Use bond command bond atom1, atom2
once you do that, any subsequent line and stick renderings will connect the atom1 and atom2 (you can right-click on the corresponding atom to see their full string representation). I assume you are trying to do something like this http://tinyurl.com/y2cdezj In this figure, metal ion was connected to its ligands by lines, not sticks. Lines become thicker once you do ray-tracing. If you want to remove the connection, use the unbond command on the same atoms. HTH, Ed. On Fri, 2010-04-16 at 14:31 +0530, Hussain Bhukyagps wrote: > Hi! > > their is no connection between the metal and ligand in my pdb.. > how can i generate bonds between them using pymol..?? > by the way the distance between ligands and metal is 1.8-2.0 Ao...?? > > Hussain > > > Send free SMS to your Friends on Mobile from your Yahoo! Messenger. > Download Now! http://messenger.yahoo.com/download.php -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore ---------------------------------------------- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. ------------------------------ / Lao Tse /
