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, Iva ________________________________ From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Wednesday, April 6, 2022 5:22:17 PM To: Lucic, Iva Cc: chimera-users@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@ca #1:323.A@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@ca :323.A@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"): <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html> ...and there are many more example atom specifications in the atom-spec help: <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.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 Apr 6, 2022, at 7:25 AM, Lucic, Iva via Chimera-users <chimera-users@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@ca - :323.A@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