VMD-L Mailing List

From: Nathan Kern (nathan.kern_at_lehigh.edu)
Date: Fri May 28 2021 - 11:49:41 CDT

Correction:

set sel1 [atomselect top {name "C5.*" "C4.*" "O4.*"}]

On Fri, May 28, 2021 at 12:48 PM Nathan Kern <nathan.kern_at_lehigh.edu> wrote:

> It's probably worth pointing out that if you don't need to do parameter
> substitution, then Tcl's literal string construct {} will tend to result in
> code that's easier to read, since you wouldn't usually need to escape
> quotes.
>
> E.g. Josh's selection example:
>
> set sel1 [atomselect top "name \"C5.*\" \"C4.*\" \"O4.*\"”]
>
> Could be rewritten as:
>
> set sel1 [atomselect top {name "C5.*" C4.*" O4.*"}]
>
>
> Nathan
>
> On Fri, May 28, 2021 at 12:42 PM Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
>> Hi Saikat,
>>
>>
>>
>> Please keep the mailinglist in your replies for context. In scripts, the
>> quotes need to be escaped, otherwise Tcl can’t determine where the strings
>> begin and end. Try:
>>
>>
>>
>> set sel1 [atomselect top "name \"C5.*\" \"C4.*\" \"O4.*\"”]
>>
>>
>>
>> When answering questions of which selection is correct, you can try
>> things like “puts [$sel2 num]”. Does it give a reasonable output? My guess
>> is that it didn’t, since I suspect that no atoms matched the sel2 selection
>> you wrote, since single quotes won’t use regular expressions.
>>
>>
>>
>> -Josh
>>
>>
>>
>> *From: *Saikat Pal <saikatpaliitg_at_yahoo.com>
>> *Date: *Friday, May 28, 2021 at 11:38 AM
>> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>
>> *Subject: *Re: vmd-l: Atom selection with asterisk atom name
>>
>>
>>
>> Thank you for your kind reply. I want to use it in tcl script. So when I
>> have tried the following command:
>>
>> set sel1 [atomselect top "name "C5.*" "C4.*" "O4.*"]
>>
>>
>>
>> It shows error:
>>
>> extra characters after close-quote
>>
>>
>>
>> But when I have used:
>>
>> set sel2 [atomselect top "name 'C5.*' 'C4.*' 'O4.*'"]
>>
>>
>>
>> There is no error. So my question is it correct?
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> Thanks and Regards,
>>
>>
>>
>> Saikat Pal
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Wednesday, 26 May, 2021, 10:33:01 pm IST, Vermaas, Josh <
>> vermaasj_at_msu.edu> wrote:
>>
>>
>>
>>
>>
>> Hi Saikat,
>>
>>
>>
>> This is in the user guide.
>> https://www.ks.uiuc.edu/Research/vmd/current/ug/node94.html
>> <https://urldefense.com/v3/__https:/www.ks.uiuc.edu/Research/vmd/current/ug/node94.html__;!!HXCxUKc!hOQRKjLoIe-uqw8ELaNnHbgk_qvvv6EL6Q1aFGxCkO9IPakikMBktMUs3Up7DQQ$>
>> .
>>
>>
>>
>> For your selection (anything starting with C1, C4, C5, or O5), I think it
>> would simplify to this:
>>
>>
>>
>> name “C[145].*” “O4.*”
>>
>>
>>
>> -Josh
>>
>>
>>
>> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Saikat Pal
>> <saikatpaliitg_at_REMOVE_yahoo.com>
>> *Date: *Wednesday, May 26, 2021 at 3:53 AM
>> *To: *VMD Mailing List <vmd-l_at_ks.uiuc.edu>
>> *Subject: *vmd-l: Atom selection with asterisk atom name
>>
>>
>>
>>
>>
>> Dear all,
>>
>>
>>
>> I want to select multiple atoms with asterisks like C5* C4* O4* C1*. So
>> what should I do?
>>
>>
>>
>>
>>
>> Thanks and Regards,
>>
>>
>>
>> Saikat Pal
>>
>>
>>
>>
>>
>>