VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 17 2014 - 10:33:02 CST

Jacob,
  Sorry for the slow reply, I was out of the office traveling for the last
several days. I was the one you probably remember meeting with
when you visited. I recall briefly showing you how to use QuickSurf for your
virus structure while you were here.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Feb 15, 2014 at 01:19:12AM -0700, Jacob Durrant wrote:
> Thanks, guys! This is exactly what I was trying to remember. ~Jacob
>
> On Wed, Feb 12, 2014 at 4:16 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
> Hi Jacob,
>
> Any of the fields that VMD stores as an integer are good candidates for
> using the modulo operation on when constructing an atom selection.
>
> residue % 3 == 0 would give you every third residue
> index % 2 == 0 would give you every other atom (by index).
>
> You might be interested in more atomselection math functions to limit
> the amount of volume that is shown at once.
> See http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node19.html for a
> simple example.
>
> -Josh Vermaas
>
> On 02/12/2014 02:37 PM, Jacob Durrant wrote:
>
> A few months ago I was visiting Klaus Schulten's group, and one of the
> VMD developers there showed me a very convenient atom selection for
> selecting every other atom, or every third atom, etc. It made viewing
> large structures much faster and easier. I've searched the internet
> and can't find that command anywhere. Can anyone here point me in the
> right direction?
> Thanks,
> Jacob
>
> --
> ==============================
> Jacob D. Durrant, PhD
> Rommie E. Amaro Research Group
> University of California, San Diego
> Connect with me on LinkedIn
> jacobdurrant_at_gmail.com
> jdurrant_at_ucsd.edu 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/