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@CA1,CA2 /c:76,79,195,109,149,150@CA1,CA2,CH2,CZ2 Error message: No atoms match given atom specifier Thanks for the help. Phil ________________________________ From: McClean, Phillip <phillip.mcclean@ndsu.edu> Sent: Tuesday, November 15, 2022 5:25 PM To: ChimeraX Users Help <chimerax-users@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@cgl.ucsf.edu> Sent: Tuesday, November 15, 2022 11:03 AM To: McClean, Phillip <phillip.mcclean@ndsu.edu> Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@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@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