Hi Joshi, The distance command doesn’t have a save-to-file option. However, you can use the “findclash” command to find all pairwise distances among a set of 2 or more atoms, and it does have a save-to-file option. You could either first select all the atoms you want and then use “sel” in the findclash command, or just list all the atoms you want directly in the findclash command, as in the example below. The trick to get all pairwise distances and not just short clash distances is to use a large negative overlap cutoff in the command, something like: findclash #0:13,48,129@ca test self overlap -100000 saveFile /Users/meng/Desktop/distances.txt There are several other options, including line width and color, and “log true” to show in the Reply Log the same thing that would be written to the saved file. See: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> The results are something like the following. You could ignore the overlap column and just look at the distance(s) in the last column: 3 contacts atom1 atom2 overlap distance ASP 13.A CA GLN 48.A CA -11.493 15.253 ASP 13.A CA ALA 129.A CA -32.639 36.399 ALA 129.A CA GLN 48.A CA -43.052 46.812 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 13, 2018, at 12:30 AM, Dhananjay <dhananjay.c.joshi@gmail.com> wrote:

Dear all, I am calculating distance between CA atoms as follows:

sel #0:13@CA, #0:129@CA color red selection distance #0:13@CA #0:129@CA

I want to save the measured distance between residue 13@CA and 129@CA in a file. I can do it using GUI. How can I do this within the command line ?

Any help would be appreciated !! Thank you -- Joshi