[chimerax-users] Distance between two atoms

[Elaine Meng]

Hi Phil,
Yes you can omit model number (#1 or whatever it is) if there is only one model, and yes, it is for when you have multiple models open.  Otherwise there would not be any way to distinguish between residue 10 in chain A of model 1 vs. residue 10 in chain A of model 2.  Several of the examples in that "target specification" page omit the model number.

The symbol # itself just means the number right after it is a model number.  You wouldn't really use the symbol by itself without a number.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Nov 16, 2022, at 7:41 AM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> 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
>