VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Fri Oct 02 2015 - 18:17:31 CDT

Not exactly sure - but maybe you can try --

Selection 1:

pick waters within a distance of atoms of interest

Selection 2:

pick waters within a distance of other waters

Final selection:

Intersection of Selection 1 and selection 2 should give you your answer
(theoretically).

Selection 1 and 2 should be simple enough - for the intersect you can try
parsing index of selected waters in selection 1 vs that in selection 2 --
This would give you waters (w1) connected to the atom (a) and to other
waters (w2). For a complete bridge lookup (w2) in selection 1. If found you
now have a bridge ...

I am not sure if a direct selection can be made or not - but I am sure the
above method would be quick to script -- however it maybe slower when
compared to a direct selection routine. However if you are doing this on a
single frame then it doesn't make a difference but if you are planning on
running it against a trajectory --- the above method might be significantly
slower - in which you might want to keep an eye for more replies against
this post.

Hope this helps,

Good luck.

Best,
/A

On Sat, Oct 3, 2015 at 11:21 AM, Yarrow Madrona <Acacia.Madrona_at_ucsf.edu>
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>
> 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
>