VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 31 2018 - 11:38:16 CDT

You should be able to align them if you use an atom selection on the
full PDB that only selects atoms that do exist in the AMBER structure,
then you can RMS align the PDB with the AMBER structure, and the
AMBER porcupine plot should then match both of them.

Best,
  John

On Tue, Jul 31, 2018 at 06:06:17PM +0200, Funzo_at_seznam.cz wrote:
> 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
> ---------- Původnà e-mail ----------
> Od: John Stone <johns_at_ks.uiuc.edu>
> Komu: Funzo_at_seznam.cz
> Datum: 31. 7. 2018 16:06:44
> PÅ*edmÄ*t: 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/ 

-- 
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/