[chimerax-users] Measuring distance between two atoms in a single protein

[Elaine Meng]

Hi Phil,
Well, the short (and likely unhelpful) answer is that you have to select only two atoms!  If you are selecting on the ribbon, for example, that will select all the atoms in the residue.  So if you're showing ribbons but not the atoms, you may need to display the atoms so that you click on exactly two.  For example, commands:

hide ribbon
show atoms

But I don't know if that is the problem in your specific case.   You can list the selection in the Log so that you can see exactly which atoms ChimeraX thinks are selected at the time, e.g. with command:

info atoms sel

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/info.html#atoms>

Also if you can really select just two atoms, if you Ctrl-click the first and Shift-Ctrl-doubleclick the second, there should be a pop-up context menu that includes the choice "Distance" (so that you don't have to start the tool to measure the distance).  See "selection context menus"
<https://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>

Finally, instead of selection, if you knew the residue numbers you could just specify the exact atoms in distance command something like:

distance #1/A:35 at CA #1/A:45 at CA

... meaning measure distance between alpha-carbons of residues 35 and 45 in chain A of model 1.
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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

> On Jul 11, 2022, at 3:14 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Chimerax Group,
> 
> I am trying to measure the distance between two atoms in a protein in Chimerax v1.4.  The .pdb file I am working with was generated using Alphafold2 in the ColabFold application.
> 
> I select the two atoms by using CTRL+SHIFT, go to the TOOL -> Structure Analysis -> Distances. The Structure Measurements panel appears in the lower right of the screen.  When I click on the Create button, a Chimerax box appears on screen with the following message:
> 
> Exactly two atoms must be selected!
> 
> I was surprised to see this message since I thought I had properly selected two atoms.
> 
> Any advice on how to calculate the distance would be greatly appreciated.
> 
> Thanks in advance for any help you can provide.
> 
> Phil McClean
> Professor
> North Dakota State University