[Chimera-users] distance measurements

Elaine Meng meng at cgl.ucsf.edu
Fri Feb 19 08:01:10 PST 2010

Thanks so much, Marco, I thought the question seemed familiar!

Yes, the possibilities are still (a) and (b) as described in my  
previous answer below, but we have made an improvement in the daily  
builds (version 1.5) in findhbond and findclash to make it easier to  
specify two groups of atoms and find only the interactions between  
those groups.  This allows you to get only the distances you want  
instead of having to sift through a lot of other output.

The improvement is also in the Find Clashes/Contacts graphical  
interface, but an example command is:

findclash :23.a,29-32.a at ca overlap -500 hbond 0 bondSep 2 log true  
test :24.a,26.a,33.a at ca

(that whole thing should be one line... the mail program may break it  

where the first group of atoms is CA atoms of residues 23 and 39-32 in  
chain A and the second group of atoms is CA atoms of residues 24, 26,  
and 33 in chain A, and the resulting 15 distances are written to the  
Reply Log.  The last column in the results is the distance.  I use a  
large negative cutoff (see keyword "overlap") to measure the distances  
even if they are far apart.  The command has many more options, such  
as saving to a file, see:


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

On Feb 19, 2010, at 3:23 AM, sette at uniroma2.it wrote:

> Hi,
> this the answer that Elaine Meng gave some times ago.
> bye
> Marco
> --------------------------------------------------
> 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
> commands.
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/distance.html
> ;
> (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.
> <http://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/findclash.html
> ;
> <http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findclash/findclash.html
> ;
> 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,
> Elaine
> 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

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