pymol-users

[PyMOL] fuse two proteins by a peptide bond

[Sheng <she...@ya...>]

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!

fuse
DESCRIPTION "fuse" joins two objects into one by forming a bond.  A copy of the object containing the first atom is moved so as to form an approximately resonable bond with the second, and is then merged with the first object. USAGE fuse (selection1), (selection2) PYMOL API cmd.fuse( string selection1="(lb)", string selection2="(lb)" ) NOTES Each selection must include a single atom in each object. The atoms can both be hydrogens, in which case they are eliminated, or they can both be non-hydrogens, in which case a bond is formed between the two atoms. 

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