From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Oct 05 2015 - 11:06:14 CDT

Hi Yarrow,

I played around a bit with atomselections in my own system that has
similar double bridging waters between two nearby glutamates, and I am
curious as to why you say it doesn't work. This is what I got to
highlight all possible bridging waters:

((water and noh) and within 3.5 of index 210 211) and ((water and noh)
and within 3.5 of ((water and noh) and within 3.5 of index 1929 1930))
or ((water and noh) and within 3.5 of index 1929 1930) and ((water and
noh) and within 3.5 of ((water and noh) and within 3.5 of index 210 211))

Its ugly as sin, but it will pick out all the atoms that are potentially
involved in such an interaction. The only difference I can see between
my approach and yours is that I'm being very explicit with my logic
operations, and I don't include hydrogens in my selection. What are you
seeing vs. what would you like to see?

-Josh Vermaas

On 10/02/2015 05:21 PM, Yarrow Madrona wrote:
> No, this doesn't actually work. Any help?
>
> On Fri, Oct 2, 2015 at 1:57 PM, Yarrow Madrona
> <Acacia.Madrona_at_ucsf.edu <mailto:Acacia.Madrona_at_ucsf.edu>> wrote:
>
> I came up with:
> ((water within 3.5 of index x) and (within 3.5 of water within 3.5
> of y)) or ((water within 3.5 of index y) and (within 3.5 of water
> within 3.5 of index x))
>
> Does the trick but maybe there is something simpler?
>
> -Yarrow
>
> On Fri, Oct 2, 2015 at 1:43 PM, Yarrow Madrona
> <Acacia.Madrona_at_ucsf.edu <mailto:Acacia.Madrona_at_ucsf.edu>> wrote:
>
>
> ---------- Forwarded message ----------
> From: *Yarrow Madrona* <yarrowmadrona_at_gmail.com
> <mailto:yarrowmadrona_at_gmail.com>>
> Date: Fri, Oct 2, 2015 at 1:42 PM
> Subject: VMD Tricky selection of protein water bridge (2
> bridge waters)
> To: vmd-l_at_ks.uiuc.edu <mailto:vmd-l_at_ks.uiuc.edu>
>
>
> Hi,
> I am trying to make a selection of a water near atom x but
> only if it is near another water that is near atom y. I am
> looking at a two water hydrogen bridge between atom x and atom y.
>
> I know this won't work:
>
> (same residue as water within 3.5 of x) or (same residue as
> water within 3.5 of y)
>
> as it gives me all waters near each residue. I have attached a
> picture. I want only the two waters between the tyrosine OH
> and the histidine NE. I have tried various "AND" selections
> such as:
> (same residue as water within 3.5 of x) and within 3.5 of
> (water within 3.5 of y)
>
> but this selection is not recognized. I would love some help
> with this. Thank you.
>
>
>
> --
> Yarrow Madrona, Ph.D.
> /Postdoctoral Scholar/
> University of California, San Francisco
> Department of Pharmaceutical Chemistry
> Rm N551, 600 16th street
> San Francisco CA, 94143
>
>
>
>
> --
> Yarrow Madrona, Ph.D.
> /Postdoctoral Scholar/
> University of California, San Francisco
> Department of Pharmaceutical Chemistry
> Rm N551, 600 16th street
> San Francisco CA, 94143
>
>
>
>
> --
> Yarrow Madrona, Ph.D.
> /Postdoctoral Scholar/
> University of California, San Francisco
> Department of Pharmaceutical Chemistry
> Rm N551, 600 16th street
> San Francisco CA, 94143