VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
Date: Fri May 28 2021 - 14:03:41 CDT

Example #101021231231231 of why copying the list is useful. I’ve been using escape characters like a noob for years!!!
-Josh

From: Nathan Kern <nathan.kern_at_lehigh.edu>
Date: Friday, May 28, 2021 at 12:49 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>
Cc: Saikat Pal <saikatpaliitg_at_yahoo.com>, VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Atom selection with asterisk atom name

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<mailto: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<mailto: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<mailto:saikatpaliitg_at_yahoo.com>>
Date: Friday, May 28, 2021 at 11:38 AM
To: "Vermaas, Josh" <vermaasj_at_msu.edu<mailto: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<mailto:vermaasj_at_msu.edu>> wrote:



Hi Saikat,



This is in the user guide. https://www.ks.uiuc.edu/Research/vmd/current/ug/node94.html$>.



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<mailto: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<mailto: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