VMD-L Mailing List

From: Ahmet Bakan (lordnapi_at_gmail.com)
Date: Wed May 15 2013 - 16:08:17 CDT

Payman,

It looks like NMWiz & ProDy did not write atom names in the NMD file.
Without atom names, VMD does not know that the complete backbone is
present. I will fix this in a day or two and send you fixed files.

On Wed, May 15, 2013 at 4:32 PM, Payman Pirzadeh <ppirzade_at_ucalgary.ca>wrote:

> Dear Ahmet,
> Thank you very much for your attention.
> Attached are the files requested. Look forward to hear from you.
> Best,
>
> Paymon
>
>
> On Wed, 2013-05-15 at 10:24 -0400, Ahmet Bakan wrote:
> > 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 options.
> >
> >
> > 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.
> >
> >
> > Ahmet
> >
> >
> > On Tue, May 14, 2013 at 8:38 PM, Payman Pirzadeh
> > <ppirzade_at_ucalgary.ca> 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
> >
> >
> >
> >
>
>