VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 31 2018 - 10:03:14 CDT

Hi,
  You could load both molecules into VMD and just hide the graphical
representation for the one from AMBER, while using its "porcupine"
arrow plot as you like. You don't necessarily have to show the
atomic structure of a given molecular in order to use the
user-drawn draw/graphics geometry that is created by tools like NMWiz.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jul 26, 2018 at 04:34:19PM +0200, Funzo_at_seznam.cz wrote:
> Dear VMD users,
> could someone help me with a visualization of a porcupine plot? I can
> create it in Amber (nmwiz.nmd) but I would like to load a full structure
> with all side chains etc into VMD and overlay the porcupine plot over
> this. Currently, I am unable to do so as I can only overlay the same
> number of atoms (i.e backbone atoms in my case).
> Thank you very much for your help
> Loki 

-- 
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/