Re: [PyMOL] Selections

[Michael G. L. <ml...@um...>]

> For example, I found a PDB online called 'pope.pdb' (a cool lipid
> bilayer; http://moose.bio.ucalgary.ca/Downloads/) and simply wanted to
> select all the hydrophobic tails and hydrophilic heads so that I may
> apply different attributes to each.  If I need to select the tails,
> which in the PDB are labeled from C10 (or so) to C50 depending on the
> molecule, can I use something like c10-c50 (experience tells me no) or
> must I do c10+c11+c12...c50?

I don't know an easy way to do this .. "like" almost does what you want,
but not quite.  You could do something like

select sol, resn sol
select heads, name N4+C5+C6+O7+O9+O10+O11+C12+C13+O14+C15+O16+C32+O33+C34+O35+P8+H1+H2+H3
select tails, not sol and not heads

Or .. even easier .. drop this in a file called something like
select_names.py

-------
#!/usr/bin/env python
from pymol import cmd,stored

def select_names(newSelectionName,selection):
    """
    Makes a new selection called <newSelectionName> comprised of
    everything that has the same atom name as something in <selection>.
    """
    stored.selected_names = []
    cmd.iterate(selection,'stored.selected_names.append(name)')
    cmd.select(newSelectionName,'name %s'%'+'.join(stored.selected_names))

cmd.extend('select_names',select_names)
-------

and type "run selected_names.py" from within PyMOL.
Now use the mouse to select one of the heads (I use shift+lb to put things
into the selection (lb).
Now type "select_names heads, lb" and you'll have a selection called
"heads" that has all of the heads.

Maybe someone who knows more about selections will know a better way,
though.

>
> So, it comes down to: do you prefer the macro method or standard; and,
> do you have any hints or tips for more accurate or powerful selections?

If you're going to be using PyMOL a lot, it's definately worth your time
to learn how to write Python scripts.  I'd also recommend looking through
the PyMOL source itself.  I don't have anything much to say about
selections, though .. I've always been quite happy with simple PyMOL
selections.

-michael

> As an example, how could I select just the tails or just the heads in
> the aforementioned pope.pdb file?
>
> Thanks.
>
> --
> Jason Vertrees
> BSCB Graduate Student @ UTMB, Galveston
> jav...@ut... :: http://www.bscb.utmb.edu
>
>
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