From: Yarrow Madrona (Acacia.Madrona_at_ucsf.edu)
Date: Fri Oct 02 2015 - 17:21:23 CDT

No, this doesn't actually work. Any help?

On Fri, Oct 2, 2015 at 1:57 PM, Yarrow Madrona <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>
> wrote:
>
>>
>> ---------- Forwarded message ----------
>> From: Yarrow Madrona <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
>>
>>
>> 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