VMD-L Mailing List

From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Fri Mar 02 2007 - 08:59:48 CST

Sorry Axel, I was not clear enough. I was just referring to $sel update
not $sel frame $i.
Your explanation is more complete. ;-)
Regards
Cesar

Axel Kohlmeyer escribió:
> On Fri, 2 Mar 2007, Cesar Luis Avila wrote:
>
> CLA> The atomselect expression is evaluated once again on each frame update,
> CLA> and the atoms matching the criterion are selected. In your example if
> CLA> you atomselect "ions within 5 of protein" this is evaluated for each
> CLA> frame. If a ion moves out of this criterion it won't be selected on that
>
> cesar,
>
> your assertion is _not_ correct. only the update subcommand re-evaluates
> the selection string and updates it (it is automatically done on
> creating a selection). if you move the selection through the trajectory
> with the frame subcommand, it will not update the selection. this is
> intentionally so, e.g. to follow a group of atoms that adhered to
> a certain condition (when you last updated the selection).
>
> please make a few experiments and you'll see.
> axel.
>
>
> CLA> frame.
> CLA> Regards
> CLA> Cesar
> CLA>
> CLA>
> CLA> Jawahar Neelankatan escribió:
> CLA> > Hi all,
> CLA> > In order to save memory and avoid using the atomselect command for
> CLA> > each frame in a trajectory, I usually do the atomselection at the
> CLA> > beginning and use either "$sel frame $i" or "$sel update" to update
> CLA> > the atomselection for each frame.
> CLA> > My question is this: exactly how does the update process work ? My
> CLA> > guess is that if X atoms are selected in the initial atomselect
> CLA> > command, the "update" command updates the coordinates of those X atoms
> CLA> > in each new frame.
> CLA> > So, if the atomselect command has a selection criterion such as
> CLA> > "within 12 of ion", then all atoms within a sphere of radius 12
> CLA> > Angstrom around the ion are selected. Let's assume there are X atoms
> CLA> > fitting this criterion, in the first frame. When the frame is switched
> CLA> > to another frame and the "update" command is used, is it those same X
> CLA> > atoms that are updated, or is the atomselection command repeated for
> CLA> > that particular frame ? My concern is that, in the new frame, an atom
> CLA> > that was previously within the 12 Angstrom sphere might have moved out
> CLA> > of the sphere, so it is pointless to update its coordinates.
> CLA> >
> CLA> > -Jawahar.
> CLA> >
> CLA> > ------------------------------------------------------------------------
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