Hi Bishwajit, Again, there is no specific tool, you would use the general tool for finding contacts. Either you would find all contacts and then determine yourself which are pi-cation, or restrict identification to only aromatic rings and cationic atom types. You would still need to check visually, however, since "contacts" depend only on distance and VDW radii, but not the angle of the interaction. Example commands: sel aromatic ring findclash sel test Ng+|N3+ overlap -1 hb 0 log true You might want to use different command options, such as saving distances to a file, different cutoff distance, including more cationic atom types, etc. <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/findclash.html> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/idatm.html> 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 9, 2012, at 7:45 AM, Bishwajit Das wrote:
how to find cation pi-interaction in a docked molecule.......plz help me