From: Axel Kohlmeyer (
Date: Fri Mar 02 2007 - 08:27:07 CST

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


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.

CLA> frame.
CLA> Regards
CLA> Cesar
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> > ------------------------------------------------------------------------
CLA> > Have a burning question? Go to Yahoo! Answers
CLA> > <;_ylc=X3oDMTFvbGNhMGE3BF9TAzM5NjU0NTEwOARfcwMzOTY1NDUxMDMEc2VjA21haWxfdGFnbGluZQRzbGsDbWFpbF90YWcx>
CLA> > and get answers from real people who know.

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.