VMD-L Mailing List

From: amin_at_imtech.res.in
Date: Sun Apr 07 2013 - 02:12:49 CDT

How about water and within 5 of name FE?

> 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. 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.
>
>
>
>
> --
> Yarrow Madrona
>
> Graduate Student
> Molecular Biology and Biochemistry Dept.
> University of California, Irvine
> Natural Sciences I, Rm 2403
> Irvine, CA 92697
>
>
>
>

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