From: M K (mahyar.karimi20_at_gmail.com)
Date: Mon Jan 25 2016 - 04:39:01 CST

ah, I think because Monika wants the "H atoms" around "H atoms", it is
tricky with exwithin :)
However, I believe it should be possible with exwithin, if we combine it
with some other keywords :)
Nothing is impossible in VMD... :-P

On Mon, Jan 25, 2016 at 8:56 PM, Ashar Malik <asharjm_at_gmail.com> wrote:

> correction to the last message:
>
> should have been $mol and not top (have a habit of doing top)
>
> set sel1 [atomselect $mol {name "H.*" and sqrt(sqr(x-$x1)+sqr(y-$y1)+
> sqr(z-$z1)) < 5}]
>
> on exwithin:
>
> If my understanding is correct - exwithin would select EVERYTHING except
> all Hydrogens?? which I think is not what Monika is trying to do??
>
>
> On Mon, Jan 25, 2016 at 10:35 PM, M K <mahyar.karimi20_at_gmail.com> wrote:
>
>> I was wondering if "exwhithin" command can be used here. For example:
>>
>> exwithin 5 of "name "H.*"
>>
>> Does it work for Monika's purpose?
>>
>> Bests
>>
>> On Mon, Jan 25, 2016 at 6:09 PM, Norman Geist <
>> norman.geist_at_uni-greifswald.de> wrote:
>>
>>> You may not nest quotes, without escaping them.
>>>
>>>
>>>
>>> set sel1 [atomselect $mol "name \"H.*\" and
>>> sqrt(sqr(x-$x1)+sqr(y-$y1)+sqr(z-$z1)) < 5"]
>>>
>>>
>>>
>>> or use single quotes within double quotes:
>>>
>>>
>>>
>>> set sel1 [atomselect $mol "name ‘H.*’ and
>>> sqrt(sqr(x-$x1)+sqr(y-$y1)+sqr(z-$z1)) < 5"]
>>>
>>>
>>>
>>>
>>>
>>> Norman Geist
>>>
>>>
>>>
>>> *Von:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *Im
>>> Auftrag von *Monika Madhavi
>>> *Gesendet:* Montag, 25. Januar 2016 06:31
>>> *An:* vmd-l_at_ks.uiuc.edu
>>> *Betreff:* vmd-l: select atoms within a sphere - atomselect
>>>
>>>
>>>
>>> Dear all,
>>>
>>>
>>>
>>> I want to select all the inter-molecular hydrogen atoms within a sphere
>>> of radius 5A from a central hydrogen atom. Coordinates of the central atom
>>> are x1,y1,z1. I tried this atomselect command.
>>>
>>>
>>>
>>> set sel1 [atomselect $mol "name "H.*" and
>>> sqrt(sqr(x-$x1)+sqr(y-$y1)+sqr(z-$z1)) < 5"]
>>>
>>>
>>>
>>> this gives me an error saying "extra characters after quoted text"
>>>
>>>
>>>
>>> Please help me to resolve this problem.
>>>
>>>
>>>
>>> Thank you.
>>>
>>> Monika
>>>
>>> --
>>>
>>> W.A.Monika Madhavi
>>>
>>> Lecturer (Probation),
>>>
>>> Department of Physics,
>>>
>>> University of Colombo.
>>>
>>
>>
>
>
> --
> Best,
> /A
>