VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Sun Apr 07 2013 - 10:30:22 CDT

W dniu 07.04.2013 03:46, Yarrow Madrona pisze:
> Hello,
>
> Does anyone know how to visualize water movement over the course of a
> trajectory?
>
> I know how to select waters within a distance for a given frame. However
> since they are entering and leaving the index numbers will change.
Select "water and same residue as within 5 of name FE" as the OP
suggested, then go to the "Trajectory" tab of the Graphical
Representations window and check "Update Selection Every Frame".
Pawel
> I can
> write out all of the PDBs and read them back in but I am wondering if
> there is some script out there that will follow only waters that show up
> within a distance of the active site regardless of the index number.
>
> For example water "1" leaves and 20 frames later water "200" enters within
> 5 angstroms of a FE atom. I want to be able to visualize the water 1 while
> it is within 5 angstroms and the water 200 while it is within 5 angstroms
> but not when they are greater than 5 angstroms. Thank you for any help you
> can provide.
>
>
>
>