VMD-L Mailing List

From: Funzo_at_seznam.cz
Date: Tue Jul 31 2018 - 11:06:17 CDT

Hi,

Thank you for your answer. The problem is I cannot superimpose them. I can
load a normal full pdb but I cannot overlay the porcupine plots.

Loki

---------- Původní e-mail ----------
Od: John Stone <johns_at_ks.uiuc.edu>
Komu: Funzo_at_seznam.cz
Datum: 31. 7. 2018 16:06:44
Předmět: Re: vmd-l: Porcupine plot with nmwiz
"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/ 
"