VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Mon Jan 25 2016 - 08:58:54 CST

Thanks all. Btw is it possible to combine something with "not" here. If I
want to select only inter-molecular H but not intra-molecular can I use
set sel1 [atomselect $mol "name \H.*\ and
sqrt(sqr(x-$x1)+sqr(y-$y1)+sqr(z-$z1)) < 5 not index $ind1"]

It is mentioned in examples that we can use ''not" command but it gives and
error "cannot parse statement"

Thank you.
Monika

On Mon, Jan 25, 2016 at 8:39 PM, M K <mahyar.karimi20_at_gmail.com> wrote:

> 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
>>
>
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.