VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Jan 25 2016 - 03:56:04 CST

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