[Chimera-users] one more suggestion in chimera

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 15 12:40:45 PDT 2018

> On Jun 14, 2018, at 8:14 PM, GLY <lcmj520 at 126.com> wrote:
> 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 at CA #1:3 at 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
> 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', 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)

Hi Guo,
Eric shared your mail with this address for Chimera user questions.  Yes, “measure distance” only gives the minimum distance, not all of the pairwise distances.

As you saw in the previous post 
… you can get multiple pairwise distances with a single “findclash” command.  Just set the overlap as a large negative number,  for example,  if you think the distances might be up to 1000 Angstroms, just use overlap -1000:

findclash #0:@CA  test #1:@CA  overlap -1000 log true

See command options here:

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

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