Re: [PyMOL] Slicing a protein (PDB Structure)

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

Hi Spyros,

This can be done pretty easily in PyMOL. Please check out the following:

Plane Wizard:
* -- http://www.pymolwiki.org/index.php/Plane_Wizard;

BNI-tools Plane Wizard
* -- http://sourceforge.net/projects/bni-tools/

Section 2.6 of the supplemental information to our PLoS paper
* -- http://pymolwiki.org/index.php/PLoS

You can use pseudoatom (http://www.pymolwiki.org/index.php/Pseudoatom)
to create three arbitrary points for the plane.

Cheers,

-- Jason


On Wed, Sep 14, 2011 at 11:38 AM, Spyros Charonis <s.c...@gm...> wrote:
> Hello PyMOLers,
>
> I have a GPCR protein molecule (pdb file) whose structure I would like to
> visualize, but instead of seeing the entire structure as one entity, I would
> like to separate it, somehow as if I was using an imaginary plane to "chop"
> the protein into two entities (extracellular interface, intracellular
> interface). Is this possible? Would it perhaps require a script?
> Many thanks for your time.
>
> Spyros
>
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-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

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