VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed May 21 2008 - 22:58:01 CDT

On Thu, 22 May 2008, Peter Jones wrote:

PJ> Hi all,
PJ>

peter,
 
you are almost there.

PJ> I'm trying to write a small tcl script that will change all the coordinates
PJ> in a simulation trajectory to nanometers (ie scale by 0.1).
PJ> I have tried-
PJ>
PJ>
PJ> set all [atomselect top "all"]
PJ> set num_steps [molinfo top get numframes]
PJ>
PJ> for {set frame 0} {$frame < $num_steps} {incr frame} {

$all frame $frame
set newcoords {}
 
PJ> foreach coord [$all get {x y z}] {
PJ> set new [vecscale 0.1 $coord]
PJ> lappend newcoords $new
PJ> }
PJ>
PJ> $all set {x y z} $newcoords }
PJ>
PJ>
PJ>
PJ> but I get an error about mismatched data sets, there seems to be twice the
PJ> number of coordinates.

because you are not clearing the list.

cheers,
   axel.
PJ>
PJ>
PJ> Any help would be greatly appreciated,
PJ>
PJ> thanks,
PJ>
PJ>
PJ> Peter Jones
PJ> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.