[Chimera-users] Creating distances using the command line

Lucic, Iva Lucic at fmp-berlin.de
Thu Apr 7 00:20:33 PDT 2022

Dear Elaine,

Yes, it helped! Thanks a lot for your fast and accurate answer :)

I will keep an eye on the two links you shared with me.

Best regards,


From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Wednesday, April 6, 2022 5:22:17 PM
To: Lucic, Iva
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Creating distances using the command line

Hi Iva,
You almost had it.   There is no dash ("-") and no spaces in the specification of each atom, so could be something like

distance #1:347.A at ca  #1:323.A at ca

...if they are really in model #1.  Or if there is only one model open anyway, you don't have to give the model number:

distance :347.A at ca  :323.A at ca

You can see what number your model is in the Model Panel (open from Favorites menu).  They start with #0 so maybe your model is #0, not #1.

The "distance" help page has a few example commands (you can also show this page with command "help distance"):

...and there are many more example atom specifications in the atom-spec help:

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

> On Apr 6, 2022, at 7:25 AM, Lucic, Iva via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I would like to measure distances between atoms in a structure by using the command line, and not manually by clicking on the atoms and then clicking on "create" button in the Structure Measurements tool.
> I would like to map many distances on the same structure (I performed a crosslinking experiments, so I would now like to map the crosslinks on the structure of my protein of interest).
> I tried something like distance #1 :347.A at ca - :323.A at ca and similar variations, hoping that I could get the distance between CA atoms of residues 347 and 323 of chain A (there are 12 chains in my protein) from model 1. But I couldn't find a good combination of commands to give me a distance.
> I would highly appreciate any advice. Otherwise, I would have to map manually over 20 crosslinks for each chain...
> Thank you in advance,
> Iva

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