From: Ahmet Bakan (
Date: Wed May 15 2013 - 09:24:15 CDT

Hi Paymon,

One thing you can do is to manage your own protein molecule
representations. Just hide the molecule controlled by NMWiz using the GUI

Another thing you can do to get proper cartoon representation for the
molecule is to extend PCA calculations to all atoms.

Also, if you don't mind sending me NMD file (and a reference PDB
structure), I can look into it to see if something went wrong. AFAIK, if
backbone atoms in the NMD file has proper geometry, STRIDE should be able
to calculate secondary structures and VMD should show you cartoon.


On Tue, May 14, 2013 at 8:38 PM, Payman Pirzadeh <>wrote:

> Hi,
> I am running VMD 1.9.1 on Linux Ubuntu 12.10. I run my simulations with
> GROMACS 4.5.4, and I upload the .gro and .xtc file in VMD to perform PCA
> analysis. I use the default NMWiz1.0 plugin. When the PCA analysis is
> done and the information is loaded, things get strange. For instance, I
> cannot change the protein presentation into new cartoon despite
> calculating the components for the backbone! If I change the
> presentation from backbone to CA, then arrows disappear, or even
> sometime the whole structure disappears and never reappear. The
> selection and redrawing, in particular, appear to be not working well. I
> found the online instructions not easy to follow. Are there any links or
> documentation with appropriate instructions/trouble shooting available
> on NMWiz?
> Thanks for your help.
> Paymon