Re: [PyMOL] Atom Connections

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

Brett,

> Thank you for your help Jason.  I think this will work for my needs.
> By one side vs. the other, I mean let's say we just look at the backbone of
> a protein consisting of 5 residues, numbered 0, 1, 2, 3, 4
> I want to click on the C-a atom of residue 3, and generate 2 selections, one
> selection will be C and O of residue 3, along with all atoms of residue 4,
> and the second selection will be N of residue 3 and all atoms of residues 0,
> 1, and 2.
> I think I can do that given the commands you suggested.
> -Brett

This sounded like a fun little programming task.  I wrote the script
to select the two halves of the protein based on an initial selection.
 That is, you select any atom, and two new selections are created when
you run the script.  The first selection has the atoms with lower IDs
and the other has the atoms with higher IDs, just as you wanted.  I
posted the script on the PyMOLWiki:

    http://www.pymolwiki.org/index.php/Split_selection


I made it pretty simple, and there are many options & pitfalls you may consider:
  (*) assumes ids are increasing with the chain
  (*) assumes your original selection has an alpha carbon
  (*) assumes you want to ignore atoms not in other objects
  (*) no cutoffs
  (*) the original selection is in neither of the two new selections
  etc...

Cheers,

-- Jason

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

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