From: Jérôme Hénin (
Date: Thu Jul 01 2004 - 04:47:55 CDT


There is a fairly simple way to do this using VMD's selections. You should
devise a selection text that selects exactly the coordinating atoms. The
simplest case being "not index 1234 and within 2.4 of index 1234" (index 1234
should be replaced by any text that selects the atom of interest). If you
build a selection (say, coordShell) using that text and the atomselect
command, then [$coordShell num] gives you the coordination number.

You may need to look at the VMD manual, as well as Tcl documentation (there is
plenty available from the Web). Several interesting scripts can be found at
Also, if you need more information on the VMD way of doing trajectory
analysis, it should be discuted on vmd-list rather than this one.


Le Jeudi 1 Juillet 2004 08:57, ying xiong a écrit :
> Dear sir,
> If I want to calculate the coodination number of some atom for each
> picosecond (or frame), could you please tell me how to write a script to
> realize it? Of course, the coordination number of A atom can be
> calculated with the criterion: if the distance between A and an atom is
> shorter than a distance value (say 2.2, 2.3 or 2.4 or 2.5 angstrom), then
> we can consider the atom coordinating to A.
> Thanks !
>         ying xiong
>           2004-07-01

Jérôme Hénin
Equipe Dynamique des Assemblages Membranaires
Université Henri Poincaré / CNRS    UMR 7565
B.P. 239	54506 Vandoeuvre-lès-Nancy Cedex
Tel : (33) 3 83 68 43 95	Fax : (33) 3 83 68 43 71

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