[Chimera-users] distance measurements

sette at uniroma2.it sette at uniroma2.it
Fri Feb 19 03:23:48 PST 2010

this the answer that Elaine Meng gave some times ago.

Hi Jean-Paul,
The possibilities I have in mind are not particularly "automatic":

(a) use multiple "distance" commands, each specifying a pair of
atoms.  You would probably want to write a script in your favorite
language to create the Chimera command file with all those distance


(b) use the "findclash" command (or GUI) with an extremely lenient
cutoff (large negative overlap), which will report all the distances
within that cutoff.  Specify finding interactions between your one
residue and all other atoms to get the distances and overlaps for all
atom-atom pairs meeting the criteria.




With (b) you would get a lot of output to sift through.  If you wanted
only certain atoms, for example CA-CA distances only, you would either
just use approach (a) or use (b) with postprocessing to extract only
the lines of interest.

I hope this helps,

Def. Quota "Bala subramanian" <bala.biophysics at gmail.com>:

> Friends,
> Greetings. I have 5Aromatic residues and 4 aliphatic residues in a loop. I
> want to calculate the CA distance between between each of Aromatic with the
> CA of each of the aliphatic residues in a single command. Can i do it in
> some fancy way. I have tried distance command but it takes exactly two
> atoms. Any example script would be of great help to me.
> Thank you,
> Bala

Dr.Marco Sette, Ph.D.

Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:        sette at uniroma2.it
e-mail:        m77it at yahoo.it
Tel.:          +39-0672594424
Fax:           +39-0672594328

This message was sent using IMP, the Internet Messaging Program.

More information about the Chimera-users mailing list