VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 21 2007 - 15:26:20 CDT

Hi,

On Wed, Mar 21, 2007 at 02:14:33PM +0000, Kailee wrote:
[...]
> 1) I tried to superimpose the hydrogen molecule trajectories, what I did
> was: select the representation of hydrogen molecule, and in the
> 'trajectory-> draw multiple frames', I changed 'now' to '0:', is it the
> right way to do this?

You'll need to have an end frame, so if you had 10 frames, you'd use "0:9"

> 2) Because I don't want to look at all the hydrogens but only hydrogens
> within a certain distance of the protein center, so in the 'selections', I
> typed 'resname H2 and (within 50 of name FE)', as I want to look at the
> hydrogen molecules within 50A of the Fe atom. However, it turned out that
> some hydrogens which are very obvious not within 50A of Fe still there.

When you use the draw multiple frames feature, the selection is not updated
as the other frames are drawn, the same selection is used to draw all of
the "multiple frames", so this could explain why you're getting extra
atoms shown. Try showing just the "now" frame and see if only the
expected atoms are shown. The other possibility is PBC as you mentioned
below:

> I am
> thinking it might because of the periodic boundary problem that some
> hydrogens flied out of the primary box and I should reimage them back to the
> central box. Is it right? And if so, how can I do it in VMD?

You could try using the PBC tools scripts (plugin in VMD 1.8.6) to
do this for you.

> 3) And also when I superimposed the hydrogen trajecotries, the
> representation of the protein residues became really not clear, I tried
> different draw styles but still can't find out how to do it.

Can you be specific as to "really not clear" means? Do you have a screen
shot that shows what you're getting?

When you use the "draw multiple timesteps" feature, it is often useful
to set the coloring method to "Timestep" so that you can differentiate
them.

> Actually I have
> attached a picture that I copied from a paper, what I want to do is almost
> exactly what he did, but just using different protein molecule, can anyone
> who is familiar with VMD guide me how to make a picture like that please?

Let me look at it and get back to you.

  John Stone
  vmd_at_ks.uiuc.edu 

-- 
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