Re: [PyMOL] side chain helper glycine

Hi Christian,

cartoon_side_chain_helper was implemented as an atom-level-setting in the latest Incentive PyMOL version. In older versions and in the current open-source, the setting is object-level. However, if you create a separate object like you said, it should work with these versions too. Just make sure you hide cartoon or unset the cartoon_side_chain_helper setting for that new object. Example:

PyMOL> fetch 1ubq, async=0
PyMOL> as cartoon
PyMOL> show sticks
PyMOL> set cartoon_side_chain_helper
PyMOL> create mygly, resi 35
PyMOL> as sticks, mygly
PyMOL> orient mygly

Cheers,
  Thomas

On 23 Jun 2014, at 14:13, Christian Roth <chr...@bb...> wrote:

> Hi there,
> 
> I used the side chain helper option to create a binding site in the 
> protein. However I want include a glycine, which doesn't show up. Even 
> when I create an extra object with the glycine and an neighbouring 
> residue I didn't get the carbonyl oxygen atom of glycine and I don't 
> want to switch of the side chain helper function for all residues.
> Is there a way to get that done without switching the helper function 
> completely off?
> 
> Thanks in advance for your help
> 
> Christian

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.