VMD-L Mailing List

From: Peter (peter.mawanga.lagos_at_gmail.com)
Date: Wed Mar 27 2024 - 01:29:46 CDT

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> 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