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@ca overlap -500 hbond 0 bondSep 2 log true test :24.a,26.a,33.a@ca (that whole thing should be one line... the mail program may break it up) 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: <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> I hope this helps, Elaine ----- 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@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

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(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

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<http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/findclash/f...

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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@gmail.com>:

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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