VMD-L Mailing List

From: Eduard Schreiner (eduard.schreiner_at_rub.de)
Date: Tue Feb 13 2007 - 06:52:21 CST

On Monday 12 February 2007 20:42, dimka wrote:
> To calculate the average structure form a trajectory I execute the
> following command executed:
> measure avpos [atomselect 0 all] first 0 last 499 step 1
>
> How can I create a new molecule (say molecule 1) that would contain
> these coordinates?
>
> dmitry
>

Hey Dmitry,
load one step of your trajectory in a new molecule and set the coordinates of the atoms
to the calculated values.
Something like this should work (I hope)

mol new TRAJECTORY type TYPE first 0 last 0
set sel1 [atomselect 0 "SEL-TEXT"]
set sel2 [atomselect 1 "SEL-TEXT"]
set newpos [measure avpos $sel1 first 0 last 499 step 1]
#note the average positions are now in a list
$sel2 lmoveto $newpos

#unset variables
$sel1 delete; unset sel1
$sel2 delete; unset sel2
unset newpos

eddi 

-- 
--
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Eduard Schreiner                     e-mail: eduard.schreiner_at_theochem.rub.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-22121
Ruhr-Universitaet Bochum - NC 03/52         Fax:   ++49 (0)234/32-14045
D-44780 Bochum                              http://www.theochem.rub.de
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