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/f... ; 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>:
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@uniroma2.it e-mail: m77it@yahoo.it Tel.: +39-0672594424 Fax: +39-0672594328 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.