[chimerax-users] issues with rotamers tool

[Elaine Meng]

Hi Alejandro,
We have not seen such a problem.  Maybe you are accidentally selecting the whole structure, or all of the residues of a certain type instead of just one residue? 

To select just one residue, you can Ctrl-click on one atom or bond in that residue, or even just its ribbon segment. Then, only that atom, bond, or ribbon segment should have a green outline.  (However, if only the ribbon is shown, it would be best to show the sidechain atoms, at least for that residue, e.g. command “show sel” … then the green outline should include that whole residue, but not anything else in the structure.)

One very important thing to understand about the Rotamers tool is that you should NOT use only the probability to choose the rotamer.
<http://rbvi.ucsf.edu/chimerax/docs/user/tools/rotamers.html>

The probability is not the overall probability considering your specific structure; instead it is based only on the backbone angles.  In other words, the rotamer with the highest probability is just the one that was seen the most often in a database of structures at positions with backbone angles similar to the backbone angles at the position in your structure. However, the sidechain in that rotamer might not fit well into your specific structure.  It might be making poor interactions with the other atoms.

Currently you can use the “swapaa” command instead of the Rotamers tool to choose the best rotamer;  by default, this command will automatically also consider also H-bonding and avoiding clashes with other atoms in your specific structure, instead of only using the database probability value.  Example commands:

swapaa sel phe
swapaa #1/A:45 ser

<http://rbvi.ucsf.edu/chimerax/docs/user/commands/swapaa.html>

Rotamers is still under development and later we will be integrating H-bond and clash measurements into that tool, but it has not been done yet.  (The Rotamers tool in Chimera has H-bond and clash measurements integrated, and we plan to do something similar for ChimeraX.)

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

> On Oct 8, 2019, at 12:05 PM, Llorente, Alejandro <alejandro.llorente at Vanderbilt.Edu> wrote:
> 
> Hi, I am new PhD student using ChimeraX and I am very interested in learning how to work with this program.
> I am trying to introduce some mutations in my protein in some specific amino acids that I have selected. When I introduce an Alanine in my position of interest (using dunbrack) I have no issues, but when I try any other amino acids (as Phe or Thy) the program has no problem giving me the prediction for the rotamers, but I have some issues. After select some of the most probable rotamers, all the amino acids of my protein change to that kind of amino acid (not just the specific one that I have selected).
> 
> 
> Another problem is that I have is that when I select a specific atom of an amino acid, the program also select similar atoms but in all the others amino acids of my protein.
> I really hope that someone can help me with these issues.
> Thank You very much
>  
> Alejandro Llorente.