VMD-L Mailing List

From: Paweł Kędzierski (pawel.kedzierski_at_pwr.wroc.pl)
Date: Tue Mar 22 2011 - 04:11:53 CDT

Hi,

On 21.03.2011 16:37, ban arn wrote:
> Dear VMD users
>
> Thanks for reply.
>
> But would like to do the same (projection of c-aplha atom coordinates
> on xy plane) for trajectories.
A quick & dirty way would be:

set sel [atomselect top "protein and name CA"]
set frames [molinfo top get numframes]
for {set i 0} {$i< $frames} {incr i} {
    $sel frame $i
    $sel set z 0
}
animate write dcd CA_z_proj.dcd sel $sel
animate write xyz CA_z_proj.xyz sel $sel

You may get the projection coordinates in any format supported by
"animate write". XYZ is the simplest text format at hand.
However you will be left with modified structure in VMD.
HTH,
Pawel