From: Thomas C. Bishop (
Date: Wed Jul 08 2015 - 09:51:10 CDT

You may have to be careful w/ the use of "" in scripts versus the gui.
e.g. here's line from a script I use.

set notwat [atomselect top {not (water or name "Cl\-" "Na\+" "K\+" ) } ]

By habit i usually  use "" 's like

set sel [atomselect top " name OH" ]
but have to use the top method with {}'s when want to include the +/- signs.

IF making a movie you can also need to pay attention to the
selection update (each frame or not) depending on what you are trying to show.

you can also select by charge if the names give you trouble :-)


On 07/07/2015 03:47 AM, Daniel Möller wrote:

try: (all within 5 of resname S2P) and resname "Na\+"

Is 'resname "Na\+"' a correct selection? Mabe 'type Na' works too. (try it
as a new representation which selection works)


Daniel Möller

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag von
Parker de Waal
Gesendet: Dienstag, 7. Juli 2015 04:57
Betreff: vmd-l: Sodium within distance

Hello Everyone,

I would like to select Na+ ions within 5A of a phosphoserine residue to
display for a movie, however the following command does not work: resname
"Na\+" within 5 of resname S2P

Does anyone have any suggestions as to how I can get this to work?