[chimerax-users] Distance between two atoms

[Elaine Meng]

Hi Phil,
When I used the selection context menu approach (pick atoms from screen) then my Log showed this:

distance /A:310 at O4 /A:236 at OD1

The / symbol means chain ID, the : symbol means residue number, and the @ symbol means atom name, as explained here:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>

There are several examples in that page if you scroll down a bit from there.

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


> On Nov 15, 2022, at 3:25 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi Elaine,
> 
> Hi Elaine,
> 
> Well I am having fish tonight 😉.  I used your suggestion select the atoms on the screen and then run the pop-up distance command and reading the results in the Log.  I am still not fully clear about defining atoms and such after reading the atoms page.  I will keep working on it.
> 
> Thanks for your help.
> 
> Phil
> From: Elaine Meng <meng at cgl.ucsf.edu>
> Sent: Tuesday, November 15, 2022 11:03 AM
> To: McClean, Phillip <phillip.mcclean at ndsu.edu>
> Cc: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
> Subject: Re: [chimerax-users] Distance between two atoms
>  
> Hi Phil,
> There is a "distance" command, use command "help distance" or see the help at our website here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/distance.html>
> 
> ...and many examples of how to specify atoms in the command line here:
> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html#hierarchy>
> 
> Why don't you give it a few tries? We need to "teach a man to fish" since we can't tell thousands of users how to write each command they need for their research.
> 
> Or you can just choose the atoms from the screen: first make sure they are displayed so you can actually see them, and then Ctrl-click one, Shift-Ctrl-doubleclick the second one and choose "Distance" from the resulting pop-up menu.  This also is described in the help  (Selection Context Menus):
> <https://rbvi.ucsf.edu/chimerax/docs/user/selection.html#context>
> 
> Best,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> > On Nov 15, 2022, at 8:30 AM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> > 
> > Hi Everyone,
> > 
> > I have a two chain model.  I would like to determine the distance between the CD1 atom of residue 77 in chain B and the CD1 atom of residue Leu 150 in chain C.  What would be the proper distance command.
> > 
> > Thanks for the help again.
> > 
> > Phil McClean