Re: [PyMOL] make bond between two atoms

[Jason V. <jas...@sc...>]

Hena,

> I created two objects as follows:
>
> pseudoatom A1, pos=[10.0, 10.0, 100.0]
> pseudoatom A2, pos=[10.0, 10.0, -200.0]
>
> I want to create a bond between these two atoms. Could you please help me? I
> need to display a 2 fold axis passing through these points.

You can create a distance measure between them as shown here,
http://www.pymolwiki.org/index.php/Pseudoatom. Or you can do this:

pseudoatom foo1, pos=[0,0,0], name=CA
pseudoatom foo2, pos=[1,1,1], name=CB

create foo, foo1 or foo2

bond foo////CA, foo////CB

which creates a single object from the two pseudoatoms and bonds the
two pseudoatoms.

Cheers,

-- Jason

--
Jason Vertrees, PhD
Director of Core Modeling Product Management
Schrödinger, Inc.

(e) Jas...@sc...
(o) +1 (603) 374-7120