[chimerax-users] Distance between two atoms

[McClean, Phillip]

Hi Elaine,

First the error in the atom designation was on my end; it should have been CD not CA.

I used your last command and found what I wanted.  My goal was to see if hydrophobic interactions were similar across the two hydrophobic faces of a heterodimer.  I was using the distance of atoms of the hydrophobic residues as a proxy for hydrophobicity.  One model contained the wild type allele of one protein of the heterodimer, while the second model contained the alternate (mutant) amino acid of the same reference protein of the complex.  I then used a T-test to determine if the distance varied between complexes.

Nice to figure the answer out with Chimerax.

Thanks again.

Phil
________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, November 16, 2022 5:06 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,
I can't tell what is wrong with your specification. From the error message, I can only say that the specification doesn't match what is in your structure.  I'm guessing the atom names are wrong because amino acids don't contain atoms named CA1 and CA2 (amino acids only have one alpha-carbon). If I recall correctly, the only one that has CH2 and CZ2 is tryptophan, but are all the residue numbers you list for chain C tryptophans? If a specific atom name only goes with one residue number, then you can interleave them, e.g.   /c:76 at ch2:149 at cb

The contacts command will already limit the results to pairs of atoms within reasonable contact distance of each other, so maybe you can just try leaving off the atom names, e.g. the following, which works for 4hhb:

contacts /b:77,81,84  /c:76,79,195,109,149,150 log true

But that will find all interactions among all those atoms.  If you want to treat them as two separate groups, then you need something like

contacts /b:77,81,84 restrict /c:76,79,195,109,149,150 log true

Or if you want only hydrophobic contacts, there are various ways to limit the set of atoms, e.g. element C (carbon) only:

contacts (/b:77,81,84 & C) restrict (/c:76,79,195,109,149,150 & C) log true

<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

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 16, 2022, at 1:42 PM, McClean, Phillip via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>
> 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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