[chimerax-users] Distance between two atoms

[McClean, Phillip]

Hi Elaine,

Yes, I picked up the command info also from the Log.  It is a good way to learn; thanks for the tip.

I had in the past tried to better understand the details in the Atom Specification page.  Some I understood, others, not so much.  What has always been a puzzle is why a model number is used?  I am assuming now that the # symbol is need to distinguish models when two are loaded in the same session.  Make sense?  Otherwise, I don't really understand the use of that symbol.

Phil
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, November 15, 2022 6:06 PM
To: McClean, Phillip <phillip.mcclean at ndsu.edu>
Cc: ChimeraX Users Help <chimerax-users at cgl.ucsf.edu>
Subject: Re: [chimerax-users] Distance between two atoms

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




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