We discussed this a bit off-list, and it looks like this was the answer:
The potentials are assigned to points in space. That's why the
isosurfaces don't change, and also why the surface coloring changes
when you change the shape of the surface.
Hope that helps anyone else who might have this question,
On 1/9/07, Michael Lerner <mglerner@...> wrote:
> I don't have time to look at this in detail right now, but .. what
> exactly do you mean that the potentials change between frames? What
> happens if you draw isosurfaces? Do they change?
> On 1/7/07, Ra=FAl Mera <butil_litio@...> wrote:
> > Dear all,
> > Two things.
> > First, I just written a small plugin that uses the
> > program "reduce" to add hydrogens to a molecule or to
> > a trajectory loaded in Pymol.(since each frame of the
> > trajectory is hydrogenated by reduce, I think that
> > protonation states could vary between frames) This
> > allow us to have a reliable protonation method in
> > PyMOL, without having to save the structure as PDB and
> > hydrogenate with another app, and using an open-source
> > (as far as I know) and easy to install application.
> > Since I don't have any website right now, I will try
> > to make it available from the Pymol Wiki. If you want
> > the plugin right now, just e-mail me.
> > The other thing is a doubt in using the APBS Tools.
> > When I use it to calculate electrostatics potentialsof
> > a trajectory (but the PQR is made by PDB2PQR from a
> > PDB made with PyMOL, i.e, only from the first
> > snapshot)
> > I get a .dx map that I think has the potentials only
> > for the first frame. When I display the potential
> > surface in the trajectory, the potentials seems to
> > change between frames, which I wouldn't expect since I
> > think that the calculation was performed only for the
> > first frame.
> > My doubt is: Are these changes alleatory due to a
> > change
> > of the structure's position changes on the grid, or
> > they have some significance?, if the latter, what
> > significance? (maybe the changes are produced by the
> > motion of polar groups?)
> > Thanks in advance,
> > Raul
> > __________________________________________________
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> Biophysics Graduate Student
> Carlson Lab, University of Michigan
> http://www.umich.edu/~mlerner http://lernerclan.net
Biophysics Graduate Student
Carlson Lab, University of Michigan