[Chimera-users] A question about "Distance Measure"

[Elaine Meng]

Hello,
Just look carefully at one protein chain first.  Distances are measured between atoms.  So you have to first figure out what atoms are at the C-term and N-term that you want to use for the measurement.  

(1) open structure, show all atoms (e.g. menu: Presets... Interactive 2 (all atoms))

(2) if you don't already know their residue numbers, find N-term and C-term.  There are many ways to do it.  One way is to show Sequence (menu: Favorites... Sequence, choose the chain that you are looking at, show its sequence), and then in the sequence window:

- draw a box to highlight the first residue in the chain (green box in sequence will be shown as selection on 3D structure)
- zoom in on and label those atoms, e.g. commands

focus sel
label sel
rlabel sel

That is just the N-terminus, decide which atom you want to use for the measurement and write it down.  E.g. my protein has these atoms at the N-terminus so I could decide to use atom "N" of residue 1 in chain A.



Then repeat to find and label the C-terminal residue (select in sequence window the last residue in the structure, focus sel, etc.).

(3) Then you have a list of the two atoms you want to use, and can use a command to add the distance, for example:

distance :1.A at N :309.A at C

...meaning measure distance between residue 1 in chain A atom N, and residue 309 in chain A atom C.

There are other ways too, e.g. Ctrl-click first atom in 3D view, then find 2nd atom and Ctrl-doubleclick, and then choose Distance from the context menu that pops up.  See examples in tutorial, and the Distance help:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#distances>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Feb 3, 2023, at 6:40 AM, squirrel via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear Ms/Mr：
> Thanks for your wonderful tool! 
> I meet a problem recently. Every proteins have N-terminations and C-terminations, and I want to measure the distance between all proteins at each other's N-C, N-N, and C-C terminals by using UCSF Chimera. But there are too many proteins for me to start.I've read Chimera's tutorials and searched my questions online. But I didn't find the answer I needed.Can you please give me some guidance or tips？ 
> 
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