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 /
|