dear Eric I sorry to trouble you. Could you just give a more function in Distances of structure analysis, please? When count the distance, we must select 2 atoms exactly. For example, use the command 'select #0:2@CA #1:3@CA' and then click create button, so that we will get the distance between the CA of residue 2 in model 0 and the CA of residue 3 in model 1. HOWEVER, if we type 'select #0:@CA #1:@CA', we can't get all the distances between all CA in model 0 and all CA in model 1! :( So, how about just adding one function, so that the Create button could count serial distance? Maybe it will just be 2 buttons, one for 'select #0:@CA' and the other for 'select #1:@CA'. I am sorry to trouble you, and many thanks. best wishes! Guo NOTE: Maybe you recommend me multiple distance! But I try a lot, such as 'measure distance #0:@CA #1:@CA multiple true'. This command just result the minimum distances between all CA in model 0 and CA in model 1, not all distances! In addition, I see the site 'http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009922.html', <http://www.cgl.ucsf.edu/pipermail/chimera-users/2014-May/009922.html',> too. I am sorry, it doesn't work for we don't know how small the overlap should be. (the smaller overlap, the more contacts would be detected)