VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue May 20 2014 - 17:39:09 CDT

Hi Bryan,

Yup. I'd use the math capabilities of the atomselection interface to
select everything within a cylinder. You want the atoms that
ax^2+bxy+cxz+dy^2+eyz+fz^2<R^2 (Note that I'm writing it mathematically,
not in strictly-correct atomselection syntax. I'm also assuming the
vector crosses through the origin). The trick is calculating a, b, c, d,
e, and f. :D Usually the easiest way to make cylindrical selections is
to align the axis of interest with x (using transvecinv,
http://www.ks.uiuc.edu/Research/vmd/current/ug/node191.html), so that
you are left with z^2+y^2<R^2. Since this is a membrane protein, you may
not want to actually rotate your coordinate space. What you'd do instead
is figure out your specific cylinder equation (See
http://en.wikipedia.org/wiki/Cylinder_%28geometry%29 for how to define a
cylinder along an arbitrary axis), and generate your atomselection that
way. If this sounds like alot of math, it is, but its all perfectly
scriptable.

-Josh Vermaas

On 5/20/14, 5:25 PM, Bryan Roessler wrote:
> The symmetry tool in VMD does a pretty god job of finding the pore
> region of my membrane protein of interest along the vertical principle
> axis of inertia. Is there a way to use this eigenvalue to select atoms
> that are within a certain distance of this axis?
>
> Thanks
>
>
> *Bryan Roessler | Graduate Research Assistant*
> UAB | The University of Alabama at Birmingham
> *_uab.edu/cmdb <http://uab.edu/cmdb>_*
> Knowledge that will change your world
>