[chimerax-users] Distance between two atoms

[McClean, Phillip]

Hi Elaine,

Rather than measure the distance atom by atom, I constructed the following command.  Again, I have two chains, and I want to limit the search just to specific atoms affiliated with those residues.  The residues I listed are hydrophobic molecules that are interacting at two hydrophobic interfaces defined by the "mlp" command.  The atoms refer to those pointing at the second interface.

Here is the command I created, and the error associated with it.

contacts /b:77,81,84 at CA1,CA2 /c:76,79,195,109,149,150 at CA1,CA2,CH2,CZ2

Error message:
No atoms match given atom specifier

Thanks for the help.

Phil
________________________________
From: McClean, Phillip <phillip.mcclean at ndsu.edu>
Sent: Tuesday, November 15, 2022 5:25 PM
To: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Distance between two atoms

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

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