VMD-L Mailing List

From: Joaquim Rui de Castro Rodrigues (joaquim.rodrigues_at_ipleiria.pt)
Date: Wed Mar 27 2024 - 06:23:54 CDT

Dear Peter,

Check this example:
https://www.ks.uiuc.edu/Research/vmd/current/ug/node20.html

that would translate to:

set x [lindex $centerofsphere 0]
set y [lindex $centerofsphere 1]
set z [lindex $centerofsphere 2]
set caatoms [atomselect top "name CA and (sqrt(sqr(x-$x) + sqr(y-$y) + sqr(z-$z)) < 22.0)"]

Hope this helps,
JR Rodrigues


________________________________
De: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> em nome de Peter <peter.mawanga.lagos_at_gmail.com>
Enviado: 27 de março de 2024 06:29
Para: Vmd l <vmd-l_at_ks.uiuc.edu>
Assunto: Re: vmd-l: Atom selection based on center of sphere

Atenção: Este email foi originado fora do Instituto Politécnico de Leiria. Por favor, não clique em links nem abra anexos, a não ser que reconheça o remetente e saiba que o conteúdo é seguro.

I think a dummy (fictitious) atom might be a better alternative to "$centerofsphere," but I was not able to figure out how to transfer the XYZ coordinates of the geometric center to such a fictitious atom for the distance calculation and the desired output.

Please suggest some method or alternative to proceed further. Thank you very much.

On Tue, Mar 26, 2024 at 5:41 PM Peter <peter.mawanga.lagos_at_gmail.com<mailto:peter.mawanga.lagos_at_gmail.com>> wrote:
Hello everyone,

I tried selecting CA atoms within a certain distance of the center of the sphere but have not been able to do so. More specifically, the "atomselect" command is not able to process the selection. Is there any way of resolving this issue?

******************************************

set allatoms [atomselect top all]

set centerofsphere [measure center $allatoms]

set caatoms [atomselect top "name CA within 22 of $centerofsphere"]

$caatoms writepdb selectedatoms.pdb

******************************************


--
Cheers
Peter


--
Cheers
Peter