From: Axel Kohlmeyer (
Date: Tue Sep 18 2007 - 08:34:29 CDT

On Tue, 18 Sep 2007, maria goranovic wrote:

MG> Hi,

hi maria,

MG> I want to change the representation of water molecules from lines to VDW
MG> when they cross a certain z-coordinate while i am making a movie using VMD.
MG> Is this possible ?


MG> Also, how can I dynamically change the selection of water molecules during
MG> an animation (without having to separate pdb files for each frame) ? The
MG> script bridging_waters.tcl in the script archive could probably do it, but
MG> its implementation is not clear. Can someone please help ?

what you want to do, can be implemented much simpler.
please create _two_ representations for your water molecules:
one with lines and one with VDW. then look up the name of the
water oxygens in the .pdb file (say OW) and use as
selection strings for the two representations:
same residue as (name OW and z < 0.0)
same residue as (name OW and z >= 0.0)

and finally click on the trajectory tab for each
representation and activate 'Update selection every frame'.

that should have all waters where the z-coordinate i positive
displayed as VDW and the others as lines. this will also work
for movies.


MG> Thank you for helping out
MG> -Maria

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.