Re: [PyMOL] Serine phosphorylation

[Thomas H. <tho...@sc...>]

Hi Wei,

Phosphorylating a serine with the builder works fine for me.

1) click "Builder" button -> opens panel and should automatically switch to "3-Button Editing" mouse mode
2) click on the serine's OG atom -> should create "pk1" selection
3) click "P=O3" button on the Builder panel

To change the orientation of the phosphate group, make sure you're in "3-Button Editing" mouse mode, then
1) double click the CB-OG bond with the *right* mouse button -> shows dihedral indicator
2) CTRL-drag any of the phosphate group atoms with the left mouse button

Cheers,
  Thomas

> On Jul 31, 2018, at 6:42 PM, Wei Song <wei...@gm...> wrote:
> 
> Hi all, 
> 
> I have a peptide structure and would like to phosphorylate one of the serine residues to test its binding capacity to a ligand. I tried the Build function with a PyMol 2.0, but only a phosphorous can be added to the serine. Does anyone have experiences of creating a phosphorylated residue with PyMol or other tools? 
> Any suggestions would be appreciated. 
> 
> Thanks,
> Wei 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.