topic in the Subject line like “showing side chains” or “pi-pi interactions.” 

I did reply to you already about the pi-pi question but perhaps you did not see the answer.  I changed the subject line because “Chimera Usage” was not descriptive.  Here is that previous answer:
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2018-December/015270.html>

To show the side chains, turn on this option of FindHBond before running the H-bond calculation: "If endpoint atom hidden, show endpoint residue”
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findhbond/findhbond.html>

If you click Help on the FindHBond dialog it would show you that page.  

Or if you are using the commands, command “help hbonds” would show you the “hbond” command help and its “reveal” option to do the same thing.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/hbonds.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco