Re: [PyMOL] fuse two proteins by a peptide bond

[Thomas H. <sp...@us...>]

Hi Sheng,

you can do this interactively in "Editing Mode". Choose "Mouse > 3
Button Editing" from the menu or click the lower-right panel in the main
window.

In Editing Mode, you can pick single atoms into named selections (pk1,
pk2, ...). So for your peptide bond, pick the N and the C, type "fuse"
and hit enter. To adjust the torsion angle, you can CTRL+Drag with the
left mouse button.

If you want to fuse non-interactively (using a script), you can select
the endpoint atoms using PyMOL's powerful selection language:

PyMOL> fuse last (obj01 and name C), first (obj02 and name N)

Hope that helps.

Cheers,
  Thomas

Sheng wrote, On 11/19/12 02:55:
> Dear,all
> I'm a new user.
> I wonder how to fuse two proteins by a peptide bond using pymol  ? (from
> 2 .pdb files into 1 file)
> I found the following description in user manual.but I don't know how to
> select a single atom.
> I know it sounds silly, but I really don't know how to do this step.
> I  really appreciate your help!

--
Thomas Holder
PyMOL Developer
Schrödinger Contractor