Re: [PyMOL] Defining and Selecting molecules

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

>> The system I am studying has an amide of interest (oleamide) in oil (At
>> the moment just dodecane molecules).
>> I have seen in the manual how to select individual elements, but is it
>> possible to select either the Nitrogen or oxygen in my oleamide
>> molecules, and then select all atoms which are bonded to this to
>> therefore select the entire oleamide molecule.

PyMOL has some powerful selection operators, here are a few that might help you:

(1) Select a complete residue based on one atom
select aRes, br. someAtom

(2) Select a complete molecule based on one atom:
select aMol, bm. someAtom

(3) Select all atoms bound to another atom:
select boundTo, neighbor someAtom

(4) Select organic small molecules
select myLig, org

So, if your case I would try:

select oleamide, bm. anyOleoAtom

If the ligand is bound to the protein, you'll get the entire object,
so try "br." instead to get just the ligand.

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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