Hi Elaine, thanks a lot!!! Very useful command :) Marco Quoting Elaine Meng <meng@cgl.ucsf.edu>:
Hi Marco, Yes, you can even do it in a single step, but not with the distance command, which takes only two things at a time (two atoms, or one atom and one axis, etc.): <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/distance.html>
To get multiple atom-atom distance measurements at once you would use Find Clashes/Contacts (in menu under Tools... Structure Analysis) or the "findclash" command. Although the cutoff you specify is the VDW overlap (distance between surfaces of VDW spheres, which can be positive or negative), it will output not only the overlaps but also the center-center distances. The output can be written to Reply Log or to a file. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclas...> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html>
For example, to measure distances between atoms named HN in model #0 and nearby atoms named HA in model #1:
findclash #0@hn test #1@ha overlap -4 hbond 0 log true
would find all HN-HA pairs with VDW surfaces within 4 angstroms of each other (make sure those are the correct atom names, and you could use larger negative cutoff to find pairs farther apart) and write all the overlaps and center-center distances of those pairs to the Reply Log. There's another example in this previous post: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008741.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 May 28, 2014, at 3:14 AM, sette@uniroma2.it wrote:
Hi Elaine, thanks a lot. It is possible, in the last version to measure distances from one (or more) single atoms and other groups of atoms? for example HN of a protein and ha of that proteins? Thanks, Marco
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 www.rete29aprile.it ---------------------------------------------------------------- Invito da parte dell'Ateneo: Il tuo futuro e quello della Ricerca Scientifica hanno bisogno del tuo aiuto. Dona il 5 x mille all'Universita' di Roma Tor Vergata codice fiscale: 80213750583 http://5x1000.uniroma2.it