From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Fri Mar 02 2007 - 07:32:01 CST

The atomselect expression is evaluated once again on each frame update,
and the atoms matching the criterion are selected. In your example if
you atomselect "ions within 5 of protein" this is evaluated for each
frame. If a ion moves out of this criterion it won't be selected on that
frame.
Regards
Cesar

Jawahar Neelankatan escribió:
> Hi all,
> In order to save memory and avoid using the atomselect command for
> each frame in a trajectory, I usually do the atomselection at the
> beginning and use either "$sel frame $i" or "$sel update" to update
> the atomselection for each frame.
> My question is this: exactly how does the update process work ? My
> guess is that if X atoms are selected in the initial atomselect
> command, the "update" command updates the coordinates of those X atoms
> in each new frame.
> So, if the atomselect command has a selection criterion such as
> "within 12 of ion", then all atoms within a sphere of radius 12
> Angstrom around the ion are selected. Let's assume there are X atoms
> fitting this criterion, in the first frame. When the frame is switched
> to another frame and the "update" command is used, is it those same X
> atoms that are updated, or is the atomselection command repeated for
> that particular frame ? My concern is that, in the new frame, an atom
> that was previously within the 12 Angstrom sphere might have moved out
> of the sphere, so it is pointless to update its coordinates.
>
> -Jawahar.
>
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