VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Feb 10 2011 - 12:56:22 CST

Hi,
  If you get "no atoms selected" then your selection wasn't including
the CA atoms. Try using the selection "all".

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Feb 08, 2011 at 05:00:43PM -0500, B.M.B. Vanschouwen wrote:
> Hello, again.
>
> Some of the PBD data that I am trying to examine contains only "CA"
> atoms (see attached example), since it was obtained from a CA-based
> principal component analysis run. However, I keep getting error
> messages along the line of "no atoms selected".
>
> What is going on?
>
> Note: I am still able to import the structures, and display them in
> "Trace" format.
>
>
> On Tue, 8 Feb 2011 14:22:21 -0600
> John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > You should be able to do this by loading all of your PDBs into
> > separate molecules, open the Extensions->Analysis->RMSD Calculator
> > tool.
> > From there set the selection to "protein" (or whatever makes sense
> > for
> > your structure), then click "all in memory", then "RMSD", then
> > "ALIGN".
> > Then change your graphical representations to color the strutures by
> > "Molecule" and you should be all set.
> >
> > If you have a proper trajectory file (rather than several PDB files)
> > you can do this much more easily using the RMSD Trajectory Tool,
> > coloring by "Timestep", and using Draw Multiple Frames feature
> > in the graphical representations "Trajectory" tab.
> >
> > Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Feb 08, 2011 at 10:19:45AM -0500, B.M.B. Vanschouwen wrote:
> > > Hello.
> > >
> > > I have a group of structures (in PDB format) for a protein that I
> > would
> > > like to display simultaneously in VMD (and possibly display each
> > > structure in a different colour), in order to get a visual
> > illustration
> > > of the motions occurring within the protein molecule.
> > >
> > > How do I do this??
> >
> > --
> > NIH Resource for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078